http://2008.igem.org/wiki/index.php?title=Special:Contributions/Logosandpathos&feed=atom&limit=50&target=Logosandpathos&year=&month=2008.igem.org - User contributions [en]2024-03-29T05:25:22ZFrom 2008.igem.orgMediaWiki 1.16.5http://2008.igem.org/Team:UC_Berkeley_ToolsTeam:UC Berkeley Tools2008-11-20T22:49:19Z<p>Logosandpathos: </p>
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<div><font size="4"><center>Winner of the "Best Software Tool" award, iGEM 2008! (see the winning presentation [https://2008.igem.org/files/video/UC_Berkeley_Tools.mp4 here])</center></font><br />
[[Image:Clotho_Title_small.png|center]]<br />
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<font size="6">W</font>ith >700 available parts and >2000 defined parts in the <A href="http://partsregistry.org/Main_Page"> MIT Registry of Standard Biological Parts</A>, additional part repositories being developed, and countless more parts local to the lab, synthetic biologists are now faced with the challenge of organizing, sorting, and editing these parts from an ever-growing collection of DNA. Computational tools are becoming increasingly needed to assist biologists to do these jobs, and it is no secret that many tools are being introduced into the community to help serve these needs. It is important that new tool developments in this area remain both firmly rooted in the realities of the present while being forward thinking and flexible.</p><br />
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<p><font size="6">C</font>lotho is a toolset designed in a <a href="http://www.gigascale.org/pubs/141.html"> platform-based design </a> paradigm to consolidate all these tools into one working, integrated toolbox. Clotho is based on a <a href = "https://2008.igem.org/Team:UC_Berkeley_Tools/Project#Project_Architecture"> core-and-hub system </a> which manages multiple connections, each connection performing tasks in some self-sufficient manner while connected to all other connections via the core. Examples of connections include sequence viewers/editors, parts database managers, assembly algorithm GUIs, and much more. Computer-savvy biologists can create new connections which will then be integrated into Clotho. These pieces can be kept locally in ones lab or made public and shared with the community. In this tool-consolidation and customization it is hoped that, in the future, biologists need not look further for a program that provides the answer to their ever growing design needs.</p><br />
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<!--- The Mission, Experiments ---><br />
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[[Image:side_by_side_screenshots.jpg|thumb|400 px|Clotho Screenshots]]<br />
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==Clotho Overview==<br />
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<html><font size="6">A</font></html>mong many possible top-level explanations of Clotho, one of the simplest is the "Clotho Data Structure"-centric view. In this view, biological part data is passed back and forth between Clotho components and to files and databases outside Clotho. Some of the possible flows of data are represented by the slew of arrows in the diagram above.<br />
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<big><b>At the Center: Clotho Data Structure</b></big><br />
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Local and standard databases vary from one lab to another, and the way to grab biological part data from one database may require a completely different route than another. The [[Team:UC_Berkeley_Tools/Project#6._Clotho_Data_Structure|'''Clotho Data Structure''']], in essence, can be viewed as the Rosetta stone of Clotho's environment. In a nutshell, it allows any developer to grab relevant information about a part from any given database. This is made possible when a developer "binds" fields in a database to specific Clotho Data Structure objects which have a specific semantic associated with them. When a user wants to grab the sequence belonging to a particular Biobrick, for example, the Clotho Data Structure, once "bound" to a particular database, will be able to grab the sequence from the database and give it to Clotho. Want to know who owned the vector from jca1021 in database A and send that information to database B? Easy. Bind the data structure with both databases, grab the data from database A, and tell Clotho where in database B to place the data. This binding not only gives unstandardized data meaning, it also provides a common language by which Clotho developers can communicate.<br />
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<big><b>Views/Functions</b></big><br />
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Each category above merits its own explanation, as each is vitally important to the project. Perhaps a good place to start are the '''views/functions'''. Here users are able to see and manipulate data, such as part information or the nucleotide sequence. Examples include the [[Team:UC_Berkeley_Tools/Project#Sequence_View|sequence view]] or the [[Team:UC_Berkeley_Tools/Project#Plate_Manager|plate manager]].<br />
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<big><b>Interfaces</b></big><br />
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Not all views/functions are self-sufficient, and so another set of components, called '''interfaces''', are involved in assisting these views/functions for functionality. Take for example the [[Team:UC_Berkeley_Tools/Project#Sequence_View|sequence view]] (a view many ApE lovers would recognize). How would the sequence view know how to highlight features or enzymes if Clotho didn't know what features or enzymes to look for? That's where the [[Team:UC_Berkeley_Tools/Project#Feature_Library_Collection|features library]] and [[Team:UC_Berkeley_Tools/Project#Enzyme_Library|enzyme library]] come in. In this particular example, the two interfaces store and manage information that the sequence view will have to frequent in order to perform vital operations. Other interfaces include a [[Team:UC_Berkeley_Tools/Project#Parts_Manager|parts manager]] and [[Team:UC_Berkeley_Tools/Project#Database_Manager|database manager]]. These allow the user to view part data and relationships. Not only can the source of parts be viewed but users can maintain personal collections of parts as well.<br />
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<big><b>Algorithm Environment</b></big><br />
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But what if you want to do ''more'' with your data you've manipulated? What if, after gathering all your parts, you want to calculate the optimal assembly scheme for a particular goal composite part? This is where the [[Team:UC_Berkeley_Tools/Project#Algorithm_Manager|'''algorithm environment''']] kicks in. The algorithm environment allows developers to make systems that take both quick one-liner inputs or more complex input from the Clotho Data Structure and spit out one-liner or more sophisticated outputs. The [[Team:UC_Berkeley_Tools/Project#Algorithm_Manager|algorithm manager]] allows not only that both approaches can be performed but each are recognized seamlessly. Let's say you wanted to program a partial matching utility into Clotho, where two sequences are given as inputs and a streamlined one-line primer match were spit back out. Algorithm manager provides you all the basic facilities to code such a utility.<br />
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<big><b>Clotho Connectors</b></big><br />
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Given all these features, there still need to be components that allow Clotho to connect to the outside world. [[Team:UC_Berkeley_Tools/Project#mySQL_Configuration_Manager|'''Clotho connectors''']], so aptly named, perform this exact purpose. These components allow users to connect to databases through internet connections, or import and export data from existing files (think .gb, .ape, .str, etc). Connectors can also translate the results of Clotho back into any number of formats if the user so wishes.<br />
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<big><b>Clotho Plug-in Environment</b></big><br />
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But last, and certainly not least, is the [[Team:UC_Berkeley_Tools/Project#7._Clotho_Plug-In_System|'''Clotho plug-in environment''']]. This powerful environment allows developers both associated and not associated with the Clotho Project to create new and customized plug-ins to integrate with their versions of Clotho. Clotho was designed to be as ''fluid'' and ''flexible'' as possible! While the project is indeed open source, and users can always make new components by making new connections (see [[Team:UC_Berkeley_Tools/Project#The_Project|Project Technical]]), developers can now program personalized tools without knowing anything about the Clotho architecture, save for the plug-in environment! Plug-ins are a bit of an intermediate between a Clotho algorithm and a Clotho connection. This allows for relative customization, but also makes the programmer's life easier. They are rooted in the [http://jpf.sourceforge.net/ Java Plugin Framework (JPF)] and should provide a powerful, community driven aspect to Clotho.<br />
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We have spent long and hard working hours to develop this tool, and we sure hope you enjoy it. Play around with it and be sure to let us know what you think!<br />
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<big><center>'''WELCOME TO CLOTHO!'''</center></big><br />
<center>''Nade, Matt, Anne, and Doug''</center><br />
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<!---The Clotho design environment is centered around the ''Clotho Data Structure''. This object unifies information about a design in a standard way. This links various pieces of data related in a design to a powerful operational semantic. This semantic allows for design information to be related to databases containing part information, infer information about parts in a design, perform part look-ups in real time, and apply algorithms to designs. By taking potentially generic external information and bringing it into the Clotho Data Structure, non-standard designs can become standardized and then disseminated to a wider design community.<br />
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Shown in the figure are the major components in the Clotho design environment. In the center of the diagram is the Clotho Data structure...yada yada.---><br />
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===Clotho Database Interaction===<br />
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<html><font size="6">A</font></html> new concept we want to introduce to the synthetic biology community is this idea of database binding. This computer science influenced concept provides software tools a way to understand biological part databases that can differ across content, ordering and/or architecture. Clotho ''understands'' a standard set of data and its semantic by translating from unstandardized sets of data, and it remembers where unstandardized data came from. This allows Clotho to export unstandardized data to files understood by the community, or to simply take in unstandardized data, manipulate it under a standardized frame, and check in the edited information back to the unstandardized database. The figure to the right illustrates this. This allows Clotho to be many things to many different designers. One can use Clotho as a scheme to import data to new or existing repositories thus allowing the rapid distribution of data, or users may create their own lab environments and use Clotho to help maintain a consistent lab database.<br />
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<!---As the synthetic biology community moves toward the standardization of parts and their repositories it is important that a design environment be agnostic when possible to the data it can begin a design with. Clotho allows for the import of both standard and non-standard data. Once the data is brought into the system it can be manipulated, analyzed, modified, and viewed. It then can either be saved back in a non-standard way as it was brought into the system initially or converted to a standardized form and distributed more widely. The figure to the right illustrates such a process.---><br />
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==Contact Us==<br />
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<b>For general information or to contribute:</b> clothodevelopment AT googlegroups DOT com<br />
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<b>For emails regarding any bugs:</b> clothobugs AT googlegroups DOT com<br />
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<b>For emails regarding any desired features:</b> clothofeatures AT googlegroups DOT com<br />
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==Sponsors==<br />
We thank our Berkeley iGEM Advisory Group: Chris Anderson, Adam Arkin, John Dueber, Jay Keasling, and Susan Marqusee for their support and guidance, our Human Practices Advisors: Gaymon Bennett, Paul Rabinow, and Anthony Stavrianakis, administration support: Kevin Costa and Kate Spohr, and the generous financial support of our sponsors: <br><br />
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<img src="https://static.igem.org/mediawiki/2008/9/95/Ucb_genentech.jpeg" width="250" height="80"><br />
</a></div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/TeamTeam:UC Berkeley Tools/Team2008-10-29T10:57:49Z<p>Logosandpathos: /* Matthew L.E. Johnson - Student Member */</p>
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== Who we are ==<br />
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'''Faculty Advisors:'''<br />
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*''' Advisor 1''': Doug Densmore, Post-Doc at UC Berkeley<br />
*'''Advisor 2''': Chris Anderson, Assistant Professor at UC Berkeley<br />
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'''Undergrads:'''<br />
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*'''Student''': Anne Van Devender, 4th year Computer Science undergraduate, Washington and Lee University<br />
*'''Student''': Matthew Johnson, 4th year Bioengineering undergraduate, UC Berkeley<br />
*'''Student''': Nade Sritanyaratana, 4th year Bioengineering undergraduate, UC Berkeley<br />
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Image:Doug_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Dr._Douglas_Densmore|Doug Densmore]]<br />
Image:Anne_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Anne_Van_Devender|Anne Van Devender]]<br />
Image:MattInStanley.png|[[Team:UC_Berkeley_Tools/Team#Matthew_Johnson|Matthew L.E. Johnson]]<br />
Image:Nade_atStanley.png|[[Team:UC_Berkeley_Tools/Team#Nade_Sritanyaratana|Nade Sritanyaratana]]<br />
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==Team Biographies==<br />
[[Image:CalCompTeam.png|The 2008 iGEM Cal Comp Team]]<br />
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===Anne Van Devender - Student Member===<br />
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[[Image:Anne_Professional.jpg|250 px|thumb|left|Anne Van Devender]]<br />
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Anne Van Devender is a 4th year undergraduate at Washington and Lee University (Lexington, VA). She is a Computer Science major with a minor in Women's Studies. After graduation she hopes to attend graduate school for either a master's degree or PhD in Human Computer Interaction. <br />
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Her main endeavor outside of academics is the Washington and Lee Women's Soccer team where she is captain and a three-year letter winner. In 2007, she was named to the NSCAA All-America team. When she is not on the field or in the classroom, she enjoys working with kids in the Lexington community including involvement in a literacy campaign and teaching middle school girls the basics of computer science.<br />
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This summer she is participating in the Summer Undergraduate Program in Engineering Research at Berkeley (SUPERB) and working with the iGEM 2008 UC Berkeley Computational Team. She is using Java to write an "Algorithm Manager" for the Clotho tool. While she has used Java extensively in her coursework at W&L, the synthetic biology aspect of the project is completely new to her. The last time she took biology was in 9th grade! She hopes this project will not only improve her research skills in computer science, but will also enlighten her to the emerging field of synthetic biology.<br />
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===Nade Sritanyaratana - Student Member===<br />
[[Image:Nade_Professional.jpg|thumb|Nade Sritanyaratana]]<br />
<!---[[Image:NadeHeadShot.png|thumb|Nade Sritanyaratana]]---><br />
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Nade Sritanyaratana is a 3rd year undergraduate at the University of California, Berkeley. He is majoring in Bioengineering with a concentration in imaging, and hopes to apply for a PhD graduate program in the upcoming year. Beyond imaging, his academic interests include Biomechanics; signals and systems; circuit analysis; systems biology; and linear optimization.<br />
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His prior research experience consists of working with [http://bioeng.berkeley.edu/cv.php?facultyid=3022 bioengineering professor Steven Conolly] in the Summer and Fall of 2007. During that summer, he designed a coil helmet with an induced [http://en.wikipedia.org/wiki/Maxwell_coil Maxwell magnetic field]. This magnetic coil could be worn on the head and activated to generate small magnetic waves, soothing the wearer. Nicknamed the “Happy Helmet”, it was designed to non-invasively treat the bipolar-depressed via magnetic stimulation. Once fully developed, the helmet was to cost a hundred-fold less than an [http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging fMRI], the current primary treatment to bipolar depression.<br />
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This summer Nade is working full-time with the iGEM 2008 Cal Computational Team. This is his first time using Java. Prior to Java, his programming experience included an introductory C++ class in the 9th grade and MATLAB experience for three years in Berkeley. He has had prior experience with computational modeling in general; last year Nade worked with LabVIEW for his introductory class to signals and systems. Last fall he graphically modeled a growing brain tumor with ADINA for his Biomechanics class, and later based his main Biofluid mechanics project on the dynamics of a atherosclerotic artery using a computational model generated by COMSOL.<br />
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===Matthew Johnson - Student Member===<br />
[[Image:Matt_Professional2.jpg|thumb|270px|Matthew L.E. Johnson]]<br />
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Matthew Johnson is currently starting up his senior year at the University of California, Berkeley. He is a Bioengineering major focusing on cell & tissue engineering, with a passionate interest in regenerative science and synthetic biology. He is also enthusiastic about nanotechnology, BioMEMS, molecular biology, product design, economics, and writing.<br />
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Matt has lofty ambitions, and thinks that applied science is the key to solving many of life's problems, maybe even including the big one at the end of it. He is very interested in how bioengineering and synthetic biology can be used to improve living conditions for people all over the world, whether through novel medical treatments, cheaper, cleaner sources of replenishable energy, or the development of heartier and healthier food crops. Outside of science, one of of his biggest interests is taekwondo, which he started his freshman year at Cal and has involved himself extensively with ever since. He believes that the discipline and physical training has improved his life, and he just loves getting a chance to compete - win or lose, there's always something to learn.<br />
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This summer was one of his first major research efforts. He'd had experience programming in Java many years before, but had to learn it again from the ground-up for iGEM, though familiarity with Perl and programming in general helped considerably. Due to a martial arts-related injury, he was gone for the last third of the summer, but he continued to code from his home in Bakersfield, CA while he recuperated. He hopes to help in the future development of Clotho in his spare time, to create an even more useful and functional tool to aid synthetic biologists in their research.<br />
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===Dr. Douglas Densmore - Instructor===<br />
[[Image:DougAtTheDOP2.png|thumb|Douglas Densmore]]<br />
Douglas Densmore received his Bachelors of Science in Engineering (Computer Engineering) from the University of Michigan in April 2001. He received his Masters of Science in Electrical Engineering in May 2004 from the University of California at Berkeley. His masters thesis was entitled, "Platform Based Reconfigurable Architecture Exploration via Boolean Constraints" and demonstrated how Boolean Satisfiability could be used to produce configurations for programmable hardware. He received his PhD in Electrical Engineering from UC Berkeley as well in May 2007. His PhD thesis, entitled "A Design Flow for the Development, Characterization, and Refinement of System Level Architecture Services", explored how electronic system level design methodologies can be abstract and modular while at the same time remaining accurate and efficient.<br />
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He is currently a UC Chancellor's post doctoral researcher at UC Berkeley studying under [http://www.eecs.berkeley.edu/~alberto Prof. Alberto Sangiovanni-Vincentelli]. His research area is in the development of System Level Design methodologies for electronic systems. Specifically, architecture modeling and refinement verification. His background and interests are in Computer Architecture, Logic Synthesis, Digital Logic Design and Synthetic Biology. <br />
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His industry experience includes four+ summers with Intel Corporation where he was involved in pre-silicon design efforts regarding chipset development, post-silicon validation of the Pentium 4 microprocessor, and chipset software validation. He has also worked as a researcher at Cypress Semiconductor and Xilinx Research Labs. He is currently a member of the [http://www.gigascale.org Gigascale Systems Research Center (GSRC)] and the [http://chess.eecs.berkeley.edu Center for Hybrid and Embedded Software Systems (CHESS)] at UC Berkeley. He has published work regarding a method of successive refinement verification of electronic systems, taxonomies of EDA design tools, and algebraic frameworks for the manipulation of functional design descriptions to expose computational parallelism. In addition he has a US patent pending regarding data characterization of programmable devices (such as field programmable gate arrays).<br />
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== What we did ==<br />
''This section briefly describes the contributions of each team member.''<br />
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===Matthew LE Johnson===<br />
Spent a lot of time working on:<br />
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* The About connection/frame<br />
* DNA analysis tools and algorithms (including Translation, G-C content, Melting Temperature, Reverse complementing, etc.)<br />
* The Enzyme Library and associated functionality<br />
* Sequence View connection (with Nade and Doug)<br />
* Compatibility with GenBank, FASTA, and ApE file formats<br />
* Support for degenerate IUPAC codes<br />
* Restriction site search and highlighting<br />
* Forward and reverse Open Reading Frame search and highlighting<br />
* Clotho Preferences for various connections<br />
* All of the Clotho Transfer Handlers<br />
* Intelligent Drag and Drop (DnD) between connections<br />
* Work on the Comp. Team Wiki<br />
* Feedback and advice on the graphic designs (seriously: thank you, Nade!)<br />
* ... and many, MANY hours of debugging!<br />
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===Anne Van Devender===<br />
Anne Van Devender was responsible for:<br />
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* The development and design of the algorithm manager<br />
* Clotho algorithm interface and initial implementation<br />
* The conversion of BioBrick assembly algorithms from Perl to Java<br />
* Aid in the development of 2ab assembly algorithms for Clotho<br />
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===Nade Sritanyaratana===<br />
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Nade Sritanyaratana, in semi-chronological order, is attributed to the following work: <br />
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* The Help connection/frame<br />
* Highlighting<br />
* Features connection<br />
* Co-coordinated Sequence View connection/frame alongside Matt and Doug<br />
* Sequence View Tools (Find/Replace)<br />
* Feature Library Collection connection/frame<br />
* File Choosers<br />
* Search Helper<br />
* .txt file Helper<br />
* Photographing at test sessions<br />
* Debugging post-test sessions<br />
* Parts Manager<br />
* Maintaining the iGEM 2008 Computational Tools Team wiki: layout and painted graphics<br />
* Maintaining the Cal College of Engineering iGEM blog alongside Marlee Tichenor and Madvhi Venkatesh of the wet team<br />
* Clotho iGEM logo and woman<br />
* Clotho iGEM t-shirt<br />
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===Dr. Douglas Densmore===<br />
Doug provided the initial Clotho software infrastructure and served as the main team lead. He helped to keep the team on track and supervised the construction and functionality of Clotho. He is the chief architect of Clotho and in charge of its maintenance, deployment, and promotion.<br />
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===Dr. Chris Anderson===<br />
Prof. Anderson provided specifications for what tools and techniques should be incorporated in Clotho. In addition he also helped to define the general assembly problem for standardized biological parts as well as provide the context in which the tool would be used. He also provided many interesting discussion regarding the Clotho data model and provided the database by which we did the majority of our testing.<br />
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===Other attribution===<br />
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Many thanks to Collin Martin for the professional photography shots, and the Comp team shot.<br />
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Shout out goes to Cici Chen of the UC Berkeley wetlab for helping design the Clotho title (alpha). Also Brian Zimmer, Bing Xia, and Roger Tu also have contributed to the development of Clotho. Josh Kittleson was instrumental in the development of the mySQL/PoBoL connection and tools. Will Deloache helped with the development of the assembly algorithms for 2ab assembly that is in the tool.<br />
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== Where we're from ==<br />
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===Dr. Douglas Densmore===<br />
Doug is from Richland, Michigan which is a small town outside of Kalamazoo. He attended the University of Michigan from 1996-2001 and has been in Berkeley, California since 2001. His family is from the Detroit area. They still live in Michigan.<br />
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===Nade Sritanyaratana===<br />
Nade is a 4th year bioengineering undergraduate at UC Berkeley. He was born in the SF Bay Area, in Hayward, CA, and has lived around the Bay Area his entire life. Both of his parents are Thai. He attended James Logan High School in Union City, CA, where his primary activities included speech and debate, Leo Club, and the swim team. His family still resides in Union City.<br />
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===Matthew L.E. Johnson===<br />
Matt is a SoCal native - born and raised in Bakersfield, CA right up until the move to Berkeley in 2005. He loves his hometown, but realizes that it is an 'acquired taste', especially during the average summer's daily triple-digit heat. Despite the vast differences between his new home and his old (with inverse climates - politically and meteorologically), he has adapted well and has been greatly enjoying his stay in the Bay Area.</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/TeamTeam:UC Berkeley Tools/Team2008-10-29T10:57:30Z<p>Logosandpathos: /* Matthew L.E. Johnson - Student Member */</p>
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== Who we are ==<br />
{|border = "0"<br />
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'''Faculty Advisors:'''<br />
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*''' Advisor 1''': Doug Densmore, Post-Doc at UC Berkeley<br />
*'''Advisor 2''': Chris Anderson, Assistant Professor at UC Berkeley<br />
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'''Undergrads:'''<br />
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*'''Student''': Anne Van Devender, 4th year Computer Science undergraduate, Washington and Lee University<br />
*'''Student''': Matthew Johnson, 4th year Bioengineering undergraduate, UC Berkeley<br />
*'''Student''': Nade Sritanyaratana, 4th year Bioengineering undergraduate, UC Berkeley<br />
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<gallery perrow="4"><br />
Image:Doug_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Dr._Douglas_Densmore|Doug Densmore]]<br />
Image:Anne_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Anne_Van_Devender|Anne Van Devender]]<br />
Image:MattInStanley.png|[[Team:UC_Berkeley_Tools/Team#Matthew_Johnson|Matthew L.E. Johnson]]<br />
Image:Nade_atStanley.png|[[Team:UC_Berkeley_Tools/Team#Nade_Sritanyaratana|Nade Sritanyaratana]]<br />
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==Team Biographies==<br />
[[Image:CalCompTeam.png|The 2008 iGEM Cal Comp Team]]<br />
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===Anne Van Devender - Student Member===<br />
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[[Image:Anne_Professional.jpg|250 px|thumb|left|Anne Van Devender]]<br />
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Anne Van Devender is a 4th year undergraduate at Washington and Lee University (Lexington, VA). She is a Computer Science major with a minor in Women's Studies. After graduation she hopes to attend graduate school for either a master's degree or PhD in Human Computer Interaction. <br />
<br />
Her main endeavor outside of academics is the Washington and Lee Women's Soccer team where she is captain and a three-year letter winner. In 2007, she was named to the NSCAA All-America team. When she is not on the field or in the classroom, she enjoys working with kids in the Lexington community including involvement in a literacy campaign and teaching middle school girls the basics of computer science.<br />
<br />
This summer she is participating in the Summer Undergraduate Program in Engineering Research at Berkeley (SUPERB) and working with the iGEM 2008 UC Berkeley Computational Team. She is using Java to write an "Algorithm Manager" for the Clotho tool. While she has used Java extensively in her coursework at W&L, the synthetic biology aspect of the project is completely new to her. The last time she took biology was in 9th grade! She hopes this project will not only improve her research skills in computer science, but will also enlighten her to the emerging field of synthetic biology.<br />
<br />
===Nade Sritanyaratana - Student Member===<br />
[[Image:Nade_Professional.jpg|thumb|Nade Sritanyaratana]]<br />
<!---[[Image:NadeHeadShot.png|thumb|Nade Sritanyaratana]]---><br />
<br />
Nade Sritanyaratana is a 3rd year undergraduate at the University of California, Berkeley. He is majoring in Bioengineering with a concentration in imaging, and hopes to apply for a PhD graduate program in the upcoming year. Beyond imaging, his academic interests include Biomechanics; signals and systems; circuit analysis; systems biology; and linear optimization.<br />
<br />
His prior research experience consists of working with [http://bioeng.berkeley.edu/cv.php?facultyid=3022 bioengineering professor Steven Conolly] in the Summer and Fall of 2007. During that summer, he designed a coil helmet with an induced [http://en.wikipedia.org/wiki/Maxwell_coil Maxwell magnetic field]. This magnetic coil could be worn on the head and activated to generate small magnetic waves, soothing the wearer. Nicknamed the “Happy Helmet”, it was designed to non-invasively treat the bipolar-depressed via magnetic stimulation. Once fully developed, the helmet was to cost a hundred-fold less than an [http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging fMRI], the current primary treatment to bipolar depression.<br />
<br />
This summer Nade is working full-time with the iGEM 2008 Cal Computational Team. This is his first time using Java. Prior to Java, his programming experience included an introductory C++ class in the 9th grade and MATLAB experience for three years in Berkeley. He has had prior experience with computational modeling in general; last year Nade worked with LabVIEW for his introductory class to signals and systems. Last fall he graphically modeled a growing brain tumor with ADINA for his Biomechanics class, and later based his main Biofluid mechanics project on the dynamics of a atherosclerotic artery using a computational model generated by COMSOL.<br />
<br />
===Matthew L.E. Johnson - Student Member===<br />
[[Image:Matt_Professional2.jpg|thumb|270px|Matthew Johnson]]<br />
<br />
Matthew Johnson is currently starting up his senior year at the University of California, Berkeley. He is a Bioengineering major focusing on cell & tissue engineering, with a passionate interest in regenerative science and synthetic biology. He is also enthusiastic about nanotechnology, BioMEMS, molecular biology, product design, economics, and writing.<br />
<br />
Matt has lofty ambitions, and thinks that applied science is the key to solving many of life's problems, maybe even including the big one at the end of it. He is very interested in how bioengineering and synthetic biology can be used to improve living conditions for people all over the world, whether through novel medical treatments, cheaper, cleaner sources of replenishable energy, or the development of heartier and healthier food crops. Outside of science, one of of his biggest interests is taekwondo, which he started his freshman year at Cal and has involved himself extensively with ever since. He believes that the discipline and physical training has improved his life, and he just loves getting a chance to compete - win or lose, there's always something to learn.<br />
<br />
This summer was one of his first major research efforts. He'd had experience programming in Java many years before, but had to learn it again from the ground-up for iGEM, though familiarity with Perl and programming in general helped considerably. Due to a martial arts-related injury, he was gone for the last third of the summer, but he continued to code from his home in Bakersfield, CA while he recuperated. He hopes to help in the future development of Clotho in his spare time, to create an even more useful and functional tool to aid synthetic biologists in their research.<br />
<br />
===Dr. Douglas Densmore - Instructor===<br />
[[Image:DougAtTheDOP2.png|thumb|Douglas Densmore]]<br />
Douglas Densmore received his Bachelors of Science in Engineering (Computer Engineering) from the University of Michigan in April 2001. He received his Masters of Science in Electrical Engineering in May 2004 from the University of California at Berkeley. His masters thesis was entitled, "Platform Based Reconfigurable Architecture Exploration via Boolean Constraints" and demonstrated how Boolean Satisfiability could be used to produce configurations for programmable hardware. He received his PhD in Electrical Engineering from UC Berkeley as well in May 2007. His PhD thesis, entitled "A Design Flow for the Development, Characterization, and Refinement of System Level Architecture Services", explored how electronic system level design methodologies can be abstract and modular while at the same time remaining accurate and efficient.<br />
<br />
He is currently a UC Chancellor's post doctoral researcher at UC Berkeley studying under [http://www.eecs.berkeley.edu/~alberto Prof. Alberto Sangiovanni-Vincentelli]. His research area is in the development of System Level Design methodologies for electronic systems. Specifically, architecture modeling and refinement verification. His background and interests are in Computer Architecture, Logic Synthesis, Digital Logic Design and Synthetic Biology. <br />
<br />
His industry experience includes four+ summers with Intel Corporation where he was involved in pre-silicon design efforts regarding chipset development, post-silicon validation of the Pentium 4 microprocessor, and chipset software validation. He has also worked as a researcher at Cypress Semiconductor and Xilinx Research Labs. He is currently a member of the [http://www.gigascale.org Gigascale Systems Research Center (GSRC)] and the [http://chess.eecs.berkeley.edu Center for Hybrid and Embedded Software Systems (CHESS)] at UC Berkeley. He has published work regarding a method of successive refinement verification of electronic systems, taxonomies of EDA design tools, and algebraic frameworks for the manipulation of functional design descriptions to expose computational parallelism. In addition he has a US patent pending regarding data characterization of programmable devices (such as field programmable gate arrays).<br />
<br />
<br clear="all"><br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
== What we did ==<br />
''This section briefly describes the contributions of each team member.''<br />
<br />
===Matthew LE Johnson===<br />
Spent a lot of time working on:<br />
<br />
* The About connection/frame<br />
* DNA analysis tools and algorithms (including Translation, G-C content, Melting Temperature, Reverse complementing, etc.)<br />
* The Enzyme Library and associated functionality<br />
* Sequence View connection (with Nade and Doug)<br />
* Compatibility with GenBank, FASTA, and ApE file formats<br />
* Support for degenerate IUPAC codes<br />
* Restriction site search and highlighting<br />
* Forward and reverse Open Reading Frame search and highlighting<br />
* Clotho Preferences for various connections<br />
* All of the Clotho Transfer Handlers<br />
* Intelligent Drag and Drop (DnD) between connections<br />
* Work on the Comp. Team Wiki<br />
* Feedback and advice on the graphic designs (seriously: thank you, Nade!)<br />
* ... and many, MANY hours of debugging!<br />
<br />
===Anne Van Devender===<br />
Anne Van Devender was responsible for:<br />
<br />
* The development and design of the algorithm manager<br />
* Clotho algorithm interface and initial implementation<br />
* The conversion of BioBrick assembly algorithms from Perl to Java<br />
* Aid in the development of 2ab assembly algorithms for Clotho<br />
<br />
===Nade Sritanyaratana===<br />
<br />
Nade Sritanyaratana, in semi-chronological order, is attributed to the following work: <br />
<br />
* The Help connection/frame<br />
* Highlighting<br />
* Features connection<br />
* Co-coordinated Sequence View connection/frame alongside Matt and Doug<br />
* Sequence View Tools (Find/Replace)<br />
* Feature Library Collection connection/frame<br />
* File Choosers<br />
* Search Helper<br />
* .txt file Helper<br />
* Photographing at test sessions<br />
* Debugging post-test sessions<br />
* Parts Manager<br />
* Maintaining the iGEM 2008 Computational Tools Team wiki: layout and painted graphics<br />
* Maintaining the Cal College of Engineering iGEM blog alongside Marlee Tichenor and Madvhi Venkatesh of the wet team<br />
* Clotho iGEM logo and woman<br />
* Clotho iGEM t-shirt<br />
<br />
===Dr. Douglas Densmore===<br />
Doug provided the initial Clotho software infrastructure and served as the main team lead. He helped to keep the team on track and supervised the construction and functionality of Clotho. He is the chief architect of Clotho and in charge of its maintenance, deployment, and promotion.<br />
<br />
===Dr. Chris Anderson===<br />
Prof. Anderson provided specifications for what tools and techniques should be incorporated in Clotho. In addition he also helped to define the general assembly problem for standardized biological parts as well as provide the context in which the tool would be used. He also provided many interesting discussion regarding the Clotho data model and provided the database by which we did the majority of our testing.<br />
<br />
===Other attribution===<br />
<br />
Many thanks to Collin Martin for the professional photography shots, and the Comp team shot.<br />
<br />
Shout out goes to Cici Chen of the UC Berkeley wetlab for helping design the Clotho title (alpha). Also Brian Zimmer, Bing Xia, and Roger Tu also have contributed to the development of Clotho. Josh Kittleson was instrumental in the development of the mySQL/PoBoL connection and tools. Will Deloache helped with the development of the assembly algorithms for 2ab assembly that is in the tool.<br />
<br />
== Where we're from ==<br />
<br />
===Dr. Douglas Densmore===<br />
Doug is from Richland, Michigan which is a small town outside of Kalamazoo. He attended the University of Michigan from 1996-2001 and has been in Berkeley, California since 2001. His family is from the Detroit area. They still live in Michigan.<br />
<br />
===Nade Sritanyaratana===<br />
Nade is a 4th year bioengineering undergraduate at UC Berkeley. He was born in the SF Bay Area, in Hayward, CA, and has lived around the Bay Area his entire life. Both of his parents are Thai. He attended James Logan High School in Union City, CA, where his primary activities included speech and debate, Leo Club, and the swim team. His family still resides in Union City.<br />
<br />
===Matthew L.E. Johnson===<br />
Matt is a SoCal native - born and raised in Bakersfield, CA right up until the move to Berkeley in 2005. He loves his hometown, but realizes that it is an 'acquired taste', especially during the average summer's daily triple-digit heat. Despite the vast differences between his new home and his old (with inverse climates - politically and meteorologically), he has adapted well and has been greatly enjoying his stay in the Bay Area.</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/TeamTeam:UC Berkeley Tools/Team2008-10-29T10:57:08Z<p>Logosandpathos: /* Matthew Johnson - Student Member */</p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<!--- <center>[http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development#Downloads_and_Information <b>The Alpha release is here.</b>]</center> ---><br />
<br />
{{Template:ClothoMenu}}<br />
__NOTOC__<br />
<br />
<br />
== Who we are ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
'''Faculty Advisors:'''<br />
<br />
*''' Advisor 1''': Doug Densmore, Post-Doc at UC Berkeley<br />
*'''Advisor 2''': Chris Anderson, Assistant Professor at UC Berkeley<br />
<br />
<br />
'''Undergrads:'''<br />
<br />
*'''Student''': Anne Van Devender, 4th year Computer Science undergraduate, Washington and Lee University<br />
*'''Student''': Matthew Johnson, 4th year Bioengineering undergraduate, UC Berkeley<br />
*'''Student''': Nade Sritanyaratana, 4th year Bioengineering undergraduate, UC Berkeley<br />
<br />
|<br />
<gallery perrow="4"><br />
Image:Doug_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Dr._Douglas_Densmore|Doug Densmore]]<br />
Image:Anne_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Anne_Van_Devender|Anne Van Devender]]<br />
Image:MattInStanley.png|[[Team:UC_Berkeley_Tools/Team#Matthew_Johnson|Matthew L.E. Johnson]]<br />
Image:Nade_atStanley.png|[[Team:UC_Berkeley_Tools/Team#Nade_Sritanyaratana|Nade Sritanyaratana]]<br />
</gallery><br />
|}<br />
<br />
==Team Biographies==<br />
[[Image:CalCompTeam.png|The 2008 iGEM Cal Comp Team]]<br />
<br />
===Anne Van Devender - Student Member===<br />
<br />
[[Image:Anne_Professional.jpg|250 px|thumb|left|Anne Van Devender]]<br />
<br />
Anne Van Devender is a 4th year undergraduate at Washington and Lee University (Lexington, VA). She is a Computer Science major with a minor in Women's Studies. After graduation she hopes to attend graduate school for either a master's degree or PhD in Human Computer Interaction. <br />
<br />
Her main endeavor outside of academics is the Washington and Lee Women's Soccer team where she is captain and a three-year letter winner. In 2007, she was named to the NSCAA All-America team. When she is not on the field or in the classroom, she enjoys working with kids in the Lexington community including involvement in a literacy campaign and teaching middle school girls the basics of computer science.<br />
<br />
This summer she is participating in the Summer Undergraduate Program in Engineering Research at Berkeley (SUPERB) and working with the iGEM 2008 UC Berkeley Computational Team. She is using Java to write an "Algorithm Manager" for the Clotho tool. While she has used Java extensively in her coursework at W&L, the synthetic biology aspect of the project is completely new to her. The last time she took biology was in 9th grade! She hopes this project will not only improve her research skills in computer science, but will also enlighten her to the emerging field of synthetic biology.<br />
<br />
===Nade Sritanyaratana - Student Member===<br />
[[Image:Nade_Professional.jpg|thumb|Nade Sritanyaratana]]<br />
<!---[[Image:NadeHeadShot.png|thumb|Nade Sritanyaratana]]---><br />
<br />
Nade Sritanyaratana is a 3rd year undergraduate at the University of California, Berkeley. He is majoring in Bioengineering with a concentration in imaging, and hopes to apply for a PhD graduate program in the upcoming year. Beyond imaging, his academic interests include Biomechanics; signals and systems; circuit analysis; systems biology; and linear optimization.<br />
<br />
His prior research experience consists of working with [http://bioeng.berkeley.edu/cv.php?facultyid=3022 bioengineering professor Steven Conolly] in the Summer and Fall of 2007. During that summer, he designed a coil helmet with an induced [http://en.wikipedia.org/wiki/Maxwell_coil Maxwell magnetic field]. This magnetic coil could be worn on the head and activated to generate small magnetic waves, soothing the wearer. Nicknamed the “Happy Helmet”, it was designed to non-invasively treat the bipolar-depressed via magnetic stimulation. Once fully developed, the helmet was to cost a hundred-fold less than an [http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging fMRI], the current primary treatment to bipolar depression.<br />
<br />
This summer Nade is working full-time with the iGEM 2008 Cal Computational Team. This is his first time using Java. Prior to Java, his programming experience included an introductory C++ class in the 9th grade and MATLAB experience for three years in Berkeley. He has had prior experience with computational modeling in general; last year Nade worked with LabVIEW for his introductory class to signals and systems. Last fall he graphically modeled a growing brain tumor with ADINA for his Biomechanics class, and later based his main Biofluid mechanics project on the dynamics of a atherosclerotic artery using a computational model generated by COMSOL.<br />
<br />
===Matthew L.E. Johnson - Student Member===<br />
[[Image:Matt_Professional2.jpg|thumb|270px|Matthew L.E. Johnson]]<br />
<br />
Matthew Johnson is currently starting up his senior year at the University of California, Berkeley. He is a Bioengineering major focusing on cell & tissue engineering, with a passionate interest in regenerative science and synthetic biology. He is also enthusiastic about nanotechnology, BioMEMS, molecular biology, product design, economics, and writing.<br />
<br />
Matt has lofty ambitions, and thinks that applied science is the key to solving many of life's problems, maybe even including the big one at the end of it. He is very interested in how bioengineering and synthetic biology can be used to improve living conditions for people all over the world, whether through novel medical treatments, cheaper, cleaner sources of replenishable energy, or the development of heartier and healthier food crops. Outside of science, one of of his biggest interests is taekwondo, which he started his freshman year at Cal and has involved himself extensively with ever since. He believes that the discipline and physical training has improved his life, and he just loves getting a chance to compete - win or lose, there's always something to learn.<br />
<br />
This summer was one of his first major research efforts. He'd had experience programming in Java many years before, but had to learn it again from the ground-up for iGEM, though familiarity with Perl and programming in general helped considerably. Due to a martial arts-related injury, he was gone for the last third of the summer, but he continued to code from his home in Bakersfield, CA while he recuperated. He hopes to help in the future development of Clotho in his spare time, to create an even more useful and functional tool to aid synthetic biologists in their research.<br />
<br />
===Dr. Douglas Densmore - Instructor===<br />
[[Image:DougAtTheDOP2.png|thumb|Douglas Densmore]]<br />
Douglas Densmore received his Bachelors of Science in Engineering (Computer Engineering) from the University of Michigan in April 2001. He received his Masters of Science in Electrical Engineering in May 2004 from the University of California at Berkeley. His masters thesis was entitled, "Platform Based Reconfigurable Architecture Exploration via Boolean Constraints" and demonstrated how Boolean Satisfiability could be used to produce configurations for programmable hardware. He received his PhD in Electrical Engineering from UC Berkeley as well in May 2007. His PhD thesis, entitled "A Design Flow for the Development, Characterization, and Refinement of System Level Architecture Services", explored how electronic system level design methodologies can be abstract and modular while at the same time remaining accurate and efficient.<br />
<br />
He is currently a UC Chancellor's post doctoral researcher at UC Berkeley studying under [http://www.eecs.berkeley.edu/~alberto Prof. Alberto Sangiovanni-Vincentelli]. His research area is in the development of System Level Design methodologies for electronic systems. Specifically, architecture modeling and refinement verification. His background and interests are in Computer Architecture, Logic Synthesis, Digital Logic Design and Synthetic Biology. <br />
<br />
His industry experience includes four+ summers with Intel Corporation where he was involved in pre-silicon design efforts regarding chipset development, post-silicon validation of the Pentium 4 microprocessor, and chipset software validation. He has also worked as a researcher at Cypress Semiconductor and Xilinx Research Labs. He is currently a member of the [http://www.gigascale.org Gigascale Systems Research Center (GSRC)] and the [http://chess.eecs.berkeley.edu Center for Hybrid and Embedded Software Systems (CHESS)] at UC Berkeley. He has published work regarding a method of successive refinement verification of electronic systems, taxonomies of EDA design tools, and algebraic frameworks for the manipulation of functional design descriptions to expose computational parallelism. In addition he has a US patent pending regarding data characterization of programmable devices (such as field programmable gate arrays).<br />
<br />
<br clear="all"><br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
== What we did ==<br />
''This section briefly describes the contributions of each team member.''<br />
<br />
===Matthew LE Johnson===<br />
Spent a lot of time working on:<br />
<br />
* The About connection/frame<br />
* DNA analysis tools and algorithms (including Translation, G-C content, Melting Temperature, Reverse complementing, etc.)<br />
* The Enzyme Library and associated functionality<br />
* Sequence View connection (with Nade and Doug)<br />
* Compatibility with GenBank, FASTA, and ApE file formats<br />
* Support for degenerate IUPAC codes<br />
* Restriction site search and highlighting<br />
* Forward and reverse Open Reading Frame search and highlighting<br />
* Clotho Preferences for various connections<br />
* All of the Clotho Transfer Handlers<br />
* Intelligent Drag and Drop (DnD) between connections<br />
* Work on the Comp. Team Wiki<br />
* Feedback and advice on the graphic designs (seriously: thank you, Nade!)<br />
* ... and many, MANY hours of debugging!<br />
<br />
===Anne Van Devender===<br />
Anne Van Devender was responsible for:<br />
<br />
* The development and design of the algorithm manager<br />
* Clotho algorithm interface and initial implementation<br />
* The conversion of BioBrick assembly algorithms from Perl to Java<br />
* Aid in the development of 2ab assembly algorithms for Clotho<br />
<br />
===Nade Sritanyaratana===<br />
<br />
Nade Sritanyaratana, in semi-chronological order, is attributed to the following work: <br />
<br />
* The Help connection/frame<br />
* Highlighting<br />
* Features connection<br />
* Co-coordinated Sequence View connection/frame alongside Matt and Doug<br />
* Sequence View Tools (Find/Replace)<br />
* Feature Library Collection connection/frame<br />
* File Choosers<br />
* Search Helper<br />
* .txt file Helper<br />
* Photographing at test sessions<br />
* Debugging post-test sessions<br />
* Parts Manager<br />
* Maintaining the iGEM 2008 Computational Tools Team wiki: layout and painted graphics<br />
* Maintaining the Cal College of Engineering iGEM blog alongside Marlee Tichenor and Madvhi Venkatesh of the wet team<br />
* Clotho iGEM logo and woman<br />
* Clotho iGEM t-shirt<br />
<br />
===Dr. Douglas Densmore===<br />
Doug provided the initial Clotho software infrastructure and served as the main team lead. He helped to keep the team on track and supervised the construction and functionality of Clotho. He is the chief architect of Clotho and in charge of its maintenance, deployment, and promotion.<br />
<br />
===Dr. Chris Anderson===<br />
Prof. Anderson provided specifications for what tools and techniques should be incorporated in Clotho. In addition he also helped to define the general assembly problem for standardized biological parts as well as provide the context in which the tool would be used. He also provided many interesting discussion regarding the Clotho data model and provided the database by which we did the majority of our testing.<br />
<br />
===Other attribution===<br />
<br />
Many thanks to Collin Martin for the professional photography shots, and the Comp team shot.<br />
<br />
Shout out goes to Cici Chen of the UC Berkeley wetlab for helping design the Clotho title (alpha). Also Brian Zimmer, Bing Xia, and Roger Tu also have contributed to the development of Clotho. Josh Kittleson was instrumental in the development of the mySQL/PoBoL connection and tools. Will Deloache helped with the development of the assembly algorithms for 2ab assembly that is in the tool.<br />
<br />
== Where we're from ==<br />
<br />
===Dr. Douglas Densmore===<br />
Doug is from Richland, Michigan which is a small town outside of Kalamazoo. He attended the University of Michigan from 1996-2001 and has been in Berkeley, California since 2001. His family is from the Detroit area. They still live in Michigan.<br />
<br />
===Nade Sritanyaratana===<br />
Nade is a 4th year bioengineering undergraduate at UC Berkeley. He was born in the SF Bay Area, in Hayward, CA, and has lived around the Bay Area his entire life. Both of his parents are Thai. He attended James Logan High School in Union City, CA, where his primary activities included speech and debate, Leo Club, and the swim team. His family still resides in Union City.<br />
<br />
===Matthew L.E. Johnson===<br />
Matt is a SoCal native - born and raised in Bakersfield, CA right up until the move to Berkeley in 2005. He loves his hometown, but realizes that it is an 'acquired taste', especially during the average summer's daily triple-digit heat. Despite the vast differences between his new home and his old (with inverse climates - politically and meteorologically), he has adapted well and has been greatly enjoying his stay in the Bay Area.</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/TeamTeam:UC Berkeley Tools/Team2008-10-29T10:56:47Z<p>Logosandpathos: /* Matthew Johnson - Student Member */</p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<!--- <center>[http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development#Downloads_and_Information <b>The Alpha release is here.</b>]</center> ---><br />
<br />
{{Template:ClothoMenu}}<br />
__NOTOC__<br />
<br />
<br />
== Who we are ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
'''Faculty Advisors:'''<br />
<br />
*''' Advisor 1''': Doug Densmore, Post-Doc at UC Berkeley<br />
*'''Advisor 2''': Chris Anderson, Assistant Professor at UC Berkeley<br />
<br />
<br />
'''Undergrads:'''<br />
<br />
*'''Student''': Anne Van Devender, 4th year Computer Science undergraduate, Washington and Lee University<br />
*'''Student''': Matthew Johnson, 4th year Bioengineering undergraduate, UC Berkeley<br />
*'''Student''': Nade Sritanyaratana, 4th year Bioengineering undergraduate, UC Berkeley<br />
<br />
|<br />
<gallery perrow="4"><br />
Image:Doug_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Dr._Douglas_Densmore|Doug Densmore]]<br />
Image:Anne_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Anne_Van_Devender|Anne Van Devender]]<br />
Image:MattInStanley.png|[[Team:UC_Berkeley_Tools/Team#Matthew_Johnson|Matthew L.E. Johnson]]<br />
Image:Nade_atStanley.png|[[Team:UC_Berkeley_Tools/Team#Nade_Sritanyaratana|Nade Sritanyaratana]]<br />
</gallery><br />
|}<br />
<br />
==Team Biographies==<br />
[[Image:CalCompTeam.png|The 2008 iGEM Cal Comp Team]]<br />
<br />
===Anne Van Devender - Student Member===<br />
<br />
[[Image:Anne_Professional.jpg|250 px|thumb|left|Anne Van Devender]]<br />
<br />
Anne Van Devender is a 4th year undergraduate at Washington and Lee University (Lexington, VA). She is a Computer Science major with a minor in Women's Studies. After graduation she hopes to attend graduate school for either a master's degree or PhD in Human Computer Interaction. <br />
<br />
Her main endeavor outside of academics is the Washington and Lee Women's Soccer team where she is captain and a three-year letter winner. In 2007, she was named to the NSCAA All-America team. When she is not on the field or in the classroom, she enjoys working with kids in the Lexington community including involvement in a literacy campaign and teaching middle school girls the basics of computer science.<br />
<br />
This summer she is participating in the Summer Undergraduate Program in Engineering Research at Berkeley (SUPERB) and working with the iGEM 2008 UC Berkeley Computational Team. She is using Java to write an "Algorithm Manager" for the Clotho tool. While she has used Java extensively in her coursework at W&L, the synthetic biology aspect of the project is completely new to her. The last time she took biology was in 9th grade! She hopes this project will not only improve her research skills in computer science, but will also enlighten her to the emerging field of synthetic biology.<br />
<br />
===Nade Sritanyaratana - Student Member===<br />
[[Image:Nade_Professional.jpg|thumb|Nade Sritanyaratana]]<br />
<!---[[Image:NadeHeadShot.png|thumb|Nade Sritanyaratana]]---><br />
<br />
Nade Sritanyaratana is a 3rd year undergraduate at the University of California, Berkeley. He is majoring in Bioengineering with a concentration in imaging, and hopes to apply for a PhD graduate program in the upcoming year. Beyond imaging, his academic interests include Biomechanics; signals and systems; circuit analysis; systems biology; and linear optimization.<br />
<br />
His prior research experience consists of working with [http://bioeng.berkeley.edu/cv.php?facultyid=3022 bioengineering professor Steven Conolly] in the Summer and Fall of 2007. During that summer, he designed a coil helmet with an induced [http://en.wikipedia.org/wiki/Maxwell_coil Maxwell magnetic field]. This magnetic coil could be worn on the head and activated to generate small magnetic waves, soothing the wearer. Nicknamed the “Happy Helmet”, it was designed to non-invasively treat the bipolar-depressed via magnetic stimulation. Once fully developed, the helmet was to cost a hundred-fold less than an [http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging fMRI], the current primary treatment to bipolar depression.<br />
<br />
This summer Nade is working full-time with the iGEM 2008 Cal Computational Team. This is his first time using Java. Prior to Java, his programming experience included an introductory C++ class in the 9th grade and MATLAB experience for three years in Berkeley. He has had prior experience with computational modeling in general; last year Nade worked with LabVIEW for his introductory class to signals and systems. Last fall he graphically modeled a growing brain tumor with ADINA for his Biomechanics class, and later based his main Biofluid mechanics project on the dynamics of a atherosclerotic artery using a computational model generated by COMSOL.<br />
<br />
===Matthew Johnson - Student Member===<br />
[[Image:Matt_Professional2.jpg|thumb|270px|Matthew L.E. Johnson]]<br />
<br />
Matthew Johnson is currently starting up his senior year at the University of California, Berkeley. He is a Bioengineering major focusing on cell & tissue engineering, with a passionate interest in regenerative science and synthetic biology. He is also enthusiastic about nanotechnology, BioMEMS, molecular biology, product design, economics, and writing.<br />
<br />
Matt has lofty ambitions, and thinks that applied science is the key to solving many of life's problems, maybe even including the big one at the end of it. He is very interested in how bioengineering and synthetic biology can be used to improve living conditions for people all over the world, whether through novel medical treatments, cheaper, cleaner sources of replenishable energy, or the development of heartier and healthier food crops. Outside of science, one of of his biggest interests is taekwondo, which he started his freshman year at Cal and has involved himself extensively with ever since. He believes that the discipline and physical training has improved his life, and he just loves getting a chance to compete - win or lose, there's always something to learn.<br />
<br />
This summer was one of his first major research efforts. He'd had experience programming in Java many years before, but had to learn it again from the ground-up for iGEM, though familiarity with Perl and programming in general helped considerably. Due to a martial arts-related injury, he was gone for the last third of the summer, but he continued to code from his home in Bakersfield, CA while he recuperated. He hopes to help in the future development of Clotho in his spare time, to create an even more useful and functional tool to aid synthetic biologists in their research.<br />
<br />
===Dr. Douglas Densmore - Instructor===<br />
[[Image:DougAtTheDOP2.png|thumb|Douglas Densmore]]<br />
Douglas Densmore received his Bachelors of Science in Engineering (Computer Engineering) from the University of Michigan in April 2001. He received his Masters of Science in Electrical Engineering in May 2004 from the University of California at Berkeley. His masters thesis was entitled, "Platform Based Reconfigurable Architecture Exploration via Boolean Constraints" and demonstrated how Boolean Satisfiability could be used to produce configurations for programmable hardware. He received his PhD in Electrical Engineering from UC Berkeley as well in May 2007. His PhD thesis, entitled "A Design Flow for the Development, Characterization, and Refinement of System Level Architecture Services", explored how electronic system level design methodologies can be abstract and modular while at the same time remaining accurate and efficient.<br />
<br />
He is currently a UC Chancellor's post doctoral researcher at UC Berkeley studying under [http://www.eecs.berkeley.edu/~alberto Prof. Alberto Sangiovanni-Vincentelli]. His research area is in the development of System Level Design methodologies for electronic systems. Specifically, architecture modeling and refinement verification. His background and interests are in Computer Architecture, Logic Synthesis, Digital Logic Design and Synthetic Biology. <br />
<br />
His industry experience includes four+ summers with Intel Corporation where he was involved in pre-silicon design efforts regarding chipset development, post-silicon validation of the Pentium 4 microprocessor, and chipset software validation. He has also worked as a researcher at Cypress Semiconductor and Xilinx Research Labs. He is currently a member of the [http://www.gigascale.org Gigascale Systems Research Center (GSRC)] and the [http://chess.eecs.berkeley.edu Center for Hybrid and Embedded Software Systems (CHESS)] at UC Berkeley. He has published work regarding a method of successive refinement verification of electronic systems, taxonomies of EDA design tools, and algebraic frameworks for the manipulation of functional design descriptions to expose computational parallelism. In addition he has a US patent pending regarding data characterization of programmable devices (such as field programmable gate arrays).<br />
<br />
<br clear="all"><br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
== What we did ==<br />
''This section briefly describes the contributions of each team member.''<br />
<br />
===Matthew LE Johnson===<br />
Spent a lot of time working on:<br />
<br />
* The About connection/frame<br />
* DNA analysis tools and algorithms (including Translation, G-C content, Melting Temperature, Reverse complementing, etc.)<br />
* The Enzyme Library and associated functionality<br />
* Sequence View connection (with Nade and Doug)<br />
* Compatibility with GenBank, FASTA, and ApE file formats<br />
* Support for degenerate IUPAC codes<br />
* Restriction site search and highlighting<br />
* Forward and reverse Open Reading Frame search and highlighting<br />
* Clotho Preferences for various connections<br />
* All of the Clotho Transfer Handlers<br />
* Intelligent Drag and Drop (DnD) between connections<br />
* Work on the Comp. Team Wiki<br />
* Feedback and advice on the graphic designs (seriously: thank you, Nade!)<br />
* ... and many, MANY hours of debugging!<br />
<br />
===Anne Van Devender===<br />
Anne Van Devender was responsible for:<br />
<br />
* The development and design of the algorithm manager<br />
* Clotho algorithm interface and initial implementation<br />
* The conversion of BioBrick assembly algorithms from Perl to Java<br />
* Aid in the development of 2ab assembly algorithms for Clotho<br />
<br />
===Nade Sritanyaratana===<br />
<br />
Nade Sritanyaratana, in semi-chronological order, is attributed to the following work: <br />
<br />
* The Help connection/frame<br />
* Highlighting<br />
* Features connection<br />
* Co-coordinated Sequence View connection/frame alongside Matt and Doug<br />
* Sequence View Tools (Find/Replace)<br />
* Feature Library Collection connection/frame<br />
* File Choosers<br />
* Search Helper<br />
* .txt file Helper<br />
* Photographing at test sessions<br />
* Debugging post-test sessions<br />
* Parts Manager<br />
* Maintaining the iGEM 2008 Computational Tools Team wiki: layout and painted graphics<br />
* Maintaining the Cal College of Engineering iGEM blog alongside Marlee Tichenor and Madvhi Venkatesh of the wet team<br />
* Clotho iGEM logo and woman<br />
* Clotho iGEM t-shirt<br />
<br />
===Dr. Douglas Densmore===<br />
Doug provided the initial Clotho software infrastructure and served as the main team lead. He helped to keep the team on track and supervised the construction and functionality of Clotho. He is the chief architect of Clotho and in charge of its maintenance, deployment, and promotion.<br />
<br />
===Dr. Chris Anderson===<br />
Prof. Anderson provided specifications for what tools and techniques should be incorporated in Clotho. In addition he also helped to define the general assembly problem for standardized biological parts as well as provide the context in which the tool would be used. He also provided many interesting discussion regarding the Clotho data model and provided the database by which we did the majority of our testing.<br />
<br />
===Other attribution===<br />
<br />
Many thanks to Collin Martin for the professional photography shots, and the Comp team shot.<br />
<br />
Shout out goes to Cici Chen of the UC Berkeley wetlab for helping design the Clotho title (alpha). Also Brian Zimmer, Bing Xia, and Roger Tu also have contributed to the development of Clotho. Josh Kittleson was instrumental in the development of the mySQL/PoBoL connection and tools. Will Deloache helped with the development of the assembly algorithms for 2ab assembly that is in the tool.<br />
<br />
== Where we're from ==<br />
<br />
===Dr. Douglas Densmore===<br />
Doug is from Richland, Michigan which is a small town outside of Kalamazoo. He attended the University of Michigan from 1996-2001 and has been in Berkeley, California since 2001. His family is from the Detroit area. They still live in Michigan.<br />
<br />
===Nade Sritanyaratana===<br />
Nade is a 4th year bioengineering undergraduate at UC Berkeley. He was born in the SF Bay Area, in Hayward, CA, and has lived around the Bay Area his entire life. Both of his parents are Thai. He attended James Logan High School in Union City, CA, where his primary activities included speech and debate, Leo Club, and the swim team. His family still resides in Union City.<br />
<br />
===Matthew L.E. Johnson===<br />
Matt is a SoCal native - born and raised in Bakersfield, CA right up until the move to Berkeley in 2005. He loves his hometown, but realizes that it is an 'acquired taste', especially during the average summer's daily triple-digit heat. Despite the vast differences between his new home and his old (with inverse climates - politically and meteorologically), he has adapted well and has been greatly enjoying his stay in the Bay Area.</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/TeamTeam:UC Berkeley Tools/Team2008-10-29T10:56:35Z<p>Logosandpathos: /* Matthew Johnson - Student Member */</p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<!--- <center>[http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development#Downloads_and_Information <b>The Alpha release is here.</b>]</center> ---><br />
<br />
{{Template:ClothoMenu}}<br />
__NOTOC__<br />
<br />
<br />
== Who we are ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
'''Faculty Advisors:'''<br />
<br />
*''' Advisor 1''': Doug Densmore, Post-Doc at UC Berkeley<br />
*'''Advisor 2''': Chris Anderson, Assistant Professor at UC Berkeley<br />
<br />
<br />
'''Undergrads:'''<br />
<br />
*'''Student''': Anne Van Devender, 4th year Computer Science undergraduate, Washington and Lee University<br />
*'''Student''': Matthew Johnson, 4th year Bioengineering undergraduate, UC Berkeley<br />
*'''Student''': Nade Sritanyaratana, 4th year Bioengineering undergraduate, UC Berkeley<br />
<br />
|<br />
<gallery perrow="4"><br />
Image:Doug_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Dr._Douglas_Densmore|Doug Densmore]]<br />
Image:Anne_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Anne_Van_Devender|Anne Van Devender]]<br />
Image:MattInStanley.png|[[Team:UC_Berkeley_Tools/Team#Matthew_Johnson|Matthew L.E. Johnson]]<br />
Image:Nade_atStanley.png|[[Team:UC_Berkeley_Tools/Team#Nade_Sritanyaratana|Nade Sritanyaratana]]<br />
</gallery><br />
|}<br />
<br />
==Team Biographies==<br />
[[Image:CalCompTeam.png|The 2008 iGEM Cal Comp Team]]<br />
<br />
===Anne Van Devender - Student Member===<br />
<br />
[[Image:Anne_Professional.jpg|250 px|thumb|left|Anne Van Devender]]<br />
<br />
Anne Van Devender is a 4th year undergraduate at Washington and Lee University (Lexington, VA). She is a Computer Science major with a minor in Women's Studies. After graduation she hopes to attend graduate school for either a master's degree or PhD in Human Computer Interaction. <br />
<br />
Her main endeavor outside of academics is the Washington and Lee Women's Soccer team where she is captain and a three-year letter winner. In 2007, she was named to the NSCAA All-America team. When she is not on the field or in the classroom, she enjoys working with kids in the Lexington community including involvement in a literacy campaign and teaching middle school girls the basics of computer science.<br />
<br />
This summer she is participating in the Summer Undergraduate Program in Engineering Research at Berkeley (SUPERB) and working with the iGEM 2008 UC Berkeley Computational Team. She is using Java to write an "Algorithm Manager" for the Clotho tool. While she has used Java extensively in her coursework at W&L, the synthetic biology aspect of the project is completely new to her. The last time she took biology was in 9th grade! She hopes this project will not only improve her research skills in computer science, but will also enlighten her to the emerging field of synthetic biology.<br />
<br />
===Nade Sritanyaratana - Student Member===<br />
[[Image:Nade_Professional.jpg|thumb|Nade Sritanyaratana]]<br />
<!---[[Image:NadeHeadShot.png|thumb|Nade Sritanyaratana]]---><br />
<br />
Nade Sritanyaratana is a 3rd year undergraduate at the University of California, Berkeley. He is majoring in Bioengineering with a concentration in imaging, and hopes to apply for a PhD graduate program in the upcoming year. Beyond imaging, his academic interests include Biomechanics; signals and systems; circuit analysis; systems biology; and linear optimization.<br />
<br />
His prior research experience consists of working with [http://bioeng.berkeley.edu/cv.php?facultyid=3022 bioengineering professor Steven Conolly] in the Summer and Fall of 2007. During that summer, he designed a coil helmet with an induced [http://en.wikipedia.org/wiki/Maxwell_coil Maxwell magnetic field]. This magnetic coil could be worn on the head and activated to generate small magnetic waves, soothing the wearer. Nicknamed the “Happy Helmet”, it was designed to non-invasively treat the bipolar-depressed via magnetic stimulation. Once fully developed, the helmet was to cost a hundred-fold less than an [http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging fMRI], the current primary treatment to bipolar depression.<br />
<br />
This summer Nade is working full-time with the iGEM 2008 Cal Computational Team. This is his first time using Java. Prior to Java, his programming experience included an introductory C++ class in the 9th grade and MATLAB experience for three years in Berkeley. He has had prior experience with computational modeling in general; last year Nade worked with LabVIEW for his introductory class to signals and systems. Last fall he graphically modeled a growing brain tumor with ADINA for his Biomechanics class, and later based his main Biofluid mechanics project on the dynamics of a atherosclerotic artery using a computational model generated by COMSOL.<br />
<br />
===Matthew Johnson - Student Member===<br />
[[Image:Matt_Professional2.jpg|thumb|300px|Matthew L.E. Johnson]]<br />
<br />
Matthew Johnson is currently starting up his senior year at the University of California, Berkeley. He is a Bioengineering major focusing on cell & tissue engineering, with a passionate interest in regenerative science and synthetic biology. He is also enthusiastic about nanotechnology, BioMEMS, molecular biology, product design, economics, and writing.<br />
<br />
Matt has lofty ambitions, and thinks that applied science is the key to solving many of life's problems, maybe even including the big one at the end of it. He is very interested in how bioengineering and synthetic biology can be used to improve living conditions for people all over the world, whether through novel medical treatments, cheaper, cleaner sources of replenishable energy, or the development of heartier and healthier food crops. Outside of science, one of of his biggest interests is taekwondo, which he started his freshman year at Cal and has involved himself extensively with ever since. He believes that the discipline and physical training has improved his life, and he just loves getting a chance to compete - win or lose, there's always something to learn.<br />
<br />
This summer was one of his first major research efforts. He'd had experience programming in Java many years before, but had to learn it again from the ground-up for iGEM, though familiarity with Perl and programming in general helped considerably. Due to a martial arts-related injury, he was gone for the last third of the summer, but he continued to code from his home in Bakersfield, CA while he recuperated. He hopes to help in the future development of Clotho in his spare time, to create an even more useful and functional tool to aid synthetic biologists in their research.<br />
<br />
===Dr. Douglas Densmore - Instructor===<br />
[[Image:DougAtTheDOP2.png|thumb|Douglas Densmore]]<br />
Douglas Densmore received his Bachelors of Science in Engineering (Computer Engineering) from the University of Michigan in April 2001. He received his Masters of Science in Electrical Engineering in May 2004 from the University of California at Berkeley. His masters thesis was entitled, "Platform Based Reconfigurable Architecture Exploration via Boolean Constraints" and demonstrated how Boolean Satisfiability could be used to produce configurations for programmable hardware. He received his PhD in Electrical Engineering from UC Berkeley as well in May 2007. His PhD thesis, entitled "A Design Flow for the Development, Characterization, and Refinement of System Level Architecture Services", explored how electronic system level design methodologies can be abstract and modular while at the same time remaining accurate and efficient.<br />
<br />
He is currently a UC Chancellor's post doctoral researcher at UC Berkeley studying under [http://www.eecs.berkeley.edu/~alberto Prof. Alberto Sangiovanni-Vincentelli]. His research area is in the development of System Level Design methodologies for electronic systems. Specifically, architecture modeling and refinement verification. His background and interests are in Computer Architecture, Logic Synthesis, Digital Logic Design and Synthetic Biology. <br />
<br />
His industry experience includes four+ summers with Intel Corporation where he was involved in pre-silicon design efforts regarding chipset development, post-silicon validation of the Pentium 4 microprocessor, and chipset software validation. He has also worked as a researcher at Cypress Semiconductor and Xilinx Research Labs. He is currently a member of the [http://www.gigascale.org Gigascale Systems Research Center (GSRC)] and the [http://chess.eecs.berkeley.edu Center for Hybrid and Embedded Software Systems (CHESS)] at UC Berkeley. He has published work regarding a method of successive refinement verification of electronic systems, taxonomies of EDA design tools, and algebraic frameworks for the manipulation of functional design descriptions to expose computational parallelism. In addition he has a US patent pending regarding data characterization of programmable devices (such as field programmable gate arrays).<br />
<br />
<br clear="all"><br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
== What we did ==<br />
''This section briefly describes the contributions of each team member.''<br />
<br />
===Matthew LE Johnson===<br />
Spent a lot of time working on:<br />
<br />
* The About connection/frame<br />
* DNA analysis tools and algorithms (including Translation, G-C content, Melting Temperature, Reverse complementing, etc.)<br />
* The Enzyme Library and associated functionality<br />
* Sequence View connection (with Nade and Doug)<br />
* Compatibility with GenBank, FASTA, and ApE file formats<br />
* Support for degenerate IUPAC codes<br />
* Restriction site search and highlighting<br />
* Forward and reverse Open Reading Frame search and highlighting<br />
* Clotho Preferences for various connections<br />
* All of the Clotho Transfer Handlers<br />
* Intelligent Drag and Drop (DnD) between connections<br />
* Work on the Comp. Team Wiki<br />
* Feedback and advice on the graphic designs (seriously: thank you, Nade!)<br />
* ... and many, MANY hours of debugging!<br />
<br />
===Anne Van Devender===<br />
Anne Van Devender was responsible for:<br />
<br />
* The development and design of the algorithm manager<br />
* Clotho algorithm interface and initial implementation<br />
* The conversion of BioBrick assembly algorithms from Perl to Java<br />
* Aid in the development of 2ab assembly algorithms for Clotho<br />
<br />
===Nade Sritanyaratana===<br />
<br />
Nade Sritanyaratana, in semi-chronological order, is attributed to the following work: <br />
<br />
* The Help connection/frame<br />
* Highlighting<br />
* Features connection<br />
* Co-coordinated Sequence View connection/frame alongside Matt and Doug<br />
* Sequence View Tools (Find/Replace)<br />
* Feature Library Collection connection/frame<br />
* File Choosers<br />
* Search Helper<br />
* .txt file Helper<br />
* Photographing at test sessions<br />
* Debugging post-test sessions<br />
* Parts Manager<br />
* Maintaining the iGEM 2008 Computational Tools Team wiki: layout and painted graphics<br />
* Maintaining the Cal College of Engineering iGEM blog alongside Marlee Tichenor and Madvhi Venkatesh of the wet team<br />
* Clotho iGEM logo and woman<br />
* Clotho iGEM t-shirt<br />
<br />
===Dr. Douglas Densmore===<br />
Doug provided the initial Clotho software infrastructure and served as the main team lead. He helped to keep the team on track and supervised the construction and functionality of Clotho. He is the chief architect of Clotho and in charge of its maintenance, deployment, and promotion.<br />
<br />
===Dr. Chris Anderson===<br />
Prof. Anderson provided specifications for what tools and techniques should be incorporated in Clotho. In addition he also helped to define the general assembly problem for standardized biological parts as well as provide the context in which the tool would be used. He also provided many interesting discussion regarding the Clotho data model and provided the database by which we did the majority of our testing.<br />
<br />
===Other attribution===<br />
<br />
Many thanks to Collin Martin for the professional photography shots, and the Comp team shot.<br />
<br />
Shout out goes to Cici Chen of the UC Berkeley wetlab for helping design the Clotho title (alpha). Also Brian Zimmer, Bing Xia, and Roger Tu also have contributed to the development of Clotho. Josh Kittleson was instrumental in the development of the mySQL/PoBoL connection and tools. Will Deloache helped with the development of the assembly algorithms for 2ab assembly that is in the tool.<br />
<br />
== Where we're from ==<br />
<br />
===Dr. Douglas Densmore===<br />
Doug is from Richland, Michigan which is a small town outside of Kalamazoo. He attended the University of Michigan from 1996-2001 and has been in Berkeley, California since 2001. His family is from the Detroit area. They still live in Michigan.<br />
<br />
===Nade Sritanyaratana===<br />
Nade is a 4th year bioengineering undergraduate at UC Berkeley. He was born in the SF Bay Area, in Hayward, CA, and has lived around the Bay Area his entire life. Both of his parents are Thai. He attended James Logan High School in Union City, CA, where his primary activities included speech and debate, Leo Club, and the swim team. His family still resides in Union City.<br />
<br />
===Matthew L.E. Johnson===<br />
Matt is a SoCal native - born and raised in Bakersfield, CA right up until the move to Berkeley in 2005. He loves his hometown, but realizes that it is an 'acquired taste', especially during the average summer's daily triple-digit heat. Despite the vast differences between his new home and his old (with inverse climates - politically and meteorologically), he has adapted well and has been greatly enjoying his stay in the Bay Area.</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/TeamTeam:UC Berkeley Tools/Team2008-10-29T10:55:55Z<p>Logosandpathos: /* Matthew Johnson - Student Member */</p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<!--- <center>[http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development#Downloads_and_Information <b>The Alpha release is here.</b>]</center> ---><br />
<br />
{{Template:ClothoMenu}}<br />
__NOTOC__<br />
<br />
<br />
== Who we are ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
'''Faculty Advisors:'''<br />
<br />
*''' Advisor 1''': Doug Densmore, Post-Doc at UC Berkeley<br />
*'''Advisor 2''': Chris Anderson, Assistant Professor at UC Berkeley<br />
<br />
<br />
'''Undergrads:'''<br />
<br />
*'''Student''': Anne Van Devender, 4th year Computer Science undergraduate, Washington and Lee University<br />
*'''Student''': Matthew Johnson, 4th year Bioengineering undergraduate, UC Berkeley<br />
*'''Student''': Nade Sritanyaratana, 4th year Bioengineering undergraduate, UC Berkeley<br />
<br />
|<br />
<gallery perrow="4"><br />
Image:Doug_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Dr._Douglas_Densmore|Doug Densmore]]<br />
Image:Anne_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Anne_Van_Devender|Anne Van Devender]]<br />
Image:MattInStanley.png|[[Team:UC_Berkeley_Tools/Team#Matthew_Johnson|Matthew L.E. Johnson]]<br />
Image:Nade_atStanley.png|[[Team:UC_Berkeley_Tools/Team#Nade_Sritanyaratana|Nade Sritanyaratana]]<br />
</gallery><br />
|}<br />
<br />
==Team Biographies==<br />
[[Image:CalCompTeam.png|The 2008 iGEM Cal Comp Team]]<br />
<br />
===Anne Van Devender - Student Member===<br />
<br />
[[Image:Anne_Professional.jpg|250 px|thumb|left|Anne Van Devender]]<br />
<br />
Anne Van Devender is a 4th year undergraduate at Washington and Lee University (Lexington, VA). She is a Computer Science major with a minor in Women's Studies. After graduation she hopes to attend graduate school for either a master's degree or PhD in Human Computer Interaction. <br />
<br />
Her main endeavor outside of academics is the Washington and Lee Women's Soccer team where she is captain and a three-year letter winner. In 2007, she was named to the NSCAA All-America team. When she is not on the field or in the classroom, she enjoys working with kids in the Lexington community including involvement in a literacy campaign and teaching middle school girls the basics of computer science.<br />
<br />
This summer she is participating in the Summer Undergraduate Program in Engineering Research at Berkeley (SUPERB) and working with the iGEM 2008 UC Berkeley Computational Team. She is using Java to write an "Algorithm Manager" for the Clotho tool. While she has used Java extensively in her coursework at W&L, the synthetic biology aspect of the project is completely new to her. The last time she took biology was in 9th grade! She hopes this project will not only improve her research skills in computer science, but will also enlighten her to the emerging field of synthetic biology.<br />
<br />
===Nade Sritanyaratana - Student Member===<br />
[[Image:Nade_Professional.jpg|thumb|Nade Sritanyaratana]]<br />
<!---[[Image:NadeHeadShot.png|thumb|Nade Sritanyaratana]]---><br />
<br />
Nade Sritanyaratana is a 3rd year undergraduate at the University of California, Berkeley. He is majoring in Bioengineering with a concentration in imaging, and hopes to apply for a PhD graduate program in the upcoming year. Beyond imaging, his academic interests include Biomechanics; signals and systems; circuit analysis; systems biology; and linear optimization.<br />
<br />
His prior research experience consists of working with [http://bioeng.berkeley.edu/cv.php?facultyid=3022 bioengineering professor Steven Conolly] in the Summer and Fall of 2007. During that summer, he designed a coil helmet with an induced [http://en.wikipedia.org/wiki/Maxwell_coil Maxwell magnetic field]. This magnetic coil could be worn on the head and activated to generate small magnetic waves, soothing the wearer. Nicknamed the “Happy Helmet”, it was designed to non-invasively treat the bipolar-depressed via magnetic stimulation. Once fully developed, the helmet was to cost a hundred-fold less than an [http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging fMRI], the current primary treatment to bipolar depression.<br />
<br />
This summer Nade is working full-time with the iGEM 2008 Cal Computational Team. This is his first time using Java. Prior to Java, his programming experience included an introductory C++ class in the 9th grade and MATLAB experience for three years in Berkeley. He has had prior experience with computational modeling in general; last year Nade worked with LabVIEW for his introductory class to signals and systems. Last fall he graphically modeled a growing brain tumor with ADINA for his Biomechanics class, and later based his main Biofluid mechanics project on the dynamics of a atherosclerotic artery using a computational model generated by COMSOL.<br />
<br />
===Matthew Johnson - Student Member===<br />
[[Image:Matt_Professional2.jpg|thumb|Matthew L.E. Johnson]]<br />
<br />
Matthew Johnson is currently starting up his senior year at the University of California, Berkeley. He is a Bioengineering major focusing on cell & tissue engineering, with a passionate interest in regenerative science and synthetic biology. He is also enthusiastic about nanotechnology, BioMEMS, molecular biology, product design, economics, and writing.<br />
<br />
Matt has lofty ambitions, and thinks that applied science is the key to solving many of life's problems, maybe even including the big one at the end of it. He is very interested in how bioengineering and synthetic biology can be used to improve living conditions for people all over the world, whether through novel medical treatments, cheaper, cleaner sources of replenishable energy, or the development of heartier and healthier food crops. Outside of science, one of of his biggest interests is taekwondo, which he started his freshman year at Cal and has involved himself extensively with ever since. He believes that the discipline and physical training has improved his life, and he just loves getting a chance to compete - win or lose, there's always something to learn.<br />
<br />
This summer was one of his first major research efforts. He'd had experience programming in Java many years before, but had to learn it again from the ground-up for iGEM, though familiarity with Perl and programming in general helped considerably. Due to a martial arts-related injury, he was gone for the last third of the summer, but he continued to code from his home in Bakersfield, CA while he recuperated. He hopes to help in the future development of Clotho in his spare time, to create an even more useful and functional tool to aid synthetic biologists in their research.<br />
<br />
===Dr. Douglas Densmore - Instructor===<br />
[[Image:DougAtTheDOP2.png|thumb|Douglas Densmore]]<br />
Douglas Densmore received his Bachelors of Science in Engineering (Computer Engineering) from the University of Michigan in April 2001. He received his Masters of Science in Electrical Engineering in May 2004 from the University of California at Berkeley. His masters thesis was entitled, "Platform Based Reconfigurable Architecture Exploration via Boolean Constraints" and demonstrated how Boolean Satisfiability could be used to produce configurations for programmable hardware. He received his PhD in Electrical Engineering from UC Berkeley as well in May 2007. His PhD thesis, entitled "A Design Flow for the Development, Characterization, and Refinement of System Level Architecture Services", explored how electronic system level design methodologies can be abstract and modular while at the same time remaining accurate and efficient.<br />
<br />
He is currently a UC Chancellor's post doctoral researcher at UC Berkeley studying under [http://www.eecs.berkeley.edu/~alberto Prof. Alberto Sangiovanni-Vincentelli]. His research area is in the development of System Level Design methodologies for electronic systems. Specifically, architecture modeling and refinement verification. His background and interests are in Computer Architecture, Logic Synthesis, Digital Logic Design and Synthetic Biology. <br />
<br />
His industry experience includes four+ summers with Intel Corporation where he was involved in pre-silicon design efforts regarding chipset development, post-silicon validation of the Pentium 4 microprocessor, and chipset software validation. He has also worked as a researcher at Cypress Semiconductor and Xilinx Research Labs. He is currently a member of the [http://www.gigascale.org Gigascale Systems Research Center (GSRC)] and the [http://chess.eecs.berkeley.edu Center for Hybrid and Embedded Software Systems (CHESS)] at UC Berkeley. He has published work regarding a method of successive refinement verification of electronic systems, taxonomies of EDA design tools, and algebraic frameworks for the manipulation of functional design descriptions to expose computational parallelism. In addition he has a US patent pending regarding data characterization of programmable devices (such as field programmable gate arrays).<br />
<br />
<br clear="all"><br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
== What we did ==<br />
''This section briefly describes the contributions of each team member.''<br />
<br />
===Matthew LE Johnson===<br />
Spent a lot of time working on:<br />
<br />
* The About connection/frame<br />
* DNA analysis tools and algorithms (including Translation, G-C content, Melting Temperature, Reverse complementing, etc.)<br />
* The Enzyme Library and associated functionality<br />
* Sequence View connection (with Nade and Doug)<br />
* Compatibility with GenBank, FASTA, and ApE file formats<br />
* Support for degenerate IUPAC codes<br />
* Restriction site search and highlighting<br />
* Forward and reverse Open Reading Frame search and highlighting<br />
* Clotho Preferences for various connections<br />
* All of the Clotho Transfer Handlers<br />
* Intelligent Drag and Drop (DnD) between connections<br />
* Work on the Comp. Team Wiki<br />
* Feedback and advice on the graphic designs (seriously: thank you, Nade!)<br />
* ... and many, MANY hours of debugging!<br />
<br />
===Anne Van Devender===<br />
Anne Van Devender was responsible for:<br />
<br />
* The development and design of the algorithm manager<br />
* Clotho algorithm interface and initial implementation<br />
* The conversion of BioBrick assembly algorithms from Perl to Java<br />
* Aid in the development of 2ab assembly algorithms for Clotho<br />
<br />
===Nade Sritanyaratana===<br />
<br />
Nade Sritanyaratana, in semi-chronological order, is attributed to the following work: <br />
<br />
* The Help connection/frame<br />
* Highlighting<br />
* Features connection<br />
* Co-coordinated Sequence View connection/frame alongside Matt and Doug<br />
* Sequence View Tools (Find/Replace)<br />
* Feature Library Collection connection/frame<br />
* File Choosers<br />
* Search Helper<br />
* .txt file Helper<br />
* Photographing at test sessions<br />
* Debugging post-test sessions<br />
* Parts Manager<br />
* Maintaining the iGEM 2008 Computational Tools Team wiki: layout and painted graphics<br />
* Maintaining the Cal College of Engineering iGEM blog alongside Marlee Tichenor and Madvhi Venkatesh of the wet team<br />
* Clotho iGEM logo and woman<br />
* Clotho iGEM t-shirt<br />
<br />
===Dr. Douglas Densmore===<br />
Doug provided the initial Clotho software infrastructure and served as the main team lead. He helped to keep the team on track and supervised the construction and functionality of Clotho. He is the chief architect of Clotho and in charge of its maintenance, deployment, and promotion.<br />
<br />
===Dr. Chris Anderson===<br />
Prof. Anderson provided specifications for what tools and techniques should be incorporated in Clotho. In addition he also helped to define the general assembly problem for standardized biological parts as well as provide the context in which the tool would be used. He also provided many interesting discussion regarding the Clotho data model and provided the database by which we did the majority of our testing.<br />
<br />
===Other attribution===<br />
<br />
Many thanks to Collin Martin for the professional photography shots, and the Comp team shot.<br />
<br />
Shout out goes to Cici Chen of the UC Berkeley wetlab for helping design the Clotho title (alpha). Also Brian Zimmer, Bing Xia, and Roger Tu also have contributed to the development of Clotho. Josh Kittleson was instrumental in the development of the mySQL/PoBoL connection and tools. Will Deloache helped with the development of the assembly algorithms for 2ab assembly that is in the tool.<br />
<br />
== Where we're from ==<br />
<br />
===Dr. Douglas Densmore===<br />
Doug is from Richland, Michigan which is a small town outside of Kalamazoo. He attended the University of Michigan from 1996-2001 and has been in Berkeley, California since 2001. His family is from the Detroit area. They still live in Michigan.<br />
<br />
===Nade Sritanyaratana===<br />
Nade is a 4th year bioengineering undergraduate at UC Berkeley. He was born in the SF Bay Area, in Hayward, CA, and has lived around the Bay Area his entire life. Both of his parents are Thai. He attended James Logan High School in Union City, CA, where his primary activities included speech and debate, Leo Club, and the swim team. His family still resides in Union City.<br />
<br />
===Matthew L.E. Johnson===<br />
Matt is a SoCal native - born and raised in Bakersfield, CA right up until the move to Berkeley in 2005. He loves his hometown, but realizes that it is an 'acquired taste', especially during the average summer's daily triple-digit heat. Despite the vast differences between his new home and his old (with inverse climates - politically and meteorologically), he has adapted well and has been greatly enjoying his stay in the Bay Area.</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/TeamTeam:UC Berkeley Tools/Team2008-10-29T10:55:09Z<p>Logosandpathos: /* Matthew Johnson - Student Member */</p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<!--- <center>[http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development#Downloads_and_Information <b>The Alpha release is here.</b>]</center> ---><br />
<br />
{{Template:ClothoMenu}}<br />
__NOTOC__<br />
<br />
<br />
== Who we are ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
'''Faculty Advisors:'''<br />
<br />
*''' Advisor 1''': Doug Densmore, Post-Doc at UC Berkeley<br />
*'''Advisor 2''': Chris Anderson, Assistant Professor at UC Berkeley<br />
<br />
<br />
'''Undergrads:'''<br />
<br />
*'''Student''': Anne Van Devender, 4th year Computer Science undergraduate, Washington and Lee University<br />
*'''Student''': Matthew Johnson, 4th year Bioengineering undergraduate, UC Berkeley<br />
*'''Student''': Nade Sritanyaratana, 4th year Bioengineering undergraduate, UC Berkeley<br />
<br />
|<br />
<gallery perrow="4"><br />
Image:Doug_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Dr._Douglas_Densmore|Doug Densmore]]<br />
Image:Anne_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Anne_Van_Devender|Anne Van Devender]]<br />
Image:MattInStanley.png|[[Team:UC_Berkeley_Tools/Team#Matthew_Johnson|Matthew L.E. Johnson]]<br />
Image:Nade_atStanley.png|[[Team:UC_Berkeley_Tools/Team#Nade_Sritanyaratana|Nade Sritanyaratana]]<br />
</gallery><br />
|}<br />
<br />
==Team Biographies==<br />
[[Image:CalCompTeam.png|The 2008 iGEM Cal Comp Team]]<br />
<br />
===Anne Van Devender - Student Member===<br />
<br />
[[Image:Anne_Professional.jpg|250 px|thumb|left|Anne Van Devender]]<br />
<br />
Anne Van Devender is a 4th year undergraduate at Washington and Lee University (Lexington, VA). She is a Computer Science major with a minor in Women's Studies. After graduation she hopes to attend graduate school for either a master's degree or PhD in Human Computer Interaction. <br />
<br />
Her main endeavor outside of academics is the Washington and Lee Women's Soccer team where she is captain and a three-year letter winner. In 2007, she was named to the NSCAA All-America team. When she is not on the field or in the classroom, she enjoys working with kids in the Lexington community including involvement in a literacy campaign and teaching middle school girls the basics of computer science.<br />
<br />
This summer she is participating in the Summer Undergraduate Program in Engineering Research at Berkeley (SUPERB) and working with the iGEM 2008 UC Berkeley Computational Team. She is using Java to write an "Algorithm Manager" for the Clotho tool. While she has used Java extensively in her coursework at W&L, the synthetic biology aspect of the project is completely new to her. The last time she took biology was in 9th grade! She hopes this project will not only improve her research skills in computer science, but will also enlighten her to the emerging field of synthetic biology.<br />
<br />
===Nade Sritanyaratana - Student Member===<br />
[[Image:Nade_Professional.jpg|thumb|Nade Sritanyaratana]]<br />
<!---[[Image:NadeHeadShot.png|thumb|Nade Sritanyaratana]]---><br />
<br />
Nade Sritanyaratana is a 3rd year undergraduate at the University of California, Berkeley. He is majoring in Bioengineering with a concentration in imaging, and hopes to apply for a PhD graduate program in the upcoming year. Beyond imaging, his academic interests include Biomechanics; signals and systems; circuit analysis; systems biology; and linear optimization.<br />
<br />
His prior research experience consists of working with [http://bioeng.berkeley.edu/cv.php?facultyid=3022 bioengineering professor Steven Conolly] in the Summer and Fall of 2007. During that summer, he designed a coil helmet with an induced [http://en.wikipedia.org/wiki/Maxwell_coil Maxwell magnetic field]. This magnetic coil could be worn on the head and activated to generate small magnetic waves, soothing the wearer. Nicknamed the “Happy Helmet”, it was designed to non-invasively treat the bipolar-depressed via magnetic stimulation. Once fully developed, the helmet was to cost a hundred-fold less than an [http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging fMRI], the current primary treatment to bipolar depression.<br />
<br />
This summer Nade is working full-time with the iGEM 2008 Cal Computational Team. This is his first time using Java. Prior to Java, his programming experience included an introductory C++ class in the 9th grade and MATLAB experience for three years in Berkeley. He has had prior experience with computational modeling in general; last year Nade worked with LabVIEW for his introductory class to signals and systems. Last fall he graphically modeled a growing brain tumor with ADINA for his Biomechanics class, and later based his main Biofluid mechanics project on the dynamics of a atherosclerotic artery using a computational model generated by COMSOL.<br />
<br />
===Matthew Johnson - Student Member===<br />
[[Image:Matt_Professional2.jpg|300 px]]<br />
<br />
Matthew Johnson is currently starting up his senior year at the University of California, Berkeley. He is a Bioengineering major focusing on cell & tissue engineering, with a passionate interest in regenerative science and synthetic biology. He is also enthusiastic about nanotechnology, BioMEMS, molecular biology, product design, economics, and writing.<br />
<br />
Matt has lofty ambitions, and thinks that applied science is the key to solving many of life's problems, maybe even including the big one at the end of it. He is very interested in how bioengineering and synthetic biology can be used to improve living conditions for people all over the world, whether through novel medical treatments, cheaper, cleaner sources of replenishable energy, or the development of heartier and healthier food crops. Outside of science, one of of his biggest interests is taekwondo, which he started his freshman year at Cal and has involved himself extensively with ever since. He believes that the discipline and physical training has improved his life, and he just loves getting a chance to compete - win or lose, there's always something to learn.<br />
<br />
This summer was one of his first major research efforts. He'd had experience programming in Java many years before, but had to learn it again from the ground-up for iGEM, though familiarity with Perl and programming in general helped considerably. Due to a martial arts-related injury, he was gone for the last third of the summer, but he continued to code from his home in Bakersfield, CA while he recuperated. He hopes to help in the future development of Clotho in his spare time, to create an even more useful and functional tool to aid synthetic biologists in their research.<br />
<br />
===Dr. Douglas Densmore - Instructor===<br />
[[Image:DougAtTheDOP2.png|thumb|Douglas Densmore]]<br />
Douglas Densmore received his Bachelors of Science in Engineering (Computer Engineering) from the University of Michigan in April 2001. He received his Masters of Science in Electrical Engineering in May 2004 from the University of California at Berkeley. His masters thesis was entitled, "Platform Based Reconfigurable Architecture Exploration via Boolean Constraints" and demonstrated how Boolean Satisfiability could be used to produce configurations for programmable hardware. He received his PhD in Electrical Engineering from UC Berkeley as well in May 2007. His PhD thesis, entitled "A Design Flow for the Development, Characterization, and Refinement of System Level Architecture Services", explored how electronic system level design methodologies can be abstract and modular while at the same time remaining accurate and efficient.<br />
<br />
He is currently a UC Chancellor's post doctoral researcher at UC Berkeley studying under [http://www.eecs.berkeley.edu/~alberto Prof. Alberto Sangiovanni-Vincentelli]. His research area is in the development of System Level Design methodologies for electronic systems. Specifically, architecture modeling and refinement verification. His background and interests are in Computer Architecture, Logic Synthesis, Digital Logic Design and Synthetic Biology. <br />
<br />
His industry experience includes four+ summers with Intel Corporation where he was involved in pre-silicon design efforts regarding chipset development, post-silicon validation of the Pentium 4 microprocessor, and chipset software validation. He has also worked as a researcher at Cypress Semiconductor and Xilinx Research Labs. He is currently a member of the [http://www.gigascale.org Gigascale Systems Research Center (GSRC)] and the [http://chess.eecs.berkeley.edu Center for Hybrid and Embedded Software Systems (CHESS)] at UC Berkeley. He has published work regarding a method of successive refinement verification of electronic systems, taxonomies of EDA design tools, and algebraic frameworks for the manipulation of functional design descriptions to expose computational parallelism. In addition he has a US patent pending regarding data characterization of programmable devices (such as field programmable gate arrays).<br />
<br />
<br clear="all"><br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
== What we did ==<br />
''This section briefly describes the contributions of each team member.''<br />
<br />
===Matthew LE Johnson===<br />
Spent a lot of time working on:<br />
<br />
* The About connection/frame<br />
* DNA analysis tools and algorithms (including Translation, G-C content, Melting Temperature, Reverse complementing, etc.)<br />
* The Enzyme Library and associated functionality<br />
* Sequence View connection (with Nade and Doug)<br />
* Compatibility with GenBank, FASTA, and ApE file formats<br />
* Support for degenerate IUPAC codes<br />
* Restriction site search and highlighting<br />
* Forward and reverse Open Reading Frame search and highlighting<br />
* Clotho Preferences for various connections<br />
* All of the Clotho Transfer Handlers<br />
* Intelligent Drag and Drop (DnD) between connections<br />
* Work on the Comp. Team Wiki<br />
* Feedback and advice on the graphic designs (seriously: thank you, Nade!)<br />
* ... and many, MANY hours of debugging!<br />
<br />
===Anne Van Devender===<br />
Anne Van Devender was responsible for:<br />
<br />
* The development and design of the algorithm manager<br />
* Clotho algorithm interface and initial implementation<br />
* The conversion of BioBrick assembly algorithms from Perl to Java<br />
* Aid in the development of 2ab assembly algorithms for Clotho<br />
<br />
===Nade Sritanyaratana===<br />
<br />
Nade Sritanyaratana, in semi-chronological order, is attributed to the following work: <br />
<br />
* The Help connection/frame<br />
* Highlighting<br />
* Features connection<br />
* Co-coordinated Sequence View connection/frame alongside Matt and Doug<br />
* Sequence View Tools (Find/Replace)<br />
* Feature Library Collection connection/frame<br />
* File Choosers<br />
* Search Helper<br />
* .txt file Helper<br />
* Photographing at test sessions<br />
* Debugging post-test sessions<br />
* Parts Manager<br />
* Maintaining the iGEM 2008 Computational Tools Team wiki: layout and painted graphics<br />
* Maintaining the Cal College of Engineering iGEM blog alongside Marlee Tichenor and Madvhi Venkatesh of the wet team<br />
* Clotho iGEM logo and woman<br />
* Clotho iGEM t-shirt<br />
<br />
===Dr. Douglas Densmore===<br />
Doug provided the initial Clotho software infrastructure and served as the main team lead. He helped to keep the team on track and supervised the construction and functionality of Clotho. He is the chief architect of Clotho and in charge of its maintenance, deployment, and promotion.<br />
<br />
===Dr. Chris Anderson===<br />
Prof. Anderson provided specifications for what tools and techniques should be incorporated in Clotho. In addition he also helped to define the general assembly problem for standardized biological parts as well as provide the context in which the tool would be used. He also provided many interesting discussion regarding the Clotho data model and provided the database by which we did the majority of our testing.<br />
<br />
===Other attribution===<br />
<br />
Many thanks to Collin Martin for the professional photography shots, and the Comp team shot.<br />
<br />
Shout out goes to Cici Chen of the UC Berkeley wetlab for helping design the Clotho title (alpha). Also Brian Zimmer, Bing Xia, and Roger Tu also have contributed to the development of Clotho. Josh Kittleson was instrumental in the development of the mySQL/PoBoL connection and tools. Will Deloache helped with the development of the assembly algorithms for 2ab assembly that is in the tool.<br />
<br />
== Where we're from ==<br />
<br />
===Dr. Douglas Densmore===<br />
Doug is from Richland, Michigan which is a small town outside of Kalamazoo. He attended the University of Michigan from 1996-2001 and has been in Berkeley, California since 2001. His family is from the Detroit area. They still live in Michigan.<br />
<br />
===Nade Sritanyaratana===<br />
Nade is a 4th year bioengineering undergraduate at UC Berkeley. He was born in the SF Bay Area, in Hayward, CA, and has lived around the Bay Area his entire life. Both of his parents are Thai. He attended James Logan High School in Union City, CA, where his primary activities included speech and debate, Leo Club, and the swim team. His family still resides in Union City.<br />
<br />
===Matthew L.E. Johnson===<br />
Matt is a SoCal native - born and raised in Bakersfield, CA right up until the move to Berkeley in 2005. He loves his hometown, but realizes that it is an 'acquired taste', especially during the average summer's daily triple-digit heat. Despite the vast differences between his new home and his old (with inverse climates - politically and meteorologically), he has adapted well and has been greatly enjoying his stay in the Bay Area.</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/TeamTeam:UC Berkeley Tools/Team2008-10-29T10:32:40Z<p>Logosandpathos: /* Matthew LE Johnson */</p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<!--- <center>[http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development#Downloads_and_Information <b>The Alpha release is here.</b>]</center> ---><br />
<br />
{{Template:ClothoMenu}}<br />
__NOTOC__<br />
<br />
<br />
== Who we are ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
'''Faculty Advisors:'''<br />
<br />
*''' Advisor 1''': Doug Densmore, Post-Doc at UC Berkeley<br />
*'''Advisor 2''': Chris Anderson, Assistant Professor at UC Berkeley<br />
<br />
<br />
'''Undergrads:'''<br />
<br />
*'''Student''': Anne Van Devender, 4th year Computer Science undergraduate, Washington and Lee University<br />
*'''Student''': Matthew Johnson, 4th year Bioengineering undergraduate, UC Berkeley<br />
*'''Student''': Nade Sritanyaratana, 4th year Bioengineering undergraduate, UC Berkeley<br />
<br />
|<br />
<gallery perrow="4"><br />
Image:Doug_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Dr._Douglas_Densmore|Doug Densmore]]<br />
Image:Anne_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Anne_Van_Devender|Anne Van Devender]]<br />
Image:MattInStanley.png|[[Team:UC_Berkeley_Tools/Team#Matthew_Johnson|Matthew L.E. Johnson]]<br />
Image:Nade_atStanley.png|[[Team:UC_Berkeley_Tools/Team#Nade_Sritanyaratana|Nade Sritanyaratana]]<br />
</gallery><br />
|}<br />
<br />
==Team Biographies==<br />
[[Image:CalCompTeam.png|The 2008 iGEM Cal Comp Team]]<br />
<br />
===Anne Van Devender - Student Member===<br />
<br />
[[Image:Anne_Professional.jpg|250 px|thumb|left|Anne Van Devender]]<br />
<br />
Anne Van Devender is a 4th year undergraduate at Washington and Lee University (Lexington, VA). She is a Computer Science major with a minor in Women's Studies. After graduation she hopes to attend graduate school for either a master's degree or PhD in Human Computer Interaction. <br />
<br />
Her main endeavor outside of academics is the Washington and Lee Women's Soccer team where she is captain and a three-year letter winner. In 2007, she was named to the NSCAA All-America team. When she is not on the field or in the classroom, she enjoys working with kids in the Lexington community including involvement in a literacy campaign and teaching middle school girls the basics of computer science.<br />
<br />
This summer she is participating in the Summer Undergraduate Program in Engineering Research at Berkeley (SUPERB) and working with the iGEM 2008 UC Berkeley Computational Team. She is using Java to write an "Algorithm Manager" for the Clotho tool. While she has used Java extensively in her coursework at W&L, the synthetic biology aspect of the project is completely new to her. The last time she took biology was in 9th grade! She hopes this project will not only improve her research skills in computer science, but will also enlighten her to the emerging field of synthetic biology.<br />
<br />
===Nade Sritanyaratana - Student Member===<br />
[[Image:Nade_Professional.jpg|thumb|Nade Sritanyaratana]]<br />
<!---[[Image:NadeHeadShot.png|thumb|Nade Sritanyaratana]]---><br />
<br />
Nade Sritanyaratana is a 3rd year undergraduate at the University of California, Berkeley. He is majoring in Bioengineering with a concentration in imaging, and hopes to apply for a PhD graduate program in the upcoming year. Beyond imaging, his academic interests include Biomechanics; signals and systems; circuit analysis; systems biology; and linear optimization.<br />
<br />
His prior research experience consists of working with [http://bioeng.berkeley.edu/cv.php?facultyid=3022 bioengineering professor Steven Conolly] in the Summer and Fall of 2007. During that summer, he designed a coil helmet with an induced [http://en.wikipedia.org/wiki/Maxwell_coil Maxwell magnetic field]. This magnetic coil could be worn on the head and activated to generate small magnetic waves, soothing the wearer. Nicknamed the “Happy Helmet”, it was designed to non-invasively treat the bipolar-depressed via magnetic stimulation. Once fully developed, the helmet was to cost a hundred-fold less than an [http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging fMRI], the current primary treatment to bipolar depression.<br />
<br />
This summer Nade is working full-time with the iGEM 2008 Cal Computational Team. This is his first time using Java. Prior to Java, his programming experience included an introductory C++ class in the 9th grade and MATLAB experience for three years in Berkeley. He has had prior experience with computational modeling in general; last year Nade worked with LabVIEW for his introductory class to signals and systems. Last fall he graphically modeled a growing brain tumor with ADINA for his Biomechanics class, and later based his main Biofluid mechanics project on the dynamics of a atherosclerotic artery using a computational model generated by COMSOL.<br />
<br />
===Matthew Johnson - Student Member===<br />
[[Image:Matt_Professional2.jpg|300 px]]<br />
<br />
===Dr. Douglas Densmore - Instructor===<br />
[[Image:DougAtTheDOP2.png|thumb|Douglas Densmore]]<br />
Douglas Densmore received his Bachelors of Science in Engineering (Computer Engineering) from the University of Michigan in April 2001. He received his Masters of Science in Electrical Engineering in May 2004 from the University of California at Berkeley. His masters thesis was entitled, "Platform Based Reconfigurable Architecture Exploration via Boolean Constraints" and demonstrated how Boolean Satisfiability could be used to produce configurations for programmable hardware. He received his PhD in Electrical Engineering from UC Berkeley as well in May 2007. His PhD thesis, entitled "A Design Flow for the Development, Characterization, and Refinement of System Level Architecture Services", explored how electronic system level design methodologies can be abstract and modular while at the same time remaining accurate and efficient.<br />
<br />
He is currently a UC Chancellor's post doctoral researcher at UC Berkeley studying under [http://www.eecs.berkeley.edu/~alberto Prof. Alberto Sangiovanni-Vincentelli]. His research area is in the development of System Level Design methodologies for electronic systems. Specifically, architecture modeling and refinement verification. His background and interests are in Computer Architecture, Logic Synthesis, Digital Logic Design and Synthetic Biology. <br />
<br />
His industry experience includes four+ summers with Intel Corporation where he was involved in pre-silicon design efforts regarding chipset development, post-silicon validation of the Pentium 4 microprocessor, and chipset software validation. He has also worked as a researcher at Cypress Semiconductor and Xilinx Research Labs. He is currently a member of the [http://www.gigascale.org Gigascale Systems Research Center (GSRC)] and the [http://chess.eecs.berkeley.edu Center for Hybrid and Embedded Software Systems (CHESS)] at UC Berkeley. He has published work regarding a method of successive refinement verification of electronic systems, taxonomies of EDA design tools, and algebraic frameworks for the manipulation of functional design descriptions to expose computational parallelism. In addition he has a US patent pending regarding data characterization of programmable devices (such as field programmable gate arrays).<br />
<br />
<br clear="all"><br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
== What we did ==<br />
''This section briefly describes the contributions of each team member.''<br />
<br />
===Matthew LE Johnson===<br />
Spent a lot of time working on:<br />
<br />
* The About connection/frame<br />
* DNA analysis tools and algorithms (including Translation, G-C content, Melting Temperature, Reverse complementing, etc.)<br />
* The Enzyme Library and associated functionality<br />
* Sequence View connection (with Nade and Doug)<br />
* Compatibility with GenBank, FASTA, and ApE file formats<br />
* Support for degenerate IUPAC codes<br />
* Restriction site search and highlighting<br />
* Forward and reverse Open Reading Frame search and highlighting<br />
* Clotho Preferences for various connections<br />
* All of the Clotho Transfer Handlers<br />
* Intelligent Drag and Drop (DnD) between connections<br />
* Work on the Comp. Team Wiki<br />
* Feedback and advice on the graphic designs (seriously: thank you, Nade!)<br />
* ... and many, MANY hours of debugging!<br />
<br />
===Anne Van Devender===<br />
Anne Van Devender was responsible for:<br />
<br />
* The development and design of the algorithm manager<br />
* Clotho algorithm interface and initial implementation<br />
* The conversion of BioBrick assembly algorithms from Perl to Java<br />
* Aid in the development of 2ab assembly algorithms for Clotho<br />
<br />
===Nade Sritanyaratana===<br />
<br />
Nade Sritanyaratana, in semi-chronological order, is attributed to the following work: <br />
<br />
* The Help connection/frame<br />
* Highlighting<br />
* Features connection<br />
* Co-coordinated Sequence View connection/frame alongside Matt and Doug<br />
* Sequence View Tools (Find/Replace)<br />
* Feature Library Collection connection/frame<br />
* File Choosers<br />
* Search Helper<br />
* .txt file Helper<br />
* Photographing at test sessions<br />
* Debugging post-test sessions<br />
* Parts Manager<br />
* Maintaining the iGEM 2008 Computational Tools Team wiki: layout and painted graphics<br />
* Maintaining the Cal College of Engineering iGEM blog alongside Marlee Tichenor and Madvhi Venkatesh of the wet team<br />
* Clotho iGEM logo and woman<br />
* Clotho iGEM t-shirt<br />
<br />
===Dr. Douglas Densmore===<br />
Doug provided the initial Clotho software infrastructure and served as the main team lead. He helped to keep the team on track and supervised the construction and functionality of Clotho. He is the chief architect of Clotho and in charge of its maintenance, deployment, and promotion.<br />
<br />
===Dr. Chris Anderson===<br />
Prof. Anderson provided specifications for what tools and techniques should be incorporated in Clotho. In addition he also helped to define the general assembly problem for standardized biological parts as well as provide the context in which the tool would be used. He also provided many interesting discussion regarding the Clotho data model and provided the database by which we did the majority of our testing.<br />
<br />
===Other attribution===<br />
<br />
Many thanks to Collin Martin for the professional photography shots, and the Comp team shot.<br />
<br />
Shout out goes to Cici Chen of the UC Berkeley wetlab for helping design the Clotho title (alpha). Also Brian Zimmer, Bing Xia, and Roger Tu also have contributed to the development of Clotho. Josh Kittleson was instrumental in the development of the mySQL/PoBoL connection and tools. Will Deloache helped with the development of the assembly algorithms for 2ab assembly that is in the tool.<br />
<br />
== Where we're from ==<br />
<br />
===Dr. Douglas Densmore===<br />
Doug is from Richland, Michigan which is a small town outside of Kalamazoo. He attended the University of Michigan from 1996-2001 and has been in Berkeley, California since 2001. His family is from the Detroit area. They still live in Michigan.<br />
<br />
===Nade Sritanyaratana===<br />
Nade is a 4th year bioengineering undergraduate at UC Berkeley. He was born in the SF Bay Area, in Hayward, CA, and has lived around the Bay Area his entire life. Both of his parents are Thai. He attended James Logan High School in Union City, CA, where his primary activities included speech and debate, Leo Club, and the swim team. His family still resides in Union City.<br />
<br />
===Matthew L.E. Johnson===<br />
Matt is a SoCal native - born and raised in Bakersfield, CA right up until the move to Berkeley in 2005. He loves his hometown, but realizes that it is an 'acquired taste', especially during the average summer's daily triple-digit heat. Despite the vast differences between his new home and his old (with inverse climates - politically and meteorologically), he has adapted well and has been greatly enjoying his stay in the Bay Area.</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/TeamTeam:UC Berkeley Tools/Team2008-10-29T10:32:16Z<p>Logosandpathos: /* Matthew LE Johnson */</p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<!--- <center>[http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development#Downloads_and_Information <b>The Alpha release is here.</b>]</center> ---><br />
<br />
{{Template:ClothoMenu}}<br />
__NOTOC__<br />
<br />
<br />
== Who we are ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
'''Faculty Advisors:'''<br />
<br />
*''' Advisor 1''': Doug Densmore, Post-Doc at UC Berkeley<br />
*'''Advisor 2''': Chris Anderson, Assistant Professor at UC Berkeley<br />
<br />
<br />
'''Undergrads:'''<br />
<br />
*'''Student''': Anne Van Devender, 4th year Computer Science undergraduate, Washington and Lee University<br />
*'''Student''': Matthew Johnson, 4th year Bioengineering undergraduate, UC Berkeley<br />
*'''Student''': Nade Sritanyaratana, 4th year Bioengineering undergraduate, UC Berkeley<br />
<br />
|<br />
<gallery perrow="4"><br />
Image:Doug_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Dr._Douglas_Densmore|Doug Densmore]]<br />
Image:Anne_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Anne_Van_Devender|Anne Van Devender]]<br />
Image:MattInStanley.png|[[Team:UC_Berkeley_Tools/Team#Matthew_Johnson|Matthew L.E. Johnson]]<br />
Image:Nade_atStanley.png|[[Team:UC_Berkeley_Tools/Team#Nade_Sritanyaratana|Nade Sritanyaratana]]<br />
</gallery><br />
|}<br />
<br />
==Team Biographies==<br />
[[Image:CalCompTeam.png|The 2008 iGEM Cal Comp Team]]<br />
<br />
===Anne Van Devender - Student Member===<br />
<br />
[[Image:Anne_Professional.jpg|250 px|thumb|left|Anne Van Devender]]<br />
<br />
Anne Van Devender is a 4th year undergraduate at Washington and Lee University (Lexington, VA). She is a Computer Science major with a minor in Women's Studies. After graduation she hopes to attend graduate school for either a master's degree or PhD in Human Computer Interaction. <br />
<br />
Her main endeavor outside of academics is the Washington and Lee Women's Soccer team where she is captain and a three-year letter winner. In 2007, she was named to the NSCAA All-America team. When she is not on the field or in the classroom, she enjoys working with kids in the Lexington community including involvement in a literacy campaign and teaching middle school girls the basics of computer science.<br />
<br />
This summer she is participating in the Summer Undergraduate Program in Engineering Research at Berkeley (SUPERB) and working with the iGEM 2008 UC Berkeley Computational Team. She is using Java to write an "Algorithm Manager" for the Clotho tool. While she has used Java extensively in her coursework at W&L, the synthetic biology aspect of the project is completely new to her. The last time she took biology was in 9th grade! She hopes this project will not only improve her research skills in computer science, but will also enlighten her to the emerging field of synthetic biology.<br />
<br />
===Nade Sritanyaratana - Student Member===<br />
[[Image:Nade_Professional.jpg|thumb|Nade Sritanyaratana]]<br />
<!---[[Image:NadeHeadShot.png|thumb|Nade Sritanyaratana]]---><br />
<br />
Nade Sritanyaratana is a 3rd year undergraduate at the University of California, Berkeley. He is majoring in Bioengineering with a concentration in imaging, and hopes to apply for a PhD graduate program in the upcoming year. Beyond imaging, his academic interests include Biomechanics; signals and systems; circuit analysis; systems biology; and linear optimization.<br />
<br />
His prior research experience consists of working with [http://bioeng.berkeley.edu/cv.php?facultyid=3022 bioengineering professor Steven Conolly] in the Summer and Fall of 2007. During that summer, he designed a coil helmet with an induced [http://en.wikipedia.org/wiki/Maxwell_coil Maxwell magnetic field]. This magnetic coil could be worn on the head and activated to generate small magnetic waves, soothing the wearer. Nicknamed the “Happy Helmet”, it was designed to non-invasively treat the bipolar-depressed via magnetic stimulation. Once fully developed, the helmet was to cost a hundred-fold less than an [http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging fMRI], the current primary treatment to bipolar depression.<br />
<br />
This summer Nade is working full-time with the iGEM 2008 Cal Computational Team. This is his first time using Java. Prior to Java, his programming experience included an introductory C++ class in the 9th grade and MATLAB experience for three years in Berkeley. He has had prior experience with computational modeling in general; last year Nade worked with LabVIEW for his introductory class to signals and systems. Last fall he graphically modeled a growing brain tumor with ADINA for his Biomechanics class, and later based his main Biofluid mechanics project on the dynamics of a atherosclerotic artery using a computational model generated by COMSOL.<br />
<br />
===Matthew Johnson - Student Member===<br />
[[Image:Matt_Professional2.jpg|300 px]]<br />
<br />
===Dr. Douglas Densmore - Instructor===<br />
[[Image:DougAtTheDOP2.png|thumb|Douglas Densmore]]<br />
Douglas Densmore received his Bachelors of Science in Engineering (Computer Engineering) from the University of Michigan in April 2001. He received his Masters of Science in Electrical Engineering in May 2004 from the University of California at Berkeley. His masters thesis was entitled, "Platform Based Reconfigurable Architecture Exploration via Boolean Constraints" and demonstrated how Boolean Satisfiability could be used to produce configurations for programmable hardware. He received his PhD in Electrical Engineering from UC Berkeley as well in May 2007. His PhD thesis, entitled "A Design Flow for the Development, Characterization, and Refinement of System Level Architecture Services", explored how electronic system level design methodologies can be abstract and modular while at the same time remaining accurate and efficient.<br />
<br />
He is currently a UC Chancellor's post doctoral researcher at UC Berkeley studying under [http://www.eecs.berkeley.edu/~alberto Prof. Alberto Sangiovanni-Vincentelli]. His research area is in the development of System Level Design methodologies for electronic systems. Specifically, architecture modeling and refinement verification. His background and interests are in Computer Architecture, Logic Synthesis, Digital Logic Design and Synthetic Biology. <br />
<br />
His industry experience includes four+ summers with Intel Corporation where he was involved in pre-silicon design efforts regarding chipset development, post-silicon validation of the Pentium 4 microprocessor, and chipset software validation. He has also worked as a researcher at Cypress Semiconductor and Xilinx Research Labs. He is currently a member of the [http://www.gigascale.org Gigascale Systems Research Center (GSRC)] and the [http://chess.eecs.berkeley.edu Center for Hybrid and Embedded Software Systems (CHESS)] at UC Berkeley. He has published work regarding a method of successive refinement verification of electronic systems, taxonomies of EDA design tools, and algebraic frameworks for the manipulation of functional design descriptions to expose computational parallelism. In addition he has a US patent pending regarding data characterization of programmable devices (such as field programmable gate arrays).<br />
<br />
<br clear="all"><br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
== What we did ==<br />
''This section briefly describes the contributions of each team member.''<br />
<br />
===Matthew LE Johnson===<br />
<br />
Helped considerably with:<br />
<br />
* The About connection/frame<br />
* DNA analysis tools and algorithms (including Translation, G-C content, Melting Temperature, Reverse complementing, etc.)<br />
* The Enzyme Library and associated functionality<br />
* Sequence View connection (with Nade and Doug)<br />
* Compatibility with GenBank, FASTA, and ApE file formats<br />
* Support for degenerate IUPAC codes<br />
* Restriction site search and highlighting<br />
* Forward and reverse Open Reading Frame search and highlighting<br />
* Clotho Preferences for various connections<br />
* All of the Clotho Transfer Handlers<br />
* Intelligent Drag and Drop (DnD) between connections<br />
* Work on the Comp. Team Wiki<br />
* Feedback and advice on the graphic designs (seriously: thank you, Nade!)<br />
* ... and many, MANY hours of debugging!<br />
<br />
===Anne Van Devender===<br />
Anne Van Devender was responsible for:<br />
<br />
* The development and design of the algorithm manager<br />
* Clotho algorithm interface and initial implementation<br />
* The conversion of BioBrick assembly algorithms from Perl to Java<br />
* Aid in the development of 2ab assembly algorithms for Clotho<br />
<br />
===Nade Sritanyaratana===<br />
<br />
Nade Sritanyaratana, in semi-chronological order, is attributed to the following work: <br />
<br />
* The Help connection/frame<br />
* Highlighting<br />
* Features connection<br />
* Co-coordinated Sequence View connection/frame alongside Matt and Doug<br />
* Sequence View Tools (Find/Replace)<br />
* Feature Library Collection connection/frame<br />
* File Choosers<br />
* Search Helper<br />
* .txt file Helper<br />
* Photographing at test sessions<br />
* Debugging post-test sessions<br />
* Parts Manager<br />
* Maintaining the iGEM 2008 Computational Tools Team wiki: layout and painted graphics<br />
* Maintaining the Cal College of Engineering iGEM blog alongside Marlee Tichenor and Madvhi Venkatesh of the wet team<br />
* Clotho iGEM logo and woman<br />
* Clotho iGEM t-shirt<br />
<br />
===Dr. Douglas Densmore===<br />
Doug provided the initial Clotho software infrastructure and served as the main team lead. He helped to keep the team on track and supervised the construction and functionality of Clotho. He is the chief architect of Clotho and in charge of its maintenance, deployment, and promotion.<br />
<br />
===Dr. Chris Anderson===<br />
Prof. Anderson provided specifications for what tools and techniques should be incorporated in Clotho. In addition he also helped to define the general assembly problem for standardized biological parts as well as provide the context in which the tool would be used. He also provided many interesting discussion regarding the Clotho data model and provided the database by which we did the majority of our testing.<br />
<br />
===Other attribution===<br />
<br />
Many thanks to Collin Martin for the professional photography shots, and the Comp team shot.<br />
<br />
Shout out goes to Cici Chen of the UC Berkeley wetlab for helping design the Clotho title (alpha). Also Brian Zimmer, Bing Xia, and Roger Tu also have contributed to the development of Clotho. Josh Kittleson was instrumental in the development of the mySQL/PoBoL connection and tools. Will Deloache helped with the development of the assembly algorithms for 2ab assembly that is in the tool.<br />
<br />
== Where we're from ==<br />
<br />
===Dr. Douglas Densmore===<br />
Doug is from Richland, Michigan which is a small town outside of Kalamazoo. He attended the University of Michigan from 1996-2001 and has been in Berkeley, California since 2001. His family is from the Detroit area. They still live in Michigan.<br />
<br />
===Nade Sritanyaratana===<br />
Nade is a 4th year bioengineering undergraduate at UC Berkeley. He was born in the SF Bay Area, in Hayward, CA, and has lived around the Bay Area his entire life. Both of his parents are Thai. He attended James Logan High School in Union City, CA, where his primary activities included speech and debate, Leo Club, and the swim team. His family still resides in Union City.<br />
<br />
===Matthew L.E. Johnson===<br />
Matt is a SoCal native - born and raised in Bakersfield, CA right up until the move to Berkeley in 2005. He loves his hometown, but realizes that it is an 'acquired taste', especially during the average summer's daily triple-digit heat. Despite the vast differences between his new home and his old (with inverse climates - politically and meteorologically), he has adapted well and has been greatly enjoying his stay in the Bay Area.</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/TeamTeam:UC Berkeley Tools/Team2008-10-29T10:29:51Z<p>Logosandpathos: /* Nade Sritanyaratana - Student Member */</p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<!--- <center>[http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development#Downloads_and_Information <b>The Alpha release is here.</b>]</center> ---><br />
<br />
{{Template:ClothoMenu}}<br />
__NOTOC__<br />
<br />
<br />
== Who we are ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
'''Faculty Advisors:'''<br />
<br />
*''' Advisor 1''': Doug Densmore, Post-Doc at UC Berkeley<br />
*'''Advisor 2''': Chris Anderson, Assistant Professor at UC Berkeley<br />
<br />
<br />
'''Undergrads:'''<br />
<br />
*'''Student''': Anne Van Devender, 4th year Computer Science undergraduate, Washington and Lee University<br />
*'''Student''': Matthew Johnson, 4th year Bioengineering undergraduate, UC Berkeley<br />
*'''Student''': Nade Sritanyaratana, 4th year Bioengineering undergraduate, UC Berkeley<br />
<br />
|<br />
<gallery perrow="4"><br />
Image:Doug_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Dr._Douglas_Densmore|Doug Densmore]]<br />
Image:Anne_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Anne_Van_Devender|Anne Van Devender]]<br />
Image:MattInStanley.png|[[Team:UC_Berkeley_Tools/Team#Matthew_Johnson|Matthew L.E. Johnson]]<br />
Image:Nade_atStanley.png|[[Team:UC_Berkeley_Tools/Team#Nade_Sritanyaratana|Nade Sritanyaratana]]<br />
</gallery><br />
|}<br />
<br />
==Team Biographies==<br />
[[Image:CalCompTeam.png|The 2008 iGEM Cal Comp Team]]<br />
<br />
===Anne Van Devender - Student Member===<br />
<br />
[[Image:Anne_Professional.jpg|250 px|thumb|left|Anne Van Devender]]<br />
<br />
Anne Van Devender is a 4th year undergraduate at Washington and Lee University (Lexington, VA). She is a Computer Science major with a minor in Women's Studies. After graduation she hopes to attend graduate school for either a master's degree or PhD in Human Computer Interaction. <br />
<br />
Her main endeavor outside of academics is the Washington and Lee Women's Soccer team where she is captain and a three-year letter winner. In 2007, she was named to the NSCAA All-America team. When she is not on the field or in the classroom, she enjoys working with kids in the Lexington community including involvement in a literacy campaign and teaching middle school girls the basics of computer science.<br />
<br />
This summer she is participating in the Summer Undergraduate Program in Engineering Research at Berkeley (SUPERB) and working with the iGEM 2008 UC Berkeley Computational Team. She is using Java to write an "Algorithm Manager" for the Clotho tool. While she has used Java extensively in her coursework at W&L, the synthetic biology aspect of the project is completely new to her. The last time she took biology was in 9th grade! She hopes this project will not only improve her research skills in computer science, but will also enlighten her to the emerging field of synthetic biology.<br />
<br />
===Nade Sritanyaratana - Student Member===<br />
[[Image:Nade_Professional.jpg|thumb|Nade Sritanyaratana]]<br />
<!---[[Image:NadeHeadShot.png|thumb|Nade Sritanyaratana]]---><br />
<br />
Nade Sritanyaratana is a 3rd year undergraduate at the University of California, Berkeley. He is majoring in Bioengineering with a concentration in imaging, and hopes to apply for a PhD graduate program in the upcoming year. Beyond imaging, his academic interests include Biomechanics; signals and systems; circuit analysis; systems biology; and linear optimization.<br />
<br />
His prior research experience consists of working with [http://bioeng.berkeley.edu/cv.php?facultyid=3022 bioengineering professor Steven Conolly] in the Summer and Fall of 2007. During that summer, he designed a coil helmet with an induced [http://en.wikipedia.org/wiki/Maxwell_coil Maxwell magnetic field]. This magnetic coil could be worn on the head and activated to generate small magnetic waves, soothing the wearer. Nicknamed the “Happy Helmet”, it was designed to non-invasively treat the bipolar-depressed via magnetic stimulation. Once fully developed, the helmet was to cost a hundred-fold less than an [http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging fMRI], the current primary treatment to bipolar depression.<br />
<br />
This summer Nade is working full-time with the iGEM 2008 Cal Computational Team. This is his first time using Java. Prior to Java, his programming experience included an introductory C++ class in the 9th grade and MATLAB experience for three years in Berkeley. He has had prior experience with computational modeling in general; last year Nade worked with LabVIEW for his introductory class to signals and systems. Last fall he graphically modeled a growing brain tumor with ADINA for his Biomechanics class, and later based his main Biofluid mechanics project on the dynamics of a atherosclerotic artery using a computational model generated by COMSOL.<br />
<br />
===Matthew Johnson - Student Member===<br />
[[Image:Matt_Professional2.jpg|300 px]]<br />
<br />
===Dr. Douglas Densmore - Instructor===<br />
[[Image:DougAtTheDOP2.png|thumb|Douglas Densmore]]<br />
Douglas Densmore received his Bachelors of Science in Engineering (Computer Engineering) from the University of Michigan in April 2001. He received his Masters of Science in Electrical Engineering in May 2004 from the University of California at Berkeley. His masters thesis was entitled, "Platform Based Reconfigurable Architecture Exploration via Boolean Constraints" and demonstrated how Boolean Satisfiability could be used to produce configurations for programmable hardware. He received his PhD in Electrical Engineering from UC Berkeley as well in May 2007. His PhD thesis, entitled "A Design Flow for the Development, Characterization, and Refinement of System Level Architecture Services", explored how electronic system level design methodologies can be abstract and modular while at the same time remaining accurate and efficient.<br />
<br />
He is currently a UC Chancellor's post doctoral researcher at UC Berkeley studying under [http://www.eecs.berkeley.edu/~alberto Prof. Alberto Sangiovanni-Vincentelli]. His research area is in the development of System Level Design methodologies for electronic systems. Specifically, architecture modeling and refinement verification. His background and interests are in Computer Architecture, Logic Synthesis, Digital Logic Design and Synthetic Biology. <br />
<br />
His industry experience includes four+ summers with Intel Corporation where he was involved in pre-silicon design efforts regarding chipset development, post-silicon validation of the Pentium 4 microprocessor, and chipset software validation. He has also worked as a researcher at Cypress Semiconductor and Xilinx Research Labs. He is currently a member of the [http://www.gigascale.org Gigascale Systems Research Center (GSRC)] and the [http://chess.eecs.berkeley.edu Center for Hybrid and Embedded Software Systems (CHESS)] at UC Berkeley. He has published work regarding a method of successive refinement verification of electronic systems, taxonomies of EDA design tools, and algebraic frameworks for the manipulation of functional design descriptions to expose computational parallelism. In addition he has a US patent pending regarding data characterization of programmable devices (such as field programmable gate arrays).<br />
<br />
<br clear="all"><br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
== What we did ==<br />
''This section briefly describes the contributions of each team member.''<br />
<br />
===Matthew LE Johnson===<br />
<br />
Give or take:<br />
<br />
* The About connection/frame<br />
* DNA analysis tools and algorithms (including Translation, G-C content, Melting Temperature, Reverse complementing, etc.)<br />
* The Enzyme Library and associated functionality<br />
* Sequence View connection (with Nade and Doug)<br />
* Compatibility with GenBank, FASTA, and ApE file formats<br />
* Support for degenerate IUPAC codes<br />
* Restriction site search and highlighting<br />
* Forward and reverse Open Reading Frame search and highlighting<br />
* Clotho Preferences for various connections<br />
* All of the Clotho Transfer Handlers<br />
* Intelligent Drag and Drop (DnD) between connections<br />
* Work on the Comp. Team Wiki<br />
* Feedback and advice on the graphic designs (seriously: thanks you, Nade!)<br />
* ... and many, MANY hours of debugging!<br />
<br />
===Anne Van Devender===<br />
Anne Van Devender was responsible for:<br />
<br />
* The development and design of the algorithm manager<br />
* Clotho algorithm interface and initial implementation<br />
* The conversion of BioBrick assembly algorithms from Perl to Java<br />
* Aid in the development of 2ab assembly algorithms for Clotho<br />
<br />
===Nade Sritanyaratana===<br />
<br />
Nade Sritanyaratana, in semi-chronological order, is attributed to the following work: <br />
<br />
* The Help connection/frame<br />
* Highlighting<br />
* Features connection<br />
* Co-coordinated Sequence View connection/frame alongside Matt and Doug<br />
* Sequence View Tools (Find/Replace)<br />
* Feature Library Collection connection/frame<br />
* File Choosers<br />
* Search Helper<br />
* .txt file Helper<br />
* Photographing at test sessions<br />
* Debugging post-test sessions<br />
* Parts Manager<br />
* Maintaining the iGEM 2008 Computational Tools Team wiki: layout and painted graphics<br />
* Maintaining the Cal College of Engineering iGEM blog alongside Marlee Tichenor and Madvhi Venkatesh of the wet team<br />
* Clotho iGEM logo and woman<br />
* Clotho iGEM t-shirt<br />
<br />
===Dr. Douglas Densmore===<br />
Doug provided the initial Clotho software infrastructure and served as the main team lead. He helped to keep the team on track and supervised the construction and functionality of Clotho. He is the chief architect of Clotho and in charge of its maintenance, deployment, and promotion.<br />
<br />
===Dr. Chris Anderson===<br />
Prof. Anderson provided specifications for what tools and techniques should be incorporated in Clotho. In addition he also helped to define the general assembly problem for standardized biological parts as well as provide the context in which the tool would be used. He also provided many interesting discussion regarding the Clotho data model and provided the database by which we did the majority of our testing.<br />
<br />
===Other attribution===<br />
<br />
Many thanks to Collin Martin for the professional photography shots, and the Comp team shot.<br />
<br />
Shout out goes to Cici Chen of the UC Berkeley wetlab for helping design the Clotho title (alpha). Also Brian Zimmer, Bing Xia, and Roger Tu also have contributed to the development of Clotho. Josh Kittleson was instrumental in the development of the mySQL/PoBoL connection and tools. Will Deloache helped with the development of the assembly algorithms for 2ab assembly that is in the tool.<br />
<br />
== Where we're from ==<br />
<br />
===Dr. Douglas Densmore===<br />
Doug is from Richland, Michigan which is a small town outside of Kalamazoo. He attended the University of Michigan from 1996-2001 and has been in Berkeley, California since 2001. His family is from the Detroit area. They still live in Michigan.<br />
<br />
===Nade Sritanyaratana===<br />
Nade is a 4th year bioengineering undergraduate at UC Berkeley. He was born in the SF Bay Area, in Hayward, CA, and has lived around the Bay Area his entire life. Both of his parents are Thai. He attended James Logan High School in Union City, CA, where his primary activities included speech and debate, Leo Club, and the swim team. His family still resides in Union City.<br />
<br />
===Matthew L.E. Johnson===<br />
Matt is a SoCal native - born and raised in Bakersfield, CA right up until the move to Berkeley in 2005. He loves his hometown, but realizes that it is an 'acquired taste', especially during the average summer's daily triple-digit heat. Despite the vast differences between his new home and his old (with inverse climates - politically and meteorologically), he has adapted well and has been greatly enjoying his stay in the Bay Area.</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/TeamTeam:UC Berkeley Tools/Team2008-10-29T10:21:29Z<p>Logosandpathos: /* What we did */</p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<!--- <center>[http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development#Downloads_and_Information <b>The Alpha release is here.</b>]</center> ---><br />
<br />
{{Template:ClothoMenu}}<br />
__NOTOC__<br />
<br />
<br />
== Who we are ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
'''Faculty Advisors:'''<br />
<br />
*''' Advisor 1''': Doug Densmore, Post-Doc at UC Berkeley<br />
*'''Advisor 2''': Chris Anderson, Assistant Professor at UC Berkeley<br />
<br />
<br />
'''Undergrads:'''<br />
<br />
*'''Student''': Anne Van Devender, 4th year Computer Science undergraduate, Washington and Lee University<br />
*'''Student''': Matthew Johnson, 4th year Bioengineering undergraduate, UC Berkeley<br />
*'''Student''': Nade Sritanyaratana, 4th year Bioengineering undergraduate, UC Berkeley<br />
<br />
|<br />
<gallery perrow="4"><br />
Image:Doug_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Dr._Douglas_Densmore|Doug Densmore]]<br />
Image:Anne_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Anne_Van_Devender|Anne Van Devender]]<br />
Image:MattInStanley.png|[[Team:UC_Berkeley_Tools/Team#Matthew_Johnson|Matthew L.E. Johnson]]<br />
Image:Nade_atStanley.png|[[Team:UC_Berkeley_Tools/Team#Nade_Sritanyaratana|Nade Sritanyaratana]]<br />
</gallery><br />
|}<br />
<br />
==Team Biographies==<br />
[[Image:CalCompTeam.png|The 2008 iGEM Cal Comp Team]]<br />
<br />
===Anne Van Devender - Student Member===<br />
<br />
[[Image:Anne_Professional.jpg|250 px|thumb|left|Anne Van Devender]]<br />
<br />
Anne Van Devender is a 4th year undergraduate at Washington and Lee University (Lexington, VA). She is a Computer Science major with a minor in Women's Studies. After graduation she hopes to attend graduate school for either a master's degree or PhD in Human Computer Interaction. <br />
<br />
Her main endeavor outside of academics is the Washington and Lee Women's Soccer team where she is captain and a three-year letter winner. In 2007, she was named to the NSCAA All-America team. When she is not on the field or in the classroom, she enjoys working with kids in the Lexington community including involvement in a literacy campaign and teaching middle school girls the basics of computer science.<br />
<br />
This summer she is participating in the Summer Undergraduate Program in Engineering Research at Berkeley (SUPERB) and working with the iGEM 2008 UC Berkeley Computational Team. She is using Java to write an "Algorithm Manager" for the Clotho tool. While she has used Java extensively in her coursework at W&L, the synthetic biology aspect of the project is completely new to her. The last time she took biology was in 9th grade! She hopes this project will not only improve her research skills in computer science, but will also enlighten her to the emerging field of synthetic biology.<br />
<br />
===Nade Sritanyaratana - Student Member===<br />
[[Image:Nade_Professional.jpg|thumb|Nade Sritanyaratana]]<br />
<!---[[Image:NadeHeadShot.png|thumb|Nade Sritanyaratana]]---><br />
<br />
Nade Sritanyaratana is a 3rd year undergraduate at the University of California, Berkeley. He is majoring in Bioengineering with a concentration in imaging, and hopes to apply for a PhD graduate program in the upcoming year. Beyond imaging, his academic interests include Biomechanics; signals and systems; circuit analysis; systems biology; and linear optimization.<br />
<br />
His prior research experience consists of working with [http://bioeng.berkeley.edu/cv.php?facultyid=3022 bioengineering professor Steven Conolly] in the Summer and Fall of 2007. During that summer, he designed a coil helmet with an induced [http://en.wikipedia.org/wiki/Maxwell_coil Maxwell magnetic field]. This magnetic coil could be worn on the head and activated to generate small magnetic waves, soothing the wearer. Nicknamed the “Happy Helmet”, it was designed to non-invasively treat the bipolar-depressed via magnetic stimulation. Once fully developed, the helmet was to cost a hundred-fold less than an [http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging fMRI], the current primary treatment to bipolar depression.<br />
<br />
This summer Nade is working full-time with the iGEM 2008 Cal Computational Team. This is his first time using Java. Prior to Java, his programming experience included an introductory C++ class in the 9th grade and MATLAB experience for three years in Berkeley. He has had prior experience with computational modelling in general; last year Nade worked with LabVIEW for his introductory class to signals and systems. Last fall he graphically modeled a growing brain tumor with ADINA for his Biomechanics class, and later based his main Biofluid mechanics project on the dynamics of a atherosclerotic artery using a computational model generated by COMSOL.<br />
<br />
===Matthew Johnson - Student Member===<br />
[[Image:Matt_Professional2.jpg|300 px]]<br />
<br />
===Dr. Douglas Densmore - Instructor===<br />
[[Image:DougAtTheDOP2.png|thumb|Douglas Densmore]]<br />
Douglas Densmore received his Bachelors of Science in Engineering (Computer Engineering) from the University of Michigan in April 2001. He received his Masters of Science in Electrical Engineering in May 2004 from the University of California at Berkeley. His masters thesis was entitled, "Platform Based Reconfigurable Architecture Exploration via Boolean Constraints" and demonstrated how Boolean Satisfiability could be used to produce configurations for programmable hardware. He received his PhD in Electrical Engineering from UC Berkeley as well in May 2007. His PhD thesis, entitled "A Design Flow for the Development, Characterization, and Refinement of System Level Architecture Services", explored how electronic system level design methodologies can be abstract and modular while at the same time remaining accurate and efficient.<br />
<br />
He is currently a UC Chancellor's post doctoral researcher at UC Berkeley studying under [http://www.eecs.berkeley.edu/~alberto Prof. Alberto Sangiovanni-Vincentelli]. His research area is in the development of System Level Design methodologies for electronic systems. Specifically, architecture modeling and refinement verification. His background and interests are in Computer Architecture, Logic Synthesis, Digital Logic Design and Synthetic Biology. <br />
<br />
His industry experience includes four+ summers with Intel Corporation where he was involved in pre-silicon design efforts regarding chipset development, post-silicon validation of the Pentium 4 microprocessor, and chipset software validation. He has also worked as a researcher at Cypress Semiconductor and Xilinx Research Labs. He is currently a member of the [http://www.gigascale.org Gigascale Systems Research Center (GSRC)] and the [http://chess.eecs.berkeley.edu Center for Hybrid and Embedded Software Systems (CHESS)] at UC Berkeley. He has published work regarding a method of successive refinement verification of electronic systems, taxonomies of EDA design tools, and algebraic frameworks for the manipulation of functional design descriptions to expose computational parallelism. In addition he has a US patent pending regarding data characterization of programmable devices (such as field programmable gate arrays).<br />
<br />
<br clear="all"><br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
== What we did ==<br />
''This section briefly describes the contributions of each team member.''<br />
<br />
===Matthew LE Johnson===<br />
<br />
Give or take:<br />
<br />
* The About connection/frame<br />
* DNA analysis tools and algorithms (including Translation, G-C content, Melting Temperature, Reverse complementing, etc.)<br />
* The Enzyme Library and associated functionality<br />
* Sequence View connection (with Nade and Doug)<br />
* Compatibility with GenBank, FASTA, and ApE file formats<br />
* Support for degenerate IUPAC codes<br />
* Restriction site search and highlighting<br />
* Forward and reverse Open Reading Frame search and highlighting<br />
* Clotho Preferences for various connections<br />
* All of the Clotho Transfer Handlers<br />
* Intelligent Drag and Drop (DnD) between connections<br />
* Work on the Comp. Team Wiki<br />
* Feedback and advice on the graphic designs (seriously: thanks you, Nade!)<br />
* ... and many, MANY hours of debugging!<br />
<br />
===Anne Van Devender===<br />
Anne Van Devender was responsible for:<br />
<br />
* The development and design of the algorithm manager<br />
* Clotho algorithm interface and initial implementation<br />
* The conversion of BioBrick assembly algorithms from Perl to Java<br />
* Aid in the development of 2ab assembly algorithms for Clotho<br />
<br />
===Nade Sritanyaratana===<br />
<br />
Nade Sritanyaratana, in semi-chronological order, is attributed to the following work: <br />
<br />
* The Help connection/frame<br />
* Highlighting<br />
* Features connection<br />
* Co-coordinated Sequence View connection/frame alongside Matt and Doug<br />
* Sequence View Tools (Find/Replace)<br />
* Feature Library Collection connection/frame<br />
* File Choosers<br />
* Search Helper<br />
* .txt file Helper<br />
* Photographing at test sessions<br />
* Debugging post-test sessions<br />
* Parts Manager<br />
* Maintaining the iGEM 2008 Computational Tools Team wiki: layout and painted graphics<br />
* Maintaining the Cal College of Engineering iGEM blog alongside Marlee Tichenor and Madvhi Venkatesh of the wet team<br />
* Clotho iGEM logo and woman<br />
* Clotho iGEM t-shirt<br />
<br />
===Dr. Douglas Densmore===<br />
Doug provided the initial Clotho software infrastructure and served as the main team lead. He helped to keep the team on track and supervised the construction and functionality of Clotho. He is the chief architect of Clotho and in charge of its maintenance, deployment, and promotion.<br />
<br />
===Dr. Chris Anderson===<br />
Prof. Anderson provided specifications for what tools and techniques should be incorporated in Clotho. In addition he also helped to define the general assembly problem for standardized biological parts as well as provide the context in which the tool would be used. He also provided many interesting discussion regarding the Clotho data model and provided the database by which we did the majority of our testing.<br />
<br />
===Other attribution===<br />
<br />
Many thanks to Collin Martin for the professional photography shots, and the Comp team shot.<br />
<br />
Shout out goes to Cici Chen of the UC Berkeley wetlab for helping design the Clotho title (alpha). Also Brian Zimmer, Bing Xia, and Roger Tu also have contributed to the development of Clotho. Josh Kittleson was instrumental in the development of the mySQL/PoBoL connection and tools. Will Deloache helped with the development of the assembly algorithms for 2ab assembly that is in the tool.<br />
<br />
== Where we're from ==<br />
<br />
===Dr. Douglas Densmore===<br />
Doug is from Richland, Michigan which is a small town outside of Kalamazoo. He attended the University of Michigan from 1996-2001 and has been in Berkeley, California since 2001. His family is from the Detroit area. They still live in Michigan.<br />
<br />
===Nade Sritanyaratana===<br />
Nade is a 4th year bioengineering undergraduate at UC Berkeley. He was born in the SF Bay Area, in Hayward, CA, and has lived around the Bay Area his entire life. Both of his parents are Thai. He attended James Logan High School in Union City, CA, where his primary activities included speech and debate, Leo Club, and the swim team. His family still resides in Union City.<br />
<br />
===Matthew L.E. Johnson===<br />
Matt is a SoCal native - born and raised in Bakersfield, CA right up until the move to Berkeley in 2005. He loves his hometown, but realizes that it is an 'acquired taste', especially during the average summer's daily triple-digit heat. Despite the vast differences between his new home and his old (with inverse climates - politically and meteorologically), he has adapted well and has been greatly enjoying his stay in the Bay Area.</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/TeamTeam:UC Berkeley Tools/Team2008-10-29T10:20:15Z<p>Logosandpathos: /* Where we're from */</p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<!--- <center>[http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development#Downloads_and_Information <b>The Alpha release is here.</b>]</center> ---><br />
<br />
{{Template:ClothoMenu}}<br />
__NOTOC__<br />
<br />
<br />
== Who we are ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
'''Faculty Advisors:'''<br />
<br />
*''' Advisor 1''': Doug Densmore, Post-Doc at UC Berkeley<br />
*'''Advisor 2''': Chris Anderson, Assistant Professor at UC Berkeley<br />
<br />
<br />
'''Undergrads:'''<br />
<br />
*'''Student''': Anne Van Devender, 4th year Computer Science undergraduate, Washington and Lee University<br />
*'''Student''': Matthew Johnson, 4th year Bioengineering undergraduate, UC Berkeley<br />
*'''Student''': Nade Sritanyaratana, 4th year Bioengineering undergraduate, UC Berkeley<br />
<br />
|<br />
<gallery perrow="4"><br />
Image:Doug_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Dr._Douglas_Densmore|Doug Densmore]]<br />
Image:Anne_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Anne_Van_Devender|Anne Van Devender]]<br />
Image:MattInStanley.png|[[Team:UC_Berkeley_Tools/Team#Matthew_Johnson|Matthew L.E. Johnson]]<br />
Image:Nade_atStanley.png|[[Team:UC_Berkeley_Tools/Team#Nade_Sritanyaratana|Nade Sritanyaratana]]<br />
</gallery><br />
|}<br />
<br />
==Team Biographies==<br />
[[Image:CalCompTeam.png|The 2008 iGEM Cal Comp Team]]<br />
<br />
===Anne Van Devender - Student Member===<br />
<br />
[[Image:Anne_Professional.jpg|250 px|thumb|left|Anne Van Devender]]<br />
<br />
Anne Van Devender is a 4th year undergraduate at Washington and Lee University (Lexington, VA). She is a Computer Science major with a minor in Women's Studies. After graduation she hopes to attend graduate school for either a master's degree or PhD in Human Computer Interaction. <br />
<br />
Her main endeavor outside of academics is the Washington and Lee Women's Soccer team where she is captain and a three-year letter winner. In 2007, she was named to the NSCAA All-America team. When she is not on the field or in the classroom, she enjoys working with kids in the Lexington community including involvement in a literacy campaign and teaching middle school girls the basics of computer science.<br />
<br />
This summer she is participating in the Summer Undergraduate Program in Engineering Research at Berkeley (SUPERB) and working with the iGEM 2008 UC Berkeley Computational Team. She is using Java to write an "Algorithm Manager" for the Clotho tool. While she has used Java extensively in her coursework at W&L, the synthetic biology aspect of the project is completely new to her. The last time she took biology was in 9th grade! She hopes this project will not only improve her research skills in computer science, but will also enlighten her to the emerging field of synthetic biology.<br />
<br />
===Nade Sritanyaratana - Student Member===<br />
[[Image:Nade_Professional.jpg|thumb|Nade Sritanyaratana]]<br />
<!---[[Image:NadeHeadShot.png|thumb|Nade Sritanyaratana]]---><br />
<br />
Nade Sritanyaratana is a 3rd year undergraduate at the University of California, Berkeley. He is majoring in Bioengineering with a concentration in imaging, and hopes to apply for a PhD graduate program in the upcoming year. Beyond imaging, his academic interests include Biomechanics; signals and systems; circuit analysis; systems biology; and linear optimization.<br />
<br />
His prior research experience consists of working with [http://bioeng.berkeley.edu/cv.php?facultyid=3022 bioengineering professor Steven Conolly] in the Summer and Fall of 2007. During that summer, he designed a coil helmet with an induced [http://en.wikipedia.org/wiki/Maxwell_coil Maxwell magnetic field]. This magnetic coil could be worn on the head and activated to generate small magnetic waves, soothing the wearer. Nicknamed the “Happy Helmet”, it was designed to non-invasively treat the bipolar-depressed via magnetic stimulation. Once fully developed, the helmet was to cost a hundred-fold less than an [http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging fMRI], the current primary treatment to bipolar depression.<br />
<br />
This summer Nade is working full-time with the iGEM 2008 Cal Computational Team. This is his first time using Java. Prior to Java, his programming experience included an introductory C++ class in the 9th grade and MATLAB experience for three years in Berkeley. He has had prior experience with computational modelling in general; last year Nade worked with LabVIEW for his introductory class to signals and systems. Last fall he graphically modeled a growing brain tumor with ADINA for his Biomechanics class, and later based his main Biofluid mechanics project on the dynamics of a atherosclerotic artery using a computational model generated by COMSOL.<br />
<br />
===Matthew Johnson - Student Member===<br />
[[Image:Matt_Professional2.jpg|300 px]]<br />
<br />
===Dr. Douglas Densmore - Instructor===<br />
[[Image:DougAtTheDOP2.png|thumb|Douglas Densmore]]<br />
Douglas Densmore received his Bachelors of Science in Engineering (Computer Engineering) from the University of Michigan in April 2001. He received his Masters of Science in Electrical Engineering in May 2004 from the University of California at Berkeley. His masters thesis was entitled, "Platform Based Reconfigurable Architecture Exploration via Boolean Constraints" and demonstrated how Boolean Satisfiability could be used to produce configurations for programmable hardware. He received his PhD in Electrical Engineering from UC Berkeley as well in May 2007. His PhD thesis, entitled "A Design Flow for the Development, Characterization, and Refinement of System Level Architecture Services", explored how electronic system level design methodologies can be abstract and modular while at the same time remaining accurate and efficient.<br />
<br />
He is currently a UC Chancellor's post doctoral researcher at UC Berkeley studying under [http://www.eecs.berkeley.edu/~alberto Prof. Alberto Sangiovanni-Vincentelli]. His research area is in the development of System Level Design methodologies for electronic systems. Specifically, architecture modeling and refinement verification. His background and interests are in Computer Architecture, Logic Synthesis, Digital Logic Design and Synthetic Biology. <br />
<br />
His industry experience includes four+ summers with Intel Corporation where he was involved in pre-silicon design efforts regarding chipset development, post-silicon validation of the Pentium 4 microprocessor, and chipset software validation. He has also worked as a researcher at Cypress Semiconductor and Xilinx Research Labs. He is currently a member of the [http://www.gigascale.org Gigascale Systems Research Center (GSRC)] and the [http://chess.eecs.berkeley.edu Center for Hybrid and Embedded Software Systems (CHESS)] at UC Berkeley. He has published work regarding a method of successive refinement verification of electronic systems, taxonomies of EDA design tools, and algebraic frameworks for the manipulation of functional design descriptions to expose computational parallelism. In addition he has a US patent pending regarding data characterization of programmable devices (such as field programmable gate arrays).<br />
<br />
<br clear="all"><br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
== What we did ==<br />
This section briefly describes the contributions of each team member.<br />
<br />
===Matthew LE Johnson===<br />
<br />
Give or take:<br />
<br />
* The About connection/frame<br />
* DNA analysis tools and algorithms (including Translation, G-C content, Melting Temperature, Reverse complementing, etc.)<br />
* The Enzyme Library and associated functionality<br />
* Sequence View connection (with Nade and Doug)<br />
* Compatibility with GenBank, FASTA, and ApE file formats<br />
* Support for degenerate IUPAC codes<br />
* Restriction site search and highlighting<br />
* Forward and reverse Open Reading Frame search and highlighting<br />
* Clotho Preferences for various connections<br />
* All of the Clotho Transfer Handlers<br />
* Intelligent Drag and Drop (DnD) between connections<br />
* Work on the Comp. Team Wiki<br />
* Feedback and advice on the graphic designs (seriously: thanks you, Nade!)<br />
* ... and many, MANY hours of debugging!<br />
<br />
===Anne Van Devender===<br />
Anne Van Devender was responsible for:<br />
<br />
* The development and design of the algorithm manager<br />
* Clotho algorithm interface and initial implementation<br />
* The conversion of BioBrick assembly algorithms from Perl to Java<br />
* Aid in the development of 2ab assembly algorithms for Clotho<br />
<br />
===Nade Sritanyaratana===<br />
<br />
Nade Sritanyaratana, in semi-chronological order, is attributed to the following work: <br />
<br />
* The Help connection/frame<br />
* Highlighting<br />
* Features connection<br />
* Co-coordinated Sequence View connection/frame alongside Matt and Doug<br />
* Sequence View Tools (Find/Replace)<br />
* Feature Library Collection connection/frame<br />
* File Choosers<br />
* Search Helper<br />
* .txt file Helper<br />
* Photographing at test sessions<br />
* Debugging post-test sessions<br />
* Parts Manager<br />
* Maintaining the iGEM 2008 Computational Tools Team wiki: layout and painted graphics<br />
* Maintaining the Cal College of Engineering iGEM blog alongside Marlee Tichenor and Madvhi Venkatesh of the wet team<br />
* Clotho iGEM logo and woman<br />
* Clotho iGEM t-shirt<br />
<br />
===Dr. Douglas Densmore===<br />
Doug provided the initial Clotho software infrastructure and served as the main team lead. He helped to keep the team on track and supervised the construction and functionality of Clotho. He is the chief architect of Clotho and in charge of its maintenance, deployment, and promotion.<br />
<br />
===Dr. Chris Anderson===<br />
Prof. Anderson provided specifications for what tools and techniques should be incorporated in Clotho. In addition he also helped to define the general assembly problem for standardized biological parts as well as provide the context in which the tool would be used. He also provided many interesting discussion regarding the Clotho data model and provided the database by which we did the majority of our testing.<br />
<br />
===Other attribution===<br />
<br />
Many thanks to Collin Martin for the professional photography shots, and the Comp team shot.<br />
<br />
Shout out goes to Cici Chen of the UC Berkeley wetlab for helping design the Clotho title (alpha). Also Brian Zimmer, Bing Xia, and Roger Tu also have contributed to the development of Clotho. Josh Kittleson was instrumental in the development of the mySQL/PoBoL connection and tools. Will Deloache helped with the development of the assembly algorithms for 2ab assembly that is in the tool.<br />
<br />
== Where we're from ==<br />
<br />
===Dr. Douglas Densmore===<br />
Doug is from Richland, Michigan which is a small town outside of Kalamazoo. He attended the University of Michigan from 1996-2001 and has been in Berkeley, California since 2001. His family is from the Detroit area. They still live in Michigan.<br />
<br />
===Nade Sritanyaratana===<br />
Nade is a 4th year bioengineering undergraduate at UC Berkeley. He was born in the SF Bay Area, in Hayward, CA, and has lived around the Bay Area his entire life. Both of his parents are Thai. He attended James Logan High School in Union City, CA, where his primary activities included speech and debate, Leo Club, and the swim team. His family still resides in Union City.<br />
<br />
===Matthew L.E. Johnson===<br />
Matt is a SoCal native - born and raised in Bakersfield, CA right up until the move to Berkeley in 2005. He loves his hometown, but realizes that it is an 'acquired taste', especially during the average summer's daily triple-digit heat. Despite the vast differences between his new home and his old (with inverse climates - politically and meteorologically), he has adapted well and has been greatly enjoying his stay in the Bay Area.</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/TeamTeam:UC Berkeley Tools/Team2008-10-29T10:13:03Z<p>Logosandpathos: /* Matthew LE Johnson */</p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<!--- <center>[http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development#Downloads_and_Information <b>The Alpha release is here.</b>]</center> ---><br />
<br />
{{Template:ClothoMenu}}<br />
__NOTOC__<br />
<br />
<br />
== Who we are ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
'''Faculty Advisors:'''<br />
<br />
*''' Advisor 1''': Doug Densmore, Post-Doc at UC Berkeley<br />
*'''Advisor 2''': Chris Anderson, Assistant Professor at UC Berkeley<br />
<br />
<br />
'''Undergrads:'''<br />
<br />
*'''Student''': Anne Van Devender, 4th year Computer Science undergraduate, Washington and Lee University<br />
*'''Student''': Matthew Johnson, 4th year Bioengineering undergraduate, UC Berkeley<br />
*'''Student''': Nade Sritanyaratana, 4th year Bioengineering undergraduate, UC Berkeley<br />
<br />
|<br />
<gallery perrow="4"><br />
Image:Doug_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Dr._Douglas_Densmore|Doug Densmore]]<br />
Image:Anne_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Anne_Van_Devender|Anne Van Devender]]<br />
Image:MattInStanley.png|[[Team:UC_Berkeley_Tools/Team#Matthew_Johnson|Matthew L.E. Johnson]]<br />
Image:Nade_atStanley.png|[[Team:UC_Berkeley_Tools/Team#Nade_Sritanyaratana|Nade Sritanyaratana]]<br />
</gallery><br />
|}<br />
<br />
==Team Biographies==<br />
[[Image:CalCompTeam.png|The 2008 iGEM Cal Comp Team]]<br />
<br />
===Anne Van Devender - Student Member===<br />
<br />
[[Image:Anne_Professional.jpg|250 px|thumb|left|Anne Van Devender]]<br />
<br />
Anne Van Devender is a 4th year undergraduate at Washington and Lee University (Lexington, VA). She is a Computer Science major with a minor in Women's Studies. After graduation she hopes to attend graduate school for either a master's degree or PhD in Human Computer Interaction. <br />
<br />
Her main endeavor outside of academics is the Washington and Lee Women's Soccer team where she is captain and a three-year letter winner. In 2007, she was named to the NSCAA All-America team. When she is not on the field or in the classroom, she enjoys working with kids in the Lexington community including involvement in a literacy campaign and teaching middle school girls the basics of computer science.<br />
<br />
This summer she is participating in the Summer Undergraduate Program in Engineering Research at Berkeley (SUPERB) and working with the iGEM 2008 UC Berkeley Computational Team. She is using Java to write an "Algorithm Manager" for the Clotho tool. While she has used Java extensively in her coursework at W&L, the synthetic biology aspect of the project is completely new to her. The last time she took biology was in 9th grade! She hopes this project will not only improve her research skills in computer science, but will also enlighten her to the emerging field of synthetic biology.<br />
<br />
===Nade Sritanyaratana - Student Member===<br />
[[Image:Nade_Professional.jpg|thumb|Nade Sritanyaratana]]<br />
<!---[[Image:NadeHeadShot.png|thumb|Nade Sritanyaratana]]---><br />
<br />
Nade Sritanyaratana is a 3rd year undergraduate at the University of California, Berkeley. He is majoring in Bioengineering with a concentration in imaging, and hopes to apply for a PhD graduate program in the upcoming year. Beyond imaging, his academic interests include Biomechanics; signals and systems; circuit analysis; systems biology; and linear optimization.<br />
<br />
His prior research experience consists of working with [http://bioeng.berkeley.edu/cv.php?facultyid=3022 bioengineering professor Steven Conolly] in the Summer and Fall of 2007. During that summer, he designed a coil helmet with an induced [http://en.wikipedia.org/wiki/Maxwell_coil Maxwell magnetic field]. This magnetic coil could be worn on the head and activated to generate small magnetic waves, soothing the wearer. Nicknamed the “Happy Helmet”, it was designed to non-invasively treat the bipolar-depressed via magnetic stimulation. Once fully developed, the helmet was to cost a hundred-fold less than an [http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging fMRI], the current primary treatment to bipolar depression.<br />
<br />
This summer Nade is working full-time with the iGEM 2008 Cal Computational Team. This is his first time using Java. Prior to Java, his programming experience included an introductory C++ class in the 9th grade and MATLAB experience for three years in Berkeley. He has had prior experience with computational modelling in general; last year Nade worked with LabVIEW for his introductory class to signals and systems. Last fall he graphically modeled a growing brain tumor with ADINA for his Biomechanics class, and later based his main Biofluid mechanics project on the dynamics of a atherosclerotic artery using a computational model generated by COMSOL.<br />
<br />
===Matthew Johnson - Student Member===<br />
[[Image:Matt_Professional2.jpg|300 px]]<br />
<br />
===Dr. Douglas Densmore - Instructor===<br />
[[Image:DougAtTheDOP2.png|thumb|Douglas Densmore]]<br />
Douglas Densmore received his Bachelors of Science in Engineering (Computer Engineering) from the University of Michigan in April 2001. He received his Masters of Science in Electrical Engineering in May 2004 from the University of California at Berkeley. His masters thesis was entitled, "Platform Based Reconfigurable Architecture Exploration via Boolean Constraints" and demonstrated how Boolean Satisfiability could be used to produce configurations for programmable hardware. He received his PhD in Electrical Engineering from UC Berkeley as well in May 2007. His PhD thesis, entitled "A Design Flow for the Development, Characterization, and Refinement of System Level Architecture Services", explored how electronic system level design methodologies can be abstract and modular while at the same time remaining accurate and efficient.<br />
<br />
He is currently a UC Chancellor's post doctoral researcher at UC Berkeley studying under [http://www.eecs.berkeley.edu/~alberto Prof. Alberto Sangiovanni-Vincentelli]. His research area is in the development of System Level Design methodologies for electronic systems. Specifically, architecture modeling and refinement verification. His background and interests are in Computer Architecture, Logic Synthesis, Digital Logic Design and Synthetic Biology. <br />
<br />
His industry experience includes four+ summers with Intel Corporation where he was involved in pre-silicon design efforts regarding chipset development, post-silicon validation of the Pentium 4 microprocessor, and chipset software validation. He has also worked as a researcher at Cypress Semiconductor and Xilinx Research Labs. He is currently a member of the [http://www.gigascale.org Gigascale Systems Research Center (GSRC)] and the [http://chess.eecs.berkeley.edu Center for Hybrid and Embedded Software Systems (CHESS)] at UC Berkeley. He has published work regarding a method of successive refinement verification of electronic systems, taxonomies of EDA design tools, and algebraic frameworks for the manipulation of functional design descriptions to expose computational parallelism. In addition he has a US patent pending regarding data characterization of programmable devices (such as field programmable gate arrays).<br />
<br />
<br clear="all"><br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
== What we did ==<br />
This section briefly describes the contributions of each team member.<br />
<br />
===Matthew LE Johnson===<br />
<br />
Give or take:<br />
<br />
* The About connection/frame<br />
* DNA analysis tools and algorithms (including Translation, G-C content, Melting Temperature, Reverse complementing, etc.)<br />
* The Enzyme Library and associated functionality<br />
* Sequence View connection (with Nade and Doug)<br />
* Compatibility with GenBank, FASTA, and ApE file formats<br />
* Support for degenerate IUPAC codes<br />
* Restriction site search and highlighting<br />
* Forward and reverse Open Reading Frame search and highlighting<br />
* Clotho Preferences for various connections<br />
* All of the Clotho Transfer Handlers<br />
* Intelligent Drag and Drop (DnD) between connections<br />
* Work on the Comp. Team Wiki<br />
* Feedback and advice on the graphic designs (seriously: thanks you, Nade!)<br />
* ... and many, MANY hours of debugging!<br />
<br />
===Anne Van Devender===<br />
Anne Van Devender was responsible for:<br />
<br />
* The development and design of the algorithm manager<br />
* Clotho algorithm interface and initial implementation<br />
* The conversion of BioBrick assembly algorithms from Perl to Java<br />
* Aid in the development of 2ab assembly algorithms for Clotho<br />
<br />
===Nade Sritanyaratana===<br />
<br />
Nade Sritanyaratana, in semi-chronological order, is attributed to the following work: <br />
<br />
* The Help connection/frame<br />
* Highlighting<br />
* Features connection<br />
* Co-coordinated Sequence View connection/frame alongside Matt and Doug<br />
* Sequence View Tools (Find/Replace)<br />
* Feature Library Collection connection/frame<br />
* File Choosers<br />
* Search Helper<br />
* .txt file Helper<br />
* Photographing at test sessions<br />
* Debugging post-test sessions<br />
* Parts Manager<br />
* Maintaining the iGEM 2008 Computational Tools Team wiki: layout and painted graphics<br />
* Maintaining the Cal College of Engineering iGEM blog alongside Marlee Tichenor and Madvhi Venkatesh of the wet team<br />
* Clotho iGEM logo and woman<br />
* Clotho iGEM t-shirt<br />
<br />
===Dr. Douglas Densmore===<br />
Doug provided the initial Clotho software infrastructure and served as the main team lead. He helped to keep the team on track and supervised the construction and functionality of Clotho. He is the chief architect of Clotho and in charge of its maintenance, deployment, and promotion.<br />
<br />
===Dr. Chris Anderson===<br />
Prof. Anderson provided specifications for what tools and techniques should be incorporated in Clotho. In addition he also helped to define the general assembly problem for standardized biological parts as well as provide the context in which the tool would be used. He also provided many interesting discussion regarding the Clotho data model and provided the database by which we did the majority of our testing.<br />
<br />
===Other attribution===<br />
<br />
Many thanks to Collin Martin for the professional photography shots, and the Comp team shot.<br />
<br />
Shout out goes to Cici Chen of the UC Berkeley wetlab for helping design the Clotho title (alpha). Also Brian Zimmer, Bing Xia, and Roger Tu also have contributed to the development of Clotho. Josh Kittleson was instrumental in the development of the mySQL/PoBoL connection and tools. Will Deloache helped with the development of the assembly algorithms for 2ab assembly that is in the tool.<br />
<br />
== Where we're from ==<br />
<br />
===Dr. Douglas Densmore===<br />
Doug is from Richland, Michigan which is a small town outside of Kalamazoo. He attended the University of Michigan from 1996-2001 and has been in Berkeley, California since 2001. His family is from the Detroit area. They still live in Michigan.<br />
<br />
===Nade Sritanyaratana===<br />
<br />
Nade is a 4th year bioengineering undergraduate at UC Berkeley. He was born in the SF Bay Area, in Hayward, CA, and has lived around the Bay Area his entire life. Both of his parents are Thai. He attended James Logan High School in Union City, CA, where his primary activities included speech and debate, Leo Club, and the swim team. His family still resides in Union City.</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/TeamTeam:UC Berkeley Tools/Team2008-10-29T10:08:48Z<p>Logosandpathos: /* Matthew LE Johnson */</p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<!--- <center>[http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development#Downloads_and_Information <b>The Alpha release is here.</b>]</center> ---><br />
<br />
{{Template:ClothoMenu}}<br />
__NOTOC__<br />
<br />
<br />
== Who we are ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
'''Faculty Advisors:'''<br />
<br />
*''' Advisor 1''': Doug Densmore, Post-Doc at UC Berkeley<br />
*'''Advisor 2''': Chris Anderson, Assistant Professor at UC Berkeley<br />
<br />
<br />
'''Undergrads:'''<br />
<br />
*'''Student''': Anne Van Devender, 4th year Computer Science undergraduate, Washington and Lee University<br />
*'''Student''': Matthew Johnson, 4th year Bioengineering undergraduate, UC Berkeley<br />
*'''Student''': Nade Sritanyaratana, 4th year Bioengineering undergraduate, UC Berkeley<br />
<br />
|<br />
<gallery perrow="4"><br />
Image:Doug_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Dr._Douglas_Densmore|Doug Densmore]]<br />
Image:Anne_Professional.jpg|[[Team:UC_Berkeley_Tools/Team#Anne_Van_Devender|Anne Van Devender]]<br />
Image:MattInStanley.png|[[Team:UC_Berkeley_Tools/Team#Matthew_Johnson|Matthew L.E. Johnson]]<br />
Image:Nade_atStanley.png|[[Team:UC_Berkeley_Tools/Team#Nade_Sritanyaratana|Nade Sritanyaratana]]<br />
</gallery><br />
|}<br />
<br />
==Team Biographies==<br />
[[Image:CalCompTeam.png|The 2008 iGEM Cal Comp Team]]<br />
<br />
===Anne Van Devender - Student Member===<br />
<br />
[[Image:Anne_Professional.jpg|250 px|thumb|left|Anne Van Devender]]<br />
<br />
Anne Van Devender is a 4th year undergraduate at Washington and Lee University (Lexington, VA). She is a Computer Science major with a minor in Women's Studies. After graduation she hopes to attend graduate school for either a master's degree or PhD in Human Computer Interaction. <br />
<br />
Her main endeavor outside of academics is the Washington and Lee Women's Soccer team where she is captain and a three-year letter winner. In 2007, she was named to the NSCAA All-America team. When she is not on the field or in the classroom, she enjoys working with kids in the Lexington community including involvement in a literacy campaign and teaching middle school girls the basics of computer science.<br />
<br />
This summer she is participating in the Summer Undergraduate Program in Engineering Research at Berkeley (SUPERB) and working with the iGEM 2008 UC Berkeley Computational Team. She is using Java to write an "Algorithm Manager" for the Clotho tool. While she has used Java extensively in her coursework at W&L, the synthetic biology aspect of the project is completely new to her. The last time she took biology was in 9th grade! She hopes this project will not only improve her research skills in computer science, but will also enlighten her to the emerging field of synthetic biology.<br />
<br />
===Nade Sritanyaratana - Student Member===<br />
[[Image:Nade_Professional.jpg|thumb|Nade Sritanyaratana]]<br />
<!---[[Image:NadeHeadShot.png|thumb|Nade Sritanyaratana]]---><br />
<br />
Nade Sritanyaratana is a 3rd year undergraduate at the University of California, Berkeley. He is majoring in Bioengineering with a concentration in imaging, and hopes to apply for a PhD graduate program in the upcoming year. Beyond imaging, his academic interests include Biomechanics; signals and systems; circuit analysis; systems biology; and linear optimization.<br />
<br />
His prior research experience consists of working with [http://bioeng.berkeley.edu/cv.php?facultyid=3022 bioengineering professor Steven Conolly] in the Summer and Fall of 2007. During that summer, he designed a coil helmet with an induced [http://en.wikipedia.org/wiki/Maxwell_coil Maxwell magnetic field]. This magnetic coil could be worn on the head and activated to generate small magnetic waves, soothing the wearer. Nicknamed the “Happy Helmet”, it was designed to non-invasively treat the bipolar-depressed via magnetic stimulation. Once fully developed, the helmet was to cost a hundred-fold less than an [http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging fMRI], the current primary treatment to bipolar depression.<br />
<br />
This summer Nade is working full-time with the iGEM 2008 Cal Computational Team. This is his first time using Java. Prior to Java, his programming experience included an introductory C++ class in the 9th grade and MATLAB experience for three years in Berkeley. He has had prior experience with computational modelling in general; last year Nade worked with LabVIEW for his introductory class to signals and systems. Last fall he graphically modeled a growing brain tumor with ADINA for his Biomechanics class, and later based his main Biofluid mechanics project on the dynamics of a atherosclerotic artery using a computational model generated by COMSOL.<br />
<br />
===Matthew Johnson - Student Member===<br />
[[Image:Matt_Professional2.jpg|300 px]]<br />
<br />
===Dr. Douglas Densmore - Instructor===<br />
[[Image:DougAtTheDOP2.png|thumb|Douglas Densmore]]<br />
Douglas Densmore received his Bachelors of Science in Engineering (Computer Engineering) from the University of Michigan in April 2001. He received his Masters of Science in Electrical Engineering in May 2004 from the University of California at Berkeley. His masters thesis was entitled, "Platform Based Reconfigurable Architecture Exploration via Boolean Constraints" and demonstrated how Boolean Satisfiability could be used to produce configurations for programmable hardware. He received his PhD in Electrical Engineering from UC Berkeley as well in May 2007. His PhD thesis, entitled "A Design Flow for the Development, Characterization, and Refinement of System Level Architecture Services", explored how electronic system level design methodologies can be abstract and modular while at the same time remaining accurate and efficient.<br />
<br />
He is currently a UC Chancellor's post doctoral researcher at UC Berkeley studying under [http://www.eecs.berkeley.edu/~alberto Prof. Alberto Sangiovanni-Vincentelli]. His research area is in the development of System Level Design methodologies for electronic systems. Specifically, architecture modeling and refinement verification. His background and interests are in Computer Architecture, Logic Synthesis, Digital Logic Design and Synthetic Biology. <br />
<br />
His industry experience includes four+ summers with Intel Corporation where he was involved in pre-silicon design efforts regarding chipset development, post-silicon validation of the Pentium 4 microprocessor, and chipset software validation. He has also worked as a researcher at Cypress Semiconductor and Xilinx Research Labs. He is currently a member of the [http://www.gigascale.org Gigascale Systems Research Center (GSRC)] and the [http://chess.eecs.berkeley.edu Center for Hybrid and Embedded Software Systems (CHESS)] at UC Berkeley. He has published work regarding a method of successive refinement verification of electronic systems, taxonomies of EDA design tools, and algebraic frameworks for the manipulation of functional design descriptions to expose computational parallelism. In addition he has a US patent pending regarding data characterization of programmable devices (such as field programmable gate arrays).<br />
<br />
<br clear="all"><br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
== What we did ==<br />
This section briefly describes the contributions of each team member.<br />
<br />
===Matthew LE Johnson===<br />
<br />
Give or take:<br />
<br />
* The About connection/frame<br />
* DNA analysis tools and algorithms<br />
(Translation, Finding Open Reading Frames, G-C content, Melting Temperature, Reverse complementing, etc.)<br />
* The Enzyme Library and associated functionality<br />
* Sequence View connection (with Nade and Doug)<br />
* Compatibility with GenBank, FASTA, and ApE file formats<br />
* Restriction site search and highlighting<br />
* Forward and reverse Open Reading Frame search and highlighting<br />
* Clotho Preferences for various connections<br />
* All of the Clotho Transfer Handlers<br />
* Intelligent Drag and Drop (DnD) between connections<br />
* ... and quite a lot of debugging!<br />
<br />
===Anne Van Devender===<br />
Anne Van Devender was responsible for:<br />
<br />
* The development and design of the algorithm manager<br />
* Clotho algorithm interface and initial implementation<br />
* The conversion of BioBrick assembly algorithms from Perl to Java<br />
* Aid in the development of 2ab assembly algorithms for Clotho<br />
<br />
===Nade Sritanyaratana===<br />
<br />
Nade Sritanyaratana, in semi-chronological order, is attributed to the following work: <br />
<br />
* The Help connection/frame<br />
* Highlighting<br />
* Features connection<br />
* Co-coordinated Sequence View connection/frame alongside Matt and Doug<br />
* Sequence View Tools (Find/Replace)<br />
* Feature Library Collection connection/frame<br />
* File Choosers<br />
* Search Helper<br />
* .txt file Helper<br />
* Photographing at test sessions<br />
* Debugging post-test sessions<br />
* Parts Manager<br />
* Maintaining the iGEM 2008 Computational Tools Team wiki: layout and painted graphics<br />
* Maintaining the Cal College of Engineering iGEM blog alongside Marlee Tichenor and Madvhi Venkatesh of the wet team<br />
* Clotho iGEM logo and woman<br />
* Clotho iGEM t-shirt<br />
<br />
===Dr. Douglas Densmore===<br />
Doug provided the initial Clotho software infrastructure and served as the main team lead. He helped to keep the team on track and supervised the construction and functionality of Clotho. He is the chief architect of Clotho and in charge of its maintenance, deployment, and promotion.<br />
<br />
===Dr. Chris Anderson===<br />
Prof. Anderson provided specifications for what tools and techniques should be incorporated in Clotho. In addition he also helped to define the general assembly problem for standardized biological parts as well as provide the context in which the tool would be used. He also provided many interesting discussion regarding the Clotho data model and provided the database by which we did the majority of our testing.<br />
<br />
===Other attribution===<br />
<br />
Many thanks to Collin Martin for the professional photography shots, and the Comp team shot.<br />
<br />
Shout out goes to Cici Chen of the UC Berkeley wetlab for helping design the Clotho title (alpha). Also Brian Zimmer, Bing Xia, and Roger Tu also have contributed to the development of Clotho. Josh Kittleson was instrumental in the development of the mySQL/PoBoL connection and tools. Will Deloache helped with the development of the assembly algorithms for 2ab assembly that is in the tool.<br />
<br />
== Where we're from ==<br />
<br />
===Dr. Douglas Densmore===<br />
Doug is from Richland, Michigan which is a small town outside of Kalamazoo. He attended the University of Michigan from 1996-2001 and has been in Berkeley, California since 2001. His family is from the Detroit area. They still live in Michigan.<br />
<br />
===Nade Sritanyaratana===<br />
<br />
Nade is a 4th year bioengineering undergraduate at UC Berkeley. He was born in the SF Bay Area, in Hayward, CA, and has lived around the Bay Area his entire life. Both of his parents are Thai. He attended James Logan High School in Union City, CA, where his primary activities included speech and debate, Leo Club, and the swim team. His family still resides in Union City.</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/DevelopmentTeam:UC Berkeley Tools/Development2008-10-29T09:52:54Z<p>Logosandpathos: /* Helping Out In The Lab: Assembly Algorithms */</p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<br />
{{Template:ClothoMenu}}<br />
__NOTOC__<br />
<br />
==Clotho Beta: Future Development==<br />
<br />
The next release of Clotho after iGEM is planned for a late Spring 2009 release. This will be the official ''Beta'' release (the other releases will have been Alpha and iGEM). The main focus of the release will be to fully implement all the features currently in Clotho as well as fix bugs that are found. Clotho testing and deployment will begin with Anderson Lab at UCB and expand to Voigt Lab at UCSF. It is our goal to have Clotho be a main software component in each lab. In addition to general robustness, Clotho Beta should also incorporate a few new features as will be described in the following sections:<br />
<br />
===New Features===<br />
[[Image:Biomek3000.jpg|thumb|right|150 px|<span style="color: white"><small>''A Biomek 3000, similar to the one we'll be working with in the lab''</small></span>]]<br />
* New design views to supplement the Sequence View and allow easier designing of basic and composite BioBrick parts. This will likely include a "schematic view" for assembling parts, similar to the one in [http://web.mit.edu/jagoler/www/biojade/overview.html BioJade]. We would also like to explore a "parts view" where the individual parts have associated icons. A design now no longer becomes writing nucleotide sequences but rather dragging around icons which have sequence data associated with them.<br />
<br />
* Ability to interface with devices, including robots that can be used for automated production of parts designed in Clotho. (In the future, this will contain a link to Anderson Lab's Biomek robot.) This aspect will be tied to the assembly algorithms already in Clotho. These algorithms will be expanded upon to deal with other assembly issues such as tracking methylated "righty" and "lefty" parts.<br />
<br />
*Increased support for other interchange format standards such as [http://www.sequenceontology.org/gff3.shtml GFF3]. This will allow us to begin to interface with such tools as BioStudio.<br />
<br />
<br />
===Improved Features:===<br />
* More database support: we plan to expand the number and variety of databases that Clotho can connect to, including [http://brickit.wiki.sourceforge.net/ BrickIt!]) and the JBEI registry. One of the databases at the top of our priority list is iGEM's own [http://partsregistry.org/Main_Page Registry of Standard Biological Parts].<br />
<br />
* Improved Plug-in environment that allows users to add even more expanded functionality to Clotho. This will include more extension points where plug-ins can be integrated and a set of more fully featured interfaces for existing extensions.<br />
<br />
<br />
==Helping Out In The Lab: Assembly Algorithms==<br />
* One of the initial algorithms we added to Clotho was an "optimal assembly" algorithm that can take in a list of goal composite parts and return a list with the minimum number of steps required to build those parts - a particularly useful feature if the goal parts utilize many of the same basic parts as subcomponents. The [https://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley UC Berkeley wet team] used these tools on a collection of 496 goal composite parts. Had no overlap been found (e.g. using naive methods), 5961 total parts would have to have been made. The program generated an assembly tree that required only 1283 total parts be built, reducing the number having to be assembled by '''4678 parts.''' This assembly took just over 4 minutes to complete using the algorithm - if this same process were attempted by hand, it would take multiple people over 3 days to complete! This saved the wet team perhaps weeks of work as well as helping them save on the cost of the reagents required for the thousands of reactions that would have been necessary.<br />
<br />
==PoBoL: BioBrick Data Sharing Made Easy==<br />
[[Image:PoBoLDiagram.png|thumb|left|200 px|<span style="color: white"><small>''A diagram representing the basic structural concepts behind PoBoL''</small></span>]]<br />
PoBoL stands for "Provisional BioBrick Language", and is the name given to a technical standard for BioBrick data in synthetic biology databases. Put simply, our implementation of PoBoL is encapsulated in the Clotho Data structure. We indicate that this is our version since it adds objects which are not part of PoBoL. These include collections of BioBricks and composite information (right and left children and order). One of the big issues current facing synthetic biology is coming up with a parts standardization. We hope that Clotho can help to raise and solve issues in this area by being a deployment vehicle for ideas. Since we have created Clotho in a highly modular way, it can be the test bed for a variety of part standardization ideas. <br />
<br />
For more information on the PoBoL standard, check out [http://www.pobol.org/ www.pobol.org]<br />
<br />
<br clear="all"><br />
<br />
==Increasing Collaboration Through Better Access To Database==<br />
A common theme with all scientific exploration is: "How will the technology you are developing have a positive impact on society". I think most people agree that Synthetic Biology has tremendous potential to be a force for good in the world. New drug delivery systems, smarter/cleaner energy sources, and improved food production capabilities are only the beginning. However for any of this to happen, there are going to have to be tools in place to help this to occur.<br />
<br />
Clotho can aid in the human practice area of synthetic biology by providing new methods to encourage sharing and innovation. Sharing is a natural aspect of Clotho with its strong connection to databases of parts. Innovation is encouraged by helping others to develop new designs more quickly and efficiently.</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/DevelopmentTeam:UC Berkeley Tools/Development2008-10-29T09:52:44Z<p>Logosandpathos: /* Helping Out In The Lab: Assembly Algorithms */</p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<br />
{{Template:ClothoMenu}}<br />
__NOTOC__<br />
<br />
==Clotho Beta: Future Development==<br />
<br />
The next release of Clotho after iGEM is planned for a late Spring 2009 release. This will be the official ''Beta'' release (the other releases will have been Alpha and iGEM). The main focus of the release will be to fully implement all the features currently in Clotho as well as fix bugs that are found. Clotho testing and deployment will begin with Anderson Lab at UCB and expand to Voigt Lab at UCSF. It is our goal to have Clotho be a main software component in each lab. In addition to general robustness, Clotho Beta should also incorporate a few new features as will be described in the following sections:<br />
<br />
===New Features===<br />
[[Image:Biomek3000.jpg|thumb|right|150 px|<span style="color: white"><small>''A Biomek 3000, similar to the one we'll be working with in the lab''</small></span>]]<br />
* New design views to supplement the Sequence View and allow easier designing of basic and composite BioBrick parts. This will likely include a "schematic view" for assembling parts, similar to the one in [http://web.mit.edu/jagoler/www/biojade/overview.html BioJade]. We would also like to explore a "parts view" where the individual parts have associated icons. A design now no longer becomes writing nucleotide sequences but rather dragging around icons which have sequence data associated with them.<br />
<br />
* Ability to interface with devices, including robots that can be used for automated production of parts designed in Clotho. (In the future, this will contain a link to Anderson Lab's Biomek robot.) This aspect will be tied to the assembly algorithms already in Clotho. These algorithms will be expanded upon to deal with other assembly issues such as tracking methylated "righty" and "lefty" parts.<br />
<br />
*Increased support for other interchange format standards such as [http://www.sequenceontology.org/gff3.shtml GFF3]. This will allow us to begin to interface with such tools as BioStudio.<br />
<br />
<br />
===Improved Features:===<br />
* More database support: we plan to expand the number and variety of databases that Clotho can connect to, including [http://brickit.wiki.sourceforge.net/ BrickIt!]) and the JBEI registry. One of the databases at the top of our priority list is iGEM's own [http://partsregistry.org/Main_Page Registry of Standard Biological Parts].<br />
<br />
* Improved Plug-in environment that allows users to add even more expanded functionality to Clotho. This will include more extension points where plug-ins can be integrated and a set of more fully featured interfaces for existing extensions.<br />
<br />
<br />
==Helping Out In The Lab: Assembly Algorithms==<br />
* One of the initial algorithms we added to Clotho was an "optimal assembly" algorithm that can take in a list of goal composite parts and return a list with the minimum number of steps required to build those parts - a particularly useful feature if the goal parts utilize many of the same basic parts as subcomponents. The [https://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley UC Berkeley wet] team used these tools on a collection of 496 goal composite parts. Had no overlap been found (e.g. using naive methods), 5961 total parts would have to have been made. The program generated an assembly tree that required only 1283 total parts be built, reducing the number having to be assembled by '''4678 parts.''' This assembly took just over 4 minutes to complete using the algorithm - if this same process were attempted by hand, it would take multiple people over 3 days to complete! This saved the wet team perhaps weeks of work as well as helping them save on the cost of the reagents required for the thousands of reactions that would have been necessary.<br />
<br />
==PoBoL: BioBrick Data Sharing Made Easy==<br />
[[Image:PoBoLDiagram.png|thumb|left|200 px|<span style="color: white"><small>''A diagram representing the basic structural concepts behind PoBoL''</small></span>]]<br />
PoBoL stands for "Provisional BioBrick Language", and is the name given to a technical standard for BioBrick data in synthetic biology databases. Put simply, our implementation of PoBoL is encapsulated in the Clotho Data structure. We indicate that this is our version since it adds objects which are not part of PoBoL. These include collections of BioBricks and composite information (right and left children and order). One of the big issues current facing synthetic biology is coming up with a parts standardization. We hope that Clotho can help to raise and solve issues in this area by being a deployment vehicle for ideas. Since we have created Clotho in a highly modular way, it can be the test bed for a variety of part standardization ideas. <br />
<br />
For more information on the PoBoL standard, check out [http://www.pobol.org/ www.pobol.org]<br />
<br />
<br clear="all"><br />
<br />
==Increasing Collaboration Through Better Access To Database==<br />
A common theme with all scientific exploration is: "How will the technology you are developing have a positive impact on society". I think most people agree that Synthetic Biology has tremendous potential to be a force for good in the world. New drug delivery systems, smarter/cleaner energy sources, and improved food production capabilities are only the beginning. However for any of this to happen, there are going to have to be tools in place to help this to occur.<br />
<br />
Clotho can aid in the human practice area of synthetic biology by providing new methods to encourage sharing and innovation. Sharing is a natural aspect of Clotho with its strong connection to databases of parts. Innovation is encouraged by helping others to develop new designs more quickly and efficiently.</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/DevelopmentTeam:UC Berkeley Tools/Development2008-10-29T09:51:10Z<p>Logosandpathos: /* Helping Out In The Lab: Assembly Algorithms */</p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<br />
{{Template:ClothoMenu}}<br />
__NOTOC__<br />
<br />
==Clotho Beta: Future Development==<br />
<br />
The next release of Clotho after iGEM is planned for a late Spring 2009 release. This will be the official ''Beta'' release (the other releases will have been Alpha and iGEM). The main focus of the release will be to fully implement all the features currently in Clotho as well as fix bugs that are found. Clotho testing and deployment will begin with Anderson Lab at UCB and expand to Voigt Lab at UCSF. It is our goal to have Clotho be a main software component in each lab. In addition to general robustness, Clotho Beta should also incorporate a few new features as will be described in the following sections:<br />
<br />
===New Features===<br />
[[Image:Biomek3000.jpg|thumb|right|150 px|<span style="color: white"><small>''A Biomek 3000, similar to the one we'll be working with in the lab''</small></span>]]<br />
* New design views to supplement the Sequence View and allow easier designing of basic and composite BioBrick parts. This will likely include a "schematic view" for assembling parts, similar to the one in [http://web.mit.edu/jagoler/www/biojade/overview.html BioJade]. We would also like to explore a "parts view" where the individual parts have associated icons. A design now no longer becomes writing nucleotide sequences but rather dragging around icons which have sequence data associated with them.<br />
<br />
* Ability to interface with devices, including robots that can be used for automated production of parts designed in Clotho. (In the future, this will contain a link to Anderson Lab's Biomek robot.) This aspect will be tied to the assembly algorithms already in Clotho. These algorithms will be expanded upon to deal with other assembly issues such as tracking methylated "righty" and "lefty" parts.<br />
<br />
*Increased support for other interchange format standards such as [http://www.sequenceontology.org/gff3.shtml GFF3]. This will allow us to begin to interface with such tools as BioStudio.<br />
<br />
<br />
===Improved Features:===<br />
* More database support: we plan to expand the number and variety of databases that Clotho can connect to, including [http://brickit.wiki.sourceforge.net/ BrickIt!]) and the JBEI registry. One of the databases at the top of our priority list is iGEM's own [http://partsregistry.org/Main_Page Registry of Standard Biological Parts].<br />
<br />
* Improved Plug-in environment that allows users to add even more expanded functionality to Clotho. This will include more extension points where plug-ins can be integrated and a set of more fully featured interfaces for existing extensions.<br />
<br />
<br />
==Helping Out In The Lab: Assembly Algorithms==<br />
* One of the initial algorithms we added to Clotho was an "optimal assembly" algorithm that can take in a list of goal composite parts and return a list with the minimum number of steps required to build those parts - a particularly useful feature if the goal parts utilize many of the same basic parts as subcomponents. The UC Berkeley wet team used these tools on a collection of 496 goal composite parts. Had no overlap been found (e.g. using naive methods), 5961 total parts would have to have been made. The program generated an assembly tree that required only 1283 total parts be built, reducing the number having to be assembled by '''4678 parts.''' This assembly took just over 4 minutes to complete using the algorithm - if this same process were attempted by hand, it would take multiple people over 3 days to complete! This saved the wet team perhaps weeks of work as well as helping them save on the cost of the reagents required for the thousands of reactions that would have been necessary.<br />
<br />
==PoBoL: BioBrick Data Sharing Made Easy==<br />
[[Image:PoBoLDiagram.png|thumb|left|200 px|<span style="color: white"><small>''A diagram representing the basic structural concepts behind PoBoL''</small></span>]]<br />
PoBoL stands for "Provisional BioBrick Language", and is the name given to a technical standard for BioBrick data in synthetic biology databases. Put simply, our implementation of PoBoL is encapsulated in the Clotho Data structure. We indicate that this is our version since it adds objects which are not part of PoBoL. These include collections of BioBricks and composite information (right and left children and order). One of the big issues current facing synthetic biology is coming up with a parts standardization. We hope that Clotho can help to raise and solve issues in this area by being a deployment vehicle for ideas. Since we have created Clotho in a highly modular way, it can be the test bed for a variety of part standardization ideas. <br />
<br />
For more information on the PoBoL standard, check out [http://www.pobol.org/ www.pobol.org]<br />
<br />
<br clear="all"><br />
<br />
==Increasing Collaboration Through Better Access To Database==<br />
A common theme with all scientific exploration is: "How will the technology you are developing have a positive impact on society". I think most people agree that Synthetic Biology has tremendous potential to be a force for good in the world. New drug delivery systems, smarter/cleaner energy sources, and improved food production capabilities are only the beginning. However for any of this to happen, there are going to have to be tools in place to help this to occur.<br />
<br />
Clotho can aid in the human practice area of synthetic biology by providing new methods to encourage sharing and innovation. Sharing is a natural aspect of Clotho with its strong connection to databases of parts. Innovation is encouraged by helping others to develop new designs more quickly and efficiently.</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Matthew%27s_NotebookTeam:UC Berkeley Tools/Notebook/Matthew's Notebook2008-10-29T09:33:31Z<p>Logosandpathos: /* October 28th, 2008 */</p>
<hr />
<div>{{Template:ClothoMenu}}<br />
<br />
[[Image:MattInStanley.png|center|frame|Matthew L.E. Johnson]]<br />
<br />
<br />
==Personal Info==<br />
<b>Name:</b> Matthew L.E. Johnson<br />
<br />
<b>Position:</b> Team member, UC_Berkeley_Tools<br />
<br />
<b>Supervisor: </b>Doug Densmore<br />
<br />
<b>Lab coworkers: </b>Nade Sritanyaratana, Anne Vandevender<br />
<br />
== Log ==<br />
=== June 3rd, 2008 ===<br />
Just received access to the wiki! Today was the first day of coding, and for me it was mostly re-familiarizing myself with Java and Swing components. We're making good progress, and if we can keep this up this amount of effort, I think we'll have something really neat to share.<br />
<br />
<br />
=== June 9th, 2008 ===<br />
Working on implementing various features already offered in ApE, including finding the melting point of a short strand of duplex DNA.<br />
<br />
<br />
=== June 16th, 2008 ===<br />
Even more functionality being added! Nearly finished with the enzyme library, need to finish figuring out the highlighting algorithms, but otherwise it's coming along nicely. I'll be working on integrating a lot of the basic DNA-related functions (reverse complementing, finding ORFs, calculating GC content and melting temp) later today.<br />
<br />
[[Image:ClothoEnzymeLib.jpg|center|frame|Example of the Clotho Enzyme Library interface. (In case you were wondering, that is the team wiki in the background!)]]<br />
<br />
=== June 28th, 2008 ===<br />
Nearly finished with the Enzyme Library - saving, loading, and searching all work. Mostly been debugging and trying to get everything currently implemented to work correctly, so that we can release a beta copy for the wet lab to play with. After this, I'd like to get started on the automatic primer and construction file generators.<br />
<br />
[[Image:EnzLibFile.jpg|center|frame|The format of the enzyme library file is modeled after ApE]]<br />
<br />
=== July 10th, 2008 ===<br />
We're going Alpha next week! We've got the basic features up and running, so it's mostly just ironing out the kinks for now, getting it all squared away. After this, 90% of our work should be on the novel features we're trying to implement, the new views and algorithms that will make our tool uniquely useful. And that will mean more updating here as I have more interesting things to talk about.<br />
<br />
=== July 31st, 2008 ===<br />
Public release of Clotho Alpha! It took a lot of work, but now we can get started on some of the more interesting features we plan on implementing, some of the alternate views and schematics to assist in designing parts and systems.<br />
<br />
=== October 17th, 2008 ===<br />
Between knee surgery and school starting up, this notebook has been looking neglected - time to spend some more time working on the wiki! Just finished writing the tutorial and taking screen shots, [https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial should be up] by the end of today!<br />
<br />
=== October 28th, 2008 ===<br />
The final night of coding before iGEM! Spent some time polishing the wiki, finishing some of the 'intelligent' Drag and Drop (DnD) support that I've been working on for weeks now, and cleaning up some of the bugs that have cropped up recently. So far, so good - we should have our code in excellent shape in time to be turned in.<br />
<br />
[[Image:ClothoDND.PNG|left|thumb|700px|Drag and Drop in Clotho, from the Parts Manager to the Sequence View]]<br />
<br />
<HTML><br />
<body><div align="right"><br />
<script language="JavaScript" src="http://www.tracemyip.org/tools/show-user-ip-info-box/ip_info_box_url.php?stlVar2=1208&rgtype=4684NR-IPIB&pidnVar2=324356580"></script><a href="http://www.tracemyip.org/" target="_blank"><img src="http://www.tracemyip.org/tools/images/trace_updater.gif" alt="Web Page Visitor Counter" border="0"></a></div><br />
</HTML></div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Matthew%27s_NotebookTeam:UC Berkeley Tools/Notebook/Matthew's Notebook2008-10-29T09:31:32Z<p>Logosandpathos: </p>
<hr />
<div>{{Template:ClothoMenu}}<br />
<br />
[[Image:MattInStanley.png|center|frame|Matthew L.E. Johnson]]<br />
<br />
<br />
==Personal Info==<br />
<b>Name:</b> Matthew L.E. Johnson<br />
<br />
<b>Position:</b> Team member, UC_Berkeley_Tools<br />
<br />
<b>Supervisor: </b>Doug Densmore<br />
<br />
<b>Lab coworkers: </b>Nade Sritanyaratana, Anne Vandevender<br />
<br />
== Log ==<br />
=== June 3rd, 2008 ===<br />
Just received access to the wiki! Today was the first day of coding, and for me it was mostly re-familiarizing myself with Java and Swing components. We're making good progress, and if we can keep this up this amount of effort, I think we'll have something really neat to share.<br />
<br />
<br />
=== June 9th, 2008 ===<br />
Working on implementing various features already offered in ApE, including finding the melting point of a short strand of duplex DNA.<br />
<br />
<br />
=== June 16th, 2008 ===<br />
Even more functionality being added! Nearly finished with the enzyme library, need to finish figuring out the highlighting algorithms, but otherwise it's coming along nicely. I'll be working on integrating a lot of the basic DNA-related functions (reverse complementing, finding ORFs, calculating GC content and melting temp) later today.<br />
<br />
[[Image:ClothoEnzymeLib.jpg|center|frame|Example of the Clotho Enzyme Library interface. (In case you were wondering, that is the team wiki in the background!)]]<br />
<br />
=== June 28th, 2008 ===<br />
Nearly finished with the Enzyme Library - saving, loading, and searching all work. Mostly been debugging and trying to get everything currently implemented to work correctly, so that we can release a beta copy for the wet lab to play with. After this, I'd like to get started on the automatic primer and construction file generators.<br />
<br />
[[Image:EnzLibFile.jpg|center|frame|The format of the enzyme library file is modeled after ApE]]<br />
<br />
=== July 10th, 2008 ===<br />
We're going Alpha next week! We've got the basic features up and running, so it's mostly just ironing out the kinks for now, getting it all squared away. After this, 90% of our work should be on the novel features we're trying to implement, the new views and algorithms that will make our tool uniquely useful. And that will mean more updating here as I have more interesting things to talk about.<br />
<br />
=== July 31st, 2008 ===<br />
Public release of Clotho Alpha! It took a lot of work, but now we can get started on some of the more interesting features we plan on implementing, some of the alternate views and schematics to assist in designing parts and systems.<br />
<br />
=== October 17th, 2008 ===<br />
Between knee surgery and school starting up, this notebook has been looking neglected - time to spend some more time working on the wiki! Just finished writing the tutorial and taking screen shots, [https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial should be up] by the end of today!<br />
<br />
=== October 28th, 2008 ===<br />
The final night of coding before iGEM! Spent some time polishing the wiki, finishing some of the 'intelligent' Drag and Drop (DnD) support that I've been working on for weeks now, and cleaning up some of the bugs that have cropped up recently. So far, so good - we should have our code in excellent shape in time to be turned in.<br />
<br />
[[Image:ClothoDND.PNG|left|thumb|600px|Drag and Drop in Clotho, from the Parts Manager to the Sequence View]]<br />
<br />
<br />
<HTML><br />
<body><div align="right"><br />
<script language="JavaScript" src="http://www.tracemyip.org/tools/show-user-ip-info-box/ip_info_box_url.php?stlVar2=1208&rgtype=4684NR-IPIB&pidnVar2=324356580"></script><a href="http://www.tracemyip.org/" target="_blank"><img src="http://www.tracemyip.org/tools/images/trace_updater.gif" alt="Web Page Visitor Counter" border="0"></a></div><br />
</HTML></div>Logosandpathoshttp://2008.igem.org/File:ClothoDND.PNGFile:ClothoDND.PNG2008-10-29T09:24:56Z<p>Logosandpathos: </p>
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<div></div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/RelatedWorkTeam:UC Berkeley Tools/RelatedWork2008-10-29T05:19:33Z<p>Logosandpathos: </p>
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<br />
=='''Related Work'''==<br />
This section will examine several tools which attempt to provide a design environment for synthetic biology. These can be divided into both academic and industrial offerings. <br />
<br />
===Academic===<br />
====APE====<br />
[[Image:ape.gif|thumb|300px|APE]]<br />
[http://www.biology.utah.edu/jorgensen/wayned/ape/ APE] (A Plasmid Editor) [6] is an editor which shows DNA sequence and translation information in a single text based viewer. It performs basic highlighting tasks for restriction sites (or user defined regions). It also shows translation, Tm, %GC, and ORF of selected DNA in real-time. It also reads DNA Strider, FASTA, Genbank and EMBL files. It has no database connectivity or notion of a larger synthetic biology community.<br />
<br />
<br clear="all"><br />
<br />
====Athena====<br />
[[Image:Athena.jpg|thumb|300px|Athena]]<br />
Athena is a tool developed at the University of Washington by Deepak Chandran, Frank Bergmann, Herbert Sauro. Here is their description from [http://openwetware.org/wiki/Computational_Tools OpenWetWare's Computational Tool Site]<br />
<br />
Athena is a tool for building, simulating, and analyzing genetic circuits (as well as metabolic/signaling networks, such as SBML files). It provides a visual interface for building biological modules that can be saved and later connected together. The connection can be achieved using either the PoPS interface or by defining overlapping molecular species (similar to the concept of module in CellML and SBML). In addition to simulation, Athena supports a few other useful features: Database of Ecoli regulatory network from RegulonDB, Graphical view of part sequence, Automated derivation of transcription rate equations, Interface to all Systems Biology Workbench programs, Interface with R statistical language, and an easy plugin architecture.<br />
<br />
You can find out more about Athena [http://www.codeplex.com/athena here]. <br />
<br />
[http://www.washington.edu/staff/deepakc/downloads/InstallAthena.exe Download Athena]<br />
<br />
<br clear="all"><br />
<br />
====BioJADE====<br />
[[Image:biojade_schem.jpg|thumb|300px|BioJADE's Schematic Aspect]]<br />
One of the early contributions in this area is [http://web.mit.edu/jagoler/www/biojade/ BioJADE] [1]. BioJADE is a design and simulation tool written in JAVA. It supports interaction with a number of part repositories including MIT's standard biological parts repository (XML interface) as well as relational database systems such as Oracle 9. It allows both the importing of devices from repositories as well as the submission of newly created parts to these same repositories. In terms of manipulating the design, BioJADE provides four ''aspects''. These are ''Schematic, DNA, Functional, and Icon''. <!--- Three views were shown in Figures [http://biocad-server.eecs.berkeley.edu/wiki/index.php/Image:Biojade_func.jpg 1], [http://biocad-server.eecs.berkeley.edu/wiki/index.php/Image:Biojade_dna.jpg 2], and [http://biocad-server.eecs.berkeley.edu/wiki/index.php/Image:Biojade_schem.jpg 3].---> As shown, Schematic presents a traditional schematic editor view for the design of logic circuits. The DNA aspect illustrates the actual DNA nucleotide sequence of the design. Functional Network presents a closer view of the layout of the DNA. It is similar to the DNA aspect but allows the user to edit the sequence. <br />
The Icon aspect allows the designer to create icons for parts to be used in the schematic aspect. Input, output, and undefined terminals are specified either as a static number or as dynamic (added at runtime). <br />
Finally, BioJADE offers a simulation mode where the design can be simulated. It interacts with simulators like Stochastirator [3] or Tabasco [4].<br />
<br />
<br clear="all"><br />
<br />
====BioStudio====<br />
BioStudio is the work of researchers at Johns Hopkins University (Joel Bader, Jef Boeke, and Sarah Richardson). <br />
<br />
''This is taken from BioStudio press release material at [http://research.microsoft.com/ur/us/fundingopps/RFPs/Synthetic_Biology_Awards_2006.aspx Computational Challenges in Synthetic Biology 2006 Awards]''<br />
<br />
We propose BioStudio as a collaborative integrated design environment (IDE) providing editing and revision control for synthetic genomes. Windows SharePoint Services and SQL Server will provide back-end support. The server middle-layer will extend existing open-source visualization-only software (GBrowse) with editing functions, including a BioBricks palette, and will communicate with the back-end using .NET and FrontPage Remote Procedure Calls. Genome sequence and annotations will be stored in XML with an adapter to the Generic Feature Format (GFF) standard. Synthetic biology teams will connect with a web browser client. Development and testing will proceed in conjunction with an in-house project to engineer a synthetic yeast cell that encodes a combinatorial satisfiability experiment to identify a minimal genome. Our physical-level editor is complementary to logical-level design tools such as BioJADE. It provides a multiscale visualization metaphor that enables non-computer-scientist teams to collaborate on documents that are too large for "Track changes" and too critical or interdependent to be consigned to a Wiki. Software will be released under a BSD license.<br />
<br />
In addition to BioStudio there is an interactive web site called [http://www.genedesign.org Gene Design].<br />
<br />
<br clear="all"><br />
<br />
====GenoCAD====<br />
[[Image:genocad.png|thumb|300px|left|GenoCAD Screen Capture]]<br />
[http://synbio.vbi.vt.edu:25500/genocad/ GenoCAD] [5] <br />
is a web based tool which guides you through the process of<br />
creating new genetic constructs by combining DNA sequences known as<br />
genetic parts or biological parts. Users can create their own account<br />
on the web site to add their new genetic parts, customize the build-in<br />
parts libraries for their own needs, and save their designs for future<br />
reference. Upon completion of the design process, the design DNA<br />
sequence can be saved as a text file for synthesis by a gene synthesis<br />
company or simply for further analysis in sequence analysis<br />
applications. GenoCAD also provides a construct validation feature (using a context free grammar (CFG) analysis)<br />
that allows users to import the sequence of a design and check its<br />
validity. GenoCAD relies on a linguistic model of the DNA sequence.<br />
The site currently supports a single proof of concept grammar that has<br />
been described in a paper published in Bioinformatics. Ongoing<br />
development efforts aim at implementing support for multiple grammars<br />
in GenoCAD.<br />
<br />
Strengths of this tool are primarily its attempt to validate the sequence and categorize parts via ''production rules'' based on 26 syntactic categories (i.e. gene coding region, terminator, stop codon, promoter, ribosome binding site, etc).<br />
<br />
For more information see: [http://bioinformatics.oxfordjournals.org/cgi/reprint/btm446v2.pdf A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts]<br />
<br />
<br clear="all"><br />
<br />
===Industrial===<br />
====Gene Designer====<br />
[[Image:gene_designer.jpg|thumb|300px|left|Gene Designer]]<br />
[http://www.dna20.com/tools/genedesigner.php Gene Designer] [2] by DNA 2.0 is a stand alone graphical software package for manipulating biological designs. The software enables you to combine building blocks such as regulatory DNA elements, amino acid sequences, affinity tags and cloning features. Additionally you can optimize expression by codon optimizing proteins for any expression host. There are two design views for the user, Icon and Sequence. The icon view encapsulates the DNA sequence as a specific icon indicating what type of part it is. The sequence view is an annotated DNA sequence corresponding to the Icon view. Gene Designer supports a wide variety of computational manipulations to the design such as codon optimization and can identify various DNA regions. Designs can be imported/exported in FASTA format for use with other tools and flows. There is not currently support for external databases (but is forthcoming in version 2.0).<br />
<br />
Here is a list of features as given by DNA 2.0:<br />
* Manage genetic elements, constructs and libraries of constructs via drag and drop<br />
* Create/Edit/Split/Merge/Save genetic elements (AA and DNA sequences)<br />
* Back-translate open reading frames using a codon bias table<br />
* Add/Remove restriction sites or other motifs (locally or globally)<br />
* Design sequencing primers for a construct, view sequencing trace files aligned construct [**]<br />
* Perform /in silico/ plasmid cloning, show circular plasmid map [**]<br />
* Annotate and Measure (TM, GC%, etc.) construct regions [**]<br />
* Create, Download, Edit & Merge codon bias tables [**]<br />
* Support user specific operations via scripting environment [**]<br />
* Import and Export various file formats Fasta, GenBank, etc. [**]<br />
* E-commerce enabled<br />
<br />
<br />
<br clear="all"><br />
<br />
==References==<br />
<br />
#J. Goler. BioJADE: A Design and Simulation Tool for Synthetic Biological Systems. Master’s thesis, MIT, MIT Computer Science and Artificial Intelligence Laboratory, May 2004.<br />
#A. Villalobos, J. E. Ness, C. Gustafsson, J. Minshull, and S. Govindarajan. Gene designer: a synthetic biology tool for constructing artificial dna segments. BMC Bioinformatics, 7:285, June 2006.<br />
#D. T. Gillespie. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics, 22(4):403–434, December 1976.<br />
#S. Kosuri, J. Kelly, and D. Endy. Tabasco: A single molecule, base-pair resolved gene expression simulator. BMC Bioinformatics, 8:480, December 2007.<br />
#Y. Cai, B. Hartnett, C. Gustafsson, and J. Peccoud. A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics, 23(20):2760–2767, October 2007.<br />
#M. W. Davis. A Plasmid Editor. World Wide Web, http://www.biology.utah.edu/jorgensen/wayned/ape/, 2008.<br />
<br />
[**]Partially implemented at present, planned for version 2 release</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/DevelopmentTeam:UC Berkeley Tools/Development2008-10-28T19:57:53Z<p>Logosandpathos: </p>
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<div>[[Image:Clotho_Title_small.png|center]]<br />
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{{Template:ClothoMenu}}<br />
__NOTOC__<br />
<br />
==Clotho Beta: Future Development==<br />
<br />
The next release of Clotho after iGEM is planned for a late Spring 2009 release. This will be the official Beta release (the other releases will have been Alpha and iGEM). The main focus of the release will be to fully implement all the features currently in Clotho as well as fix bugs that are found. Clotho testing and deployment will begin with Anderson Lab at UCB and expand to Voigt Lab at UCSF. In addition to general robustness, Clotho Beta should also incorporate a few new features.<br />
<br />
===New Features===<br />
[[Image:Biomek3000.jpg|thumb|right|150 px|<span style="color: blue"><small>''A Biomek 3000, similar to the we'll be working with in the lab''</small></span>]]<br />
* New design views to supplement the Sequence View and allow easier designing of basic and composite BioBrick parts. This will likely include a 'schematic view' for assembling parts, similar to the one in [http://web.mit.edu/jagoler/www/biojade/overview.html BioJade].<br />
<br />
* Ability to interface with devices, including robots that can be used for automated production of parts designed in Clotho. (In the future, this will contain a link to Anderson Lab's Biomek robot.)<br />
<br />
*<br />
<br />
<br />
<br />
<br />
<br />
<br />
===Improved Features:===<br />
* More database support: we plan to expand the number and variety of databases that Clotho can connect to, including [http://brickit.wiki.sourceforge.net/ BrickIt!]) and the JBEI registry. One of the databases at the top of our priority list is iGEM's own [http://partsregistry.org/Main_Page Registry of Standard Biological Parts].<br />
<br />
* Improved Plug-in environment that allows users to add even more expanded functionality to Clotho. This will include more extension points where plug-ins can be integrated and a set of more fully featured interfaces for existing extensions.<br />
<br />
<br />
==Helping Out In The Lab: Assembly Algorithms==<br />
* One of the initial algorithms we added to Clotho was an "optimal assembly" algorithm that can take in a list of goal composite parts and return a list with the minimum number of steps required to build those parts - a particularly useful feature if the goal parts utilize many of the same basic parts as subcomponents.<br />
** EXPAND HERE **<br />
<br />
==PoBoL: BioBrick Data Sharing Made Easy==<br />
[[Image:PoBoLDiagram.png|thumb|left|200 px|<span style="color: blue"><small>''A diagram representing the basic structural concepts behind PoBoL''</small></span>]]<br />
PoBoL stands for "Provisional BioBrick Language", and is the name given to a technical standard for BioBrick data in synthetic biology databases. Put simply, our implementation of PoBoL<br />
<br />
<br />
For more information on the PoBoL standard, check out [http://www.pobol.org/ www.pobol.org]<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
==Increasing Collaboration Through Better Access To Database==<br />
Through a combination of PoBoL</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/DevelopmentTeam:UC Berkeley Tools/Development2008-10-28T19:29:22Z<p>Logosandpathos: </p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<br />
{{Template:ClothoMenu}}<br />
__NOTOC__<br />
<br />
==Clotho Beta: Future Development==<br />
<br />
The next release of Clotho after iGEM is planned for a late Spring 2009 release. This will be the official Beta release (the other releases will have been Alpha and iGEM). The main focus of the release will be to fully implement all the features currently in Clotho as well as fix bugs that are found. Clotho testing and deployment will begin with Anderson Lab at UCB and expand to Voigt Lab at UCSF. In addition to general robustness, Clotho Beta should also incorporate a few new features.<br />
<br />
===New Features===<br />
[[Image:Biomek3000.jpg|thumb|right|150 px|<span style="color: blue"><small>''A Biomek 3000, similar to the we'll be working with in the lab''</small></span>']]<br />
* New design views to supplement the Sequence View and allow easier designing of basic and composite BioBrick parts. This will likely include a 'schematic view' for assembling parts, similar to the one in [http://web.mit.edu/jagoler/www/biojade/overview.html BioJade].<br />
<br />
* Ability to interface with devices, including robots that can be used for automated production of parts designed in Clotho. (In the future, this will contain a link to Anderson Lab's Biomek robot.)<br />
<br />
*<br />
<br />
<br />
<br />
<br />
<br />
<br />
===Improved Features:===<br />
* More database support (systems like [http://brickit.wiki.sourceforge.net/ BrickIt!]). We plan to test this one a wide variety of databases including JBEI's registry.<br />
<br />
* Improved Plug-in environment that allows users to add even more expanded functionality to Clotho. This will take the form of more plug in extension points and more fully featured interfaces for the existing ones.<br />
<br />
<br />
==Helping Out In The Lab: Assembly Algorithms==<br />
* Using the assembly algorithms, helped <br />
<br />
==PoBoL: BioBrick Data Sharing Made Easy==<br />
PoBoL stands for "Provisional BioBrick Language", and is the name given to a technical standard for BioBrick data in synthetic biology databases. Put simply, our implementation of PoBoL<br />
<br />
[[Image:PoBoLDiagram.png]]<br />
<br />
For more information on the PoBoL standard, check out [http://www.pobol.org/ www.pobol.org]<br />
<br />
==Increasing Collaboration Through Better Access To Database==<br />
Through a combination of PoBoL</div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/DevelopmentTeam:UC Berkeley Tools/Development2008-10-24T08:56:49Z<p>Logosandpathos: </p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<br />
{{Template:ClothoMenu}}<br />
<br />
<br />
==Clotho Beta: Future Development==<br />
===New Features===<br />
* New design views to supplement the Sequence View and allow easier designing of basic and composite BioBrick parts<br />
* Ability to interface with devices, including robots that can be used for automated production of parts designed in Clotho.<br />
[[Image:Biomek3000.jpg|200 px|A Biomek 3000 Pippeting Robot]]<br />
<br />
===Improved Features:===<br />
* More database support (systems like [http://brickit.wiki.sourceforge.net/ BrickIt!])<br />
* Improved Plug-in environment that allows users to add even more expanded functionality to Clotho<br />
<br />
<br />
==Helping Out In The Lab: Assembly Algorithms==<br />
* Using the assembly algorithms, helped <br />
<br />
==PoBoL: BioBrick Data Sharing Made Easy==<br />
PoBoL stands for "Provisional BioBrick Language", and is the name given to a technical standard for BioBrick data in synthetic biology databases. Put simply, our implementation of PoBoL<br />
<br />
[[Image:PoBoLDiagram.png]]<br />
<br />
For more information on the PoBoL standard, check out [http://www.pobol.org/ www.pobol.org]<br />
<br />
==Increasing Collaboration Through Better Access To Database==<br />
Through a combination of PoBoL</div>Logosandpathoshttp://2008.igem.org/File:PoBoLDiagram.pngFile:PoBoLDiagram.png2008-10-24T05:02:15Z<p>Logosandpathos: </p>
<hr />
<div></div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/DevelopmentTeam:UC Berkeley Tools/Development2008-10-24T04:48:44Z<p>Logosandpathos: </p>
<hr />
<div>[[Image:Clotho_Title_small.png|center]]<br />
<br />
{{Template:ClothoMenu}}<br />
<br />
<br />
==Clotho Beta: Future Development==<br />
===New Features===<br />
* New design views to supplement the Sequence View and allow easier designing of basic and composite BioBrick parts.<br />
* Ability to interface with devices, including robots that can be used for automated production of parts designed in Clotho.<br />
[[Image:Biomek3000.jpg|200 px|A Biomek 3000 Pippeting Robot]]<br />
<br />
===Improved Features:===<br />
* More Database support (systems like [http://brickit.wiki.sourceforge.net/ BrickIt!])<br />
*<br />
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==Helping Out In The Lab: Assembly Algorithms==<br />
* Using the assembly algorithms, helped <br />
<br />
==PoBoL: BioBrick Data Sharing Made Easy==<br />
PoBoL stands for "Provisional BioBrick Language", and is the name given to a technical standard for BioBrick data in synthetic biology databases. Put simply, our implementation of PoBoL<br />
<br />
For more information on the PoBoL standard, check out [http://www.pobol.org/]<br />
<br />
==Increasing Collaboration Through Better Access To Database==<br />
Through a combination of PoBoL</div>Logosandpathoshttp://2008.igem.org/File:Biomek3000.jpgFile:Biomek3000.jpg2008-10-24T03:54:43Z<p>Logosandpathos: </p>
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<a title="Clotho: Development and Impacts" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Development">Clotho: Development and Impacts</a><br />
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<a title="The Team" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Team">Who Are We?</a><br />
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<a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook"><br />
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<a title="Doug's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Doug's_Notebook">Doug's Notebook</a><br />
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<a title="Anne's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Anne's_Notebook">Anne's Notebook</a><br />
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<a title="Matt's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Matthew's_Notebook">Matt's Notebook</a><br />
</li><br />
<li><br />
<a title="Nade's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Nade's_Notebook">Nade's Notebook</a><br />
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<a title="Download Now!" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Downloads" class="menu">Get Clotho Now!</a><br />
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<h3 class="headerbar">Clotho Tutorial</h3><br />
<ul><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial">Introduction/Main Toolbar</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/Preferences">Preferences</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/SequenceView">Sequence View I</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/FeatureHighlighting">Feature Highlighting</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/RestrictionSiteHighlighting">Restriction Site Highlighting</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/SequenceView2">Sequence View II</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/Database">Connecting to a Database</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/PoBoL">PoBoL</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/PartsAndPlatesManager">Parts Manager/Plate Manager</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/AlgorithmManager">Algorithm Manager</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/OtherInfo">Other Information</a></li><br />
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<h3 class="headerbar">Clotho Tutorial</h3><br />
<ul><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial">Introduction/Main Toolbar</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/Preferences">Preferences</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/SequenceView">Sequence View I</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/FeatureHighlighting">Feature Highlighting</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/RestrictionSiteHighlighting">Restriction Site Highlighting</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/SequenceView2">Sequence View II</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/Database">Connecting to a Database</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/PoBoL">PoBoL</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/PartsAndPlatesManager">Parts Manager/Plate Manager</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/AlgorithmManager">Algorithm Manager</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/OtherInfo">Other Information</a></li><br />
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<h3 class="headerbar">Clotho Tutorial</h3><br />
<ul><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial">Introduction/Main Toolbar</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/Preferences">Preferences</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/SequenceView">Sequence View I</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/FeatureHighlighting">Feature Highlighting</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/RestrictionSiteHighlighting">Restriction Site Highlighting</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/SequenceView2">Sequence View II</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/Database">Connecting to a Database</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/PoBoL">PoBoL</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/PartsAndPlatesManager">Parts Manager/Plate Manager</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/AlgorithmManager">Algorithm Manager</a></li><br />
<li><a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/OtherInfo">Other Information</a></li><br />
</ul><br />
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<p>'''<<< Previous''' | [[Team:UC_Berkeley_Tools/Project/Tutorial/Preferences|'''Next >>>''']]</p><br />
<p><strong>1) The Main Toolbar</strong><br /><br />
This is the center of Clotho: the main toolbar. From here, you can open up any of the Clotho connections. The connections are separated into four categories: I/O, Tools, View, and Interfaces. &quot;I/O&quot; contains the connections that link Clotho to outside resources and databases. &quot;Tools&quot; contains the connections that provide functionality to Clotho. &quot;Views&quot; contains ways of viewing and manipulating information, including sequence data. &quot;Interfaces&quot; contains the connections that provide the user a way of interfacing with data, such as libraries of parts and feature annotations. From here, you can also access the Start, Help, and Options menus. For now, let's open up the options menu and select &quot;Preferences&quot;</p><br />
[[Image:Tut1.PNG|center]] <p>&nbsp;</p><br />
</div><br />
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'''<<< Previous''' | [[Team:UC_Berkeley_Tools/Project/Tutorial/Preferences|'''Next >>>''']]</div>Logosandpathoshttp://2008.igem.org/Template:ClothoMenuTemplate:ClothoMenu2008-10-24T02:33:02Z<p>Logosandpathos: </p>
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<a title="Clotho Tutorial" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project">Technical Description</a><br />
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<a title="For Judges" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Judging">For Judges</a><br />
</li><br />
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</ul><br />
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<li><br />
<a class="menu">The Team</a><br />
<ul><br />
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</li><br />
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<li><br />
<a href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook"><br />
<span class="drop"><br />
<span>Notebooks</span><br />
>><br />
</span><br />
</a><br />
<ul><br />
<li><br />
<a title="Doug's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Doug's_Notebook">Doug's Notebook</a><br />
</li><br />
<li><br />
<a title="Anne's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Anne's_Notebook">Anne's Notebook</a><br />
</li><br />
<li><br />
<a title="Matt's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Matthew's_Notebook">Matt's Notebook</a><br />
</li><br />
<li><br />
<a title="Nade's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Nade's_Notebook">Nade's Notebook</a><br />
</li><br />
</ul><br />
<br />
</ul><br />
</li><br />
</ul><br />
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<li><br />
<a class="menu">Resources</a><br />
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</li><br />
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</li><br />
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<a title="External Links" href="https://2008.igem.org/Team:UC_Berkeley_Tools/ExternalLinks">External Links</a><br />
</li><br />
<br />
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</li><br />
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<a title="Technical Information" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Tutorial">Clotho Tutorial</a><br />
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<a title="Clotho Tutorial" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project">Technical Description</a><br />
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<a title="For Judges" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Judging">For Judges</a><br />
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<span>Notebooks</span><br />
>><br />
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<a title="Doug's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Doug's_Notebook">Doug's Notebook</a><br />
</li><br />
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<a title="Anne's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Anne's_Notebook">Anne's Notebook</a><br />
</li><br />
<li><br />
<a title="Matt's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Matthew's_Notebook">Matt's Notebook</a><br />
</li><br />
<li><br />
<a title="Nade's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Nade's_Notebook">Nade's Notebook</a><br />
</li><br />
</ul><br />
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</li><br />
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<ul><br />
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<a title="Technical Information" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Tutorial">Clotho Tutorial</a><br />
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<a title="Clotho Tutorial" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Project">Technical Description</a><br />
</li><br />
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<a class="menu">Resources</a><br />
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<a title="The Team" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Team">The Team</a><br />
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<a title="Related Work" href="https://2008.igem.org/Team:UC_Berkeley_Tools/RelatedWork">Related Work</a><br />
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<a title="For Judges" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Judging">For Judges</a><br />
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<a href="."><br />
<span class="drop"><br />
<span>Notebooks</span><br />
>><br />
</span><br />
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<ul><br />
<li><br />
<a title="Doug's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Doug's_Notebook">Doug's Notebook</a><br />
</li><br />
<li><br />
<a title="Anne's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Anne's_Notebook">Anne's Notebook</a><br />
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<a title="Matt's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Matthew's_Notebook">Matt's Notebook</a><br />
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<a title="Nade's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Nade's_Notebook">Nade's Notebook</a><br />
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</html></div>Logosandpathoshttp://2008.igem.org/Template:ClothoMenuTemplate:ClothoMenu2008-10-24T02:18:03Z<p>Logosandpathos: </p>
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<span>Notebooks</span><br />
>><br />
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<ul><br />
<li><br />
<a title="Doug's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Doug's_Notebook">Doug's Notebook</a><br />
</li><br />
<li><br />
<a title="Anne's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Anne's_Notebook">Anne's Notebook</a><br />
</li><br />
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<a title="Matt's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Matthew's_Notebook">Matt's Notebook</a><br />
</li><br />
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<a title="Nade's Notebook" href="https://2008.igem.org/Team:UC_Berkeley_Tools/Notebook/Nade's_Notebook">Nade's Notebook</a><br />
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</html></div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/OtherInfoTeam:UC Berkeley Tools/Project/Tutorial/OtherInfo2008-10-24T01:49:47Z<p>Logosandpathos: </p>
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<p><br><br>[[Team:UC_Berkeley_Tools/Project/Tutorial/AlgorithmManager|'''<<< Previous''']] | '''Next >>>'''</p><br />
<p><strong>11) Other Information</strong></p><br />
<p>From here, feel free to explore Clotho! More detailed information on the different connections can be found in the Help menu.</p><br />
<p>&nbsp;</p> [[Image:Tut11.PNG|center]] <p>&nbsp;</p><br />
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<p>[[Team:UC_Berkeley_Tools/Project/Tutorial/AlgorithmManager|'''<<< Previous''']] | '''Next >>>'''</p></div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/AlgorithmManagerTeam:UC Berkeley Tools/Project/Tutorial/AlgorithmManager2008-10-24T01:48:13Z<p>Logosandpathos: </p>
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<p><strong>10) Algorithm Manager</strong></p><br />
<p>From the Main Toolbar select &quot;Algorithm Manager&quot; from the Tools drop down menu. The Algorithm Manager is a straightforward but robust tool - you take some input, select an algorithm, and it gives you an output. Each algorithm has its own rules for its use, including the proper inputs and syntax. After selecting any algorithm from the 'Algorithms' drop down box, select &quot;Get Instructions for Algorithm&quot; to get information on how to get it up and running. After finding an appropriate input (whether entered manually, imported from a file, or exported from another connection) select the &quot;Run&quot; button, and the output should appear in the 'Output' box. From here you can view or save the information in a number of different formats, graphically or textually. The default Optimal Assembly and 2abAssembly algorithms provide methods for optimizing the number of steps required to create composite parts.</p><br />
[[Image:Tut10.PNG|center]] <p>&nbsp;</p><br />
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<p>[[Team:UC_Berkeley_Tools/Project/Tutorial/PartsAndPlatesManager|'''<<< Previous''']] | [[Team:UC_Berkeley_Tools/Project/Tutorial/OtherInfo|'''Next >>>''']]</p></div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/AlgorithmManagerTeam:UC Berkeley Tools/Project/Tutorial/AlgorithmManager2008-10-24T01:48:01Z<p>Logosandpathos: </p>
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<p><strong>10) Algorithm Manager</strong></p><br />
<p>From the Main Toolbar select &quot;Algorithm Manager&quot; from the Tools drop down menu. The Algorithm Manager is a straightforward but robust tool - you take some input, select an algorithm, and it gives you an output. Each algorithm has its own rules for its use, including the proper inputs and syntax. After selecting any algorithm from the 'Algorithms' drop down box, select &quot;Get Instructions for Algorithm&quot; to get information on how to get it up and running. After finding an appropriate input (whether entered manually, imported from a file, or exported from another connection) select the &quot;Run&quot; button, and the output should appear in the 'Output' box. From here you can view or save the information in a number of different formats, graphically or textually. The default Optimal Assembly and 2abAssembly algorithms provide methods for optimizing the number of steps required to create composite parts.</p><br />
[[Image:Tut10.PNG|center]] <p>&nbsp;</p><br />
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<p>[[Team:UC_Berkeley_Tools/Project/Tutorial/PartsAndPlatesManager|'''<<< Previous''']] | [[Team:UC_Berkeley_Tools/Project/Tutorial/OtherInfo|'''Next >>>''']]</p></div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/PartsAndPlatesManagerTeam:UC Berkeley Tools/Project/Tutorial/PartsAndPlatesManager2008-10-24T01:47:04Z<p>Logosandpathos: </p>
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<p><strong>9) Parts Manager and Plate Manager</strong></p><br />
<p>Two Clotho connections so far utilize the PoBoL-based mySQL connection: the Parts Manager and the Plate Manager. On the Main Toolbar select &quot;Parts Manager&quot; from the Interfaces drop down menu, bring up the Parts Manager window. The Parts Manager allows you to look at BioBrick parts in the database. It contains a lot of information on each part, including the part and vector nicknames, the parts status, who submitted it, its location in the lab, the amount left, and more. In the future, you will be able to add, delete, and edit parts in the database through this window, as well as looking up more detailed information on the part.</p><br />
[[Image:Tut9a.PNG|center]]<br />
<p>Close the Parts Manager, and on the Main Toolbar select &quot;Plate Manager&quot; from the Tools drop down menu, bringing up the Plate Manager window. The Plate Manager lets you keep track of the contents and locations of plates in the lab. From the drop down menu below the 'Zoom' buttons, select **PLATE NAME*, click the &quot;Select&quot; button, and select 'Yes' in the following pop-up box - this should load up a 96-well plate from the database. Information on the plate itself can be found in the 'Plate Information' box. Clicking on any of the occupied wells will fill out the 'Sample Information' box with information on the contents of the well. The data that gets displayed can be changed in the Plate Manager preferences window, by going to the Edit menu item, selecting &quot;Preferences&quot;, and changing the the labels. For now, let's close the Plate Manager window and go back to the Main Toolbar.</p><br />
[[Image:Tut9b.PNG|center]] <p>&nbsp;</p><br />
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<p>[[Team:UC_Berkeley_Tools/Project/Tutorial/PoBoL|'''<<< Previous''']] | [[Team:UC_Berkeley_Tools/Project/Tutorial/AlgorithmManager|'''Next >>>''']]</p></div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/PoBoLTeam:UC Berkeley Tools/Project/Tutorial/PoBoL2008-10-24T01:46:21Z<p>Logosandpathos: </p>
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<p><strong>8) PoBoL</strong></p><br />
<p>PoBoL stands for &quot;Provisional Biobrick Language&quot;, and represents a way to translate different databases into one common language. The binding file is a way of specifying which tables and entries from the database correspond to which PoBoL data types. Ideally, you would be able to download a binding file for any given database, saving you the trouble - for our tutorial database, such a file can be found **HERE** - just copy and paste the contents of the text file into the 'Binding Configuration' window. If no such file existed though, you would have to create it manually: first you would select a Table and then a Field from the 'Database Information' box, and then a corresponding Object and Field from the 'PoBoL fields' box, and click &quot;Bind&quot;. This would have to be done for all the tables and fields you wish to use from the database. Fortunately, you only have to create the mySQL connection and its corresponding PoBoL binding file once. Now click &quot;Save/Connect&quot;, and select 'Yes' when the message box appears. Now Clotho is connected! (Note: In future uses, you will only have to enter the user name and password and click &quot;Connect&quot;.)</p><br />
<p>More information on PoBoL can be found **HERE**.</p><br />
[[Image:Tut8.PNG|center]] <p>&nbsp;</p><br />
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<p>[[Team:UC_Berkeley_Tools/Project/Tutorial/Database|'''<<< Previous''']] | [[Team:UC_Berkeley_Tools/Project/Tutorial/PartsAndPlatesManager|'''Next >>>''']]</p></div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/DatabaseTeam:UC Berkeley Tools/Project/Tutorial/Database2008-10-24T01:44:57Z<p>Logosandpathos: </p>
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<p><strong>7) Connecting to a Database</strong></p><br />
[[Image:Tut7.PNG|right]]<br />
<p>Some of Clotho's most interesting features can only be utilized once we've connected to a database. Let's try setting up a mySQL connection: on the Main Toolbar select &quot;PoBoL based mySQL&quot; from the I/O drop down menu. This should bring up the mySQL/PoBoL Configuration window. The first two boxes are username and password, but don't put anything in them just yet. First, select the &quot;Create New Connection&quot; tab, and enter the following information:</p><br />
<p>Name:<br /><br />
Host:<br /><br />
Port:<br /><br />
Database:</p><br />
<p>After you're done, click &quot;Create&quot; and go to the &quot;Existing Connections&quot; tab. Select the connection you just made from the &quot;Connection Available&quot; drop down menu. In the appropriate boxes, put in the username **USERNAME** and password **PASSWORD**. Then click &quot;Set as Next, we'll setup the PoBoL binding file: click the &quot;View PoBoL Binding&quot; button, and it should bring up the PoBoL Binding window.</p><br />
<p>&nbsp;</p><br />
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<p>[[Team:UC_Berkeley_Tools/Project/Tutorial/SequenceView2|'''<<< Previous''']] | [[Team:UC_Berkeley_Tools/Project/Tutorial/PoBoL|'''Next >>>''']]</p></div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/SequenceView2Team:UC Berkeley Tools/Project/Tutorial/SequenceView22008-10-24T01:44:04Z<p>Logosandpathos: </p>
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<p><strong>6) Sequence View II</strong><br /><br />
Now let's play with some of the other basic tools in the Sequence View. First, let's find an open reading frame - place your cursor anywhere in the sequence, go to the &quot;ORFs&quot; menu and select &quot;Find Next ORF&quot;. Alternatively, you can use the shortcut and press [Ctrl + .]. This will place line a light green line underneath the next open reading frame found in the sequence after the cursor (if other alternate start codons are enabled in the preferences, their reading frames will be shown using yellow or red lines). Highlight this sequence with the mouse and select the &quot;Translate&quot; option from the &quot;Tools&quot; menu (or press [Ctrl + T]). The protein translation of this reading frame will be printed to the 'Output Data' window. Similiarly, if you select &quot;Reverse Complement&quot; [Ctrl + /], the reverse complement of the sequence will be printed. &quot;Find Reverse ORF&quot; and &quot;Reverse Translate&quot; operate in the same fashion, but they look at the reverse complement of the sequence. &quot;UPPER CASE&quot;, &quot;Switch Case&quot;, and &quot;lower case&quot; all operate on any portion of the sequence you care to highlight (case has no effect on sequence analysis and is treated as aesthetic). Highlighting a string of nucleotides also displays information like G-C content and melting temperature. Additionally, you can open up a tools menu under &quot;Tools&quot; [Ctrl + F] to peform find and replace operations on the sequence. Let's leave the Sequnce View for now - either select &quot;Exit Sequence View&quot; from the File menu or click the 'X' in the corner and select &quot;Yes close&quot; from the resulting pop-up box.</p><br />
[[Image:Tut6.PNG|center]] <p>&nbsp;</p><br />
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<p>[[Team:UC_Berkeley_Tools/Project/Tutorial/RestrictionSiteHighlighting|'''<<< Previous''']] | [[Team:UC_Berkeley_Tools/Project/Tutorial/Database|'''Next >>>''']]</p></div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/RestrictionSiteHighlightingTeam:UC Berkeley Tools/Project/Tutorial/RestrictionSiteHighlighting2008-10-24T01:42:49Z<p>Logosandpathos: </p>
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<p><strong>5) Restriction Site Highlighting</strong><br /><br />
The Enzyme Library contains a list of restriction enzymes that you can search for in the sequence. You can select each enzyme individually, search for them by name or sequence, or select a pre-assigned group of enzymes. Let's try selecting the standard four BioBrick enzymes [EcoRI, PstI, SpeI, and XbaI]: you can do this by selecting them manually or by going to &quot;Select by Group&quot; and picking the &quot;BBa Enzymes&quot; group. Select the &quot;Highlight Enzymes&quot; button, and open the Sequence View window, but don't close the Enzyme Library just yet. You should see new orange highlights in the sequence corresponding to the selected restriction, and just like features, running the mouse cursor over the highlights shows the corresponding restriction enzyme. [Clotho supports multiple highlighting, so you may see features and restriction sequences overlapping one another, and in that case both names will be shown].</p><br />
[[Image:Tut5a.PNG|center]] <p>&nbsp;</p><br />
[[Image:Tut5b.PNG|center]] <p>&nbsp;</p><br />
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<p>[[Team:UC_Berkeley_Tools/Project/Tutorial/FeatureHighlighting|'''<<< Previous''']] | [[Team:UC_Berkeley_Tools/Project/Tutorial/SequenceView2|'''Next >>>''']]</p></div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/RestrictionSiteHighlightingTeam:UC Berkeley Tools/Project/Tutorial/RestrictionSiteHighlighting2008-10-24T01:42:14Z<p>Logosandpathos: </p>
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<p><strong>5) Restriction Site Highlighting</strong><br /><br />
The Enzyme Library contains a list of restriction enzymes that you can search for in the sequence. You can select each enzyme individually, search for them by name or sequence, or select a pre-assigned group of enzymes. Let's try selecting the standard four BioBrick enzymes [EcoRI, PstI, SpeI, and XbaI]: you can do this by selecting them manually or by going to &quot;Select by Group&quot; and picking the &quot;BBa Enzymes&quot; group. Select the &quot;Highlight Enzymes&quot; button, and open the Sequence View window, but don't close the Enzyme Library just yet. You should see new orange highlights in the sequence corresponding to the selected restriction, and just like features, running the mouse cursor over the highlights shows the corresponding restriction enzyme. [Clotho supports multiple highlighting, so you may see features and restriction sequences overlapping one another, and in that case both names will be shown].</p><br />
[[Image:Tut5a.PNG|center]] <p>&nbsp;</p><br />
[[Image:Tut5b.PNG|center]] <p>&nbsp;</p></div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/FeatureHighlightingTeam:UC Berkeley Tools/Project/Tutorial/FeatureHighlighting2008-10-24T01:40:24Z<p>Logosandpathos: </p>
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<p><strong>4) Feature Highlighting</strong><br /><br />
The Features Library manages the local libraries of feature annotations for sequences. From here you can create, load, or remove libraries, examine features from within these libraries, and select which libraries you want to use for highlighting. (Additionally, you can drag features from a library into the Sequence View and place them anywhere in the sequence.) For now, let's select default library and hit the &quot;Highlight&quot; button. Close the Feature Library and go back to the Sequence View, and you'll see that several features have been highlighted in different colors. If you run the mouse cursor over any of the highlights, the name of the feature will pop-up on the info bar just above the sequence box. Knowing where our features of interest are helps, but let's find some restriction sites where we might want to cut our sequence. Go to the Highlighting menu, and select &quot;Open Enzyme Library&quot;.</p><br />
[[Image:Tut4a.PNG|center]] <p>&nbsp;</p><br />
[[Image:Tut4b.PNG|center]] <p>&nbsp;</p><br />
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<p>[[Team:UC_Berkeley_Tools/Project/Tutorial/SequenceView|'''<<< Previous''']] | [[Team:UC_Berkeley_Tools/Project/Tutorial/RestrictionSiteHighlighting|'''Next >>>''']]</p></div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/Project/Tutorial/SequenceViewTeam:UC Berkeley Tools/Project/Tutorial/SequenceView2008-10-24T01:39:18Z<p>Logosandpathos: </p>
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<p><strong>3) Sequence View I</strong><br /><br />
Now that we've got it everything looking spiffy, let's try out one of the main view of the tool - the Sequence View. On the main toolbar select &quot;Sequence View&quot; from the View drop down menu. This should bring up the Sequence View window. From here you have many options - you can load a sequence from a GenBank or FASTA file, drag in a sequence from another connection, copy and paste your chosen sequence, or enter it manually. Let's try opening a GenBank file ([http://openwetware.org/images/3/39/JCAseq_pSB1A2-Bca9128.str like this one], for example). Go to File, and select 'Load Sequence File' - this should bring up a window allowing you to choose what file you want to open. Go to the directory you saved the file to, select it, and click open (if the directory has many files in it, you can go to the 'Files of Type' drop down menu and filter it to only show GenBank or FASTA files). This will load the sequence into the current Sequence View window. From here, you can edit the sequence or perform a number of operations on it. But first, let's try adding some informative highlights to this plain text sequence. Go to the Highlighting menu, and select &quot;Open Feature Library Connection&quot;.</p><br />
[[Image:Tut3b.PNG|center]] <p>&nbsp;</p><br />
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<p>[[Team:UC_Berkeley_Tools/Project/Tutorial/Preferences|'''<<< Previous''']] | [[Team:UC_Berkeley_Tools/Project/Tutorial/FeatureHighlighting|'''Next >>>''']]</p></div>Logosandpathoshttp://2008.igem.org/Team:UC_Berkeley_Tools/Project/TutorialTeam:UC Berkeley Tools/Project/Tutorial2008-10-24T01:37:45Z<p>Logosandpathos: </p>
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<p align="center" class="style1">'''Welcome to Clotho!'''</p><br />
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<p><strong>1) The Main Toolbar</strong><br /><br />
This is the center of Clotho: the main toolbar. From here, you can open up any of the Clotho connections. The connections are separated into four categories: I/O, Tools, View, and Interfaces. &quot;I/O&quot; contains the connections that link Clotho to outside resources and databases. &quot;Tools&quot; contains the connections that provide functionality to Clotho. &quot;Views&quot; contains ways of viewing and manipulating information, including sequence data. &quot;Interfaces&quot; contains the connections that provide the user a way of interfacing with data, such as libraries of parts and feature annotations. From here, you can also access the Start, Help, and Options menus. For now, let's open up the options menu and select &quot;Preferences&quot;</p><br />
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