Team:UC Berkeley Tools

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<h1 class="firstHeading">BioCad</h1>
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<h3 id="siteSub">From PBD of Synthetic Biological Tools</h3>
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<p><big><b>Welcome to the "Platform-Based Design of Synthetic Biological Tools" Wiki</b></big>
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</p><p>This website provides information and tools for the design of synthetic biological systems using the notions of Platform-based design from the EDA community in electrical engineering and computer science. The work is based at UC Berkeley but includes participants from a number of universities and organizations.
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</p><p><br />
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</p>
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<table id="toc" class="toc" summary="Contents"><tr><td><div id="toctitle"><h2>Contents</h2></div>
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<ul>
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<li class="toclevel-1"><a href="#Overview"><span class="tocnumber">1</span> <span class="toctext">Overview</span></a></li>
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<li class="toclevel-1"><a href="#News"><span class="tocnumber">2</span> <span class="toctext">News</span></a>
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<ul>
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<li class="toclevel-2"><a href="#7.2F15.2F08_-__Clotho_Alpha_Release_Coming.21"><span class="tocnumber">2.1</span> <span class="toctext">7/15/08 -  Clotho Alpha Release Coming!</span></a></li>
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<li class="toclevel-2"><a href="#7.2F26.2F08_-_Clotho_Alpha_Release"><span class="tocnumber">2.2</span> <span class="toctext">7/26/08 - Clotho Alpha Release</span></a></li>
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<li class="toclevel-2"><a href="#7.2F27.2F08_-_Clotho_Alpha_Release_1.1"><span class="tocnumber">2.3</span> <span class="toctext">7/27/08 - Clotho Alpha Release 1.1</span></a></li>
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<li class="toclevel-2"><a href="#7.2F28.2F08_-_iGEM_Blog"><span class="tocnumber">2.4</span> <span class="toctext">7/28/08 - iGEM Blog</span></a></li>
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<li class="toclevel-2"><a href="#7.2F29.2F08_-_Clotho_Alpha_Source_Code_Available"><span class="tocnumber">2.5</span> <span class="toctext">7/29/08 - Clotho Alpha Source Code Available</span></a></li>
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</ul>
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</li>
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<li class="toclevel-1"><a href="#People"><span class="tocnumber">3</span> <span class="toctext">People</span></a></li>
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<li class="toclevel-1"><a href="#More_Information"><span class="tocnumber">4</span> <span class="toctext">More Information</span></a></li>
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</ul>
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<a name="Overview"></a><h2> <span class="mw-headline">Overview</span></h2>
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<p>Genomics has reached the stage at which the amount of DNA sequence information in existing databases is quite large. Moreover, synthetic biology now is using these databases to catalog sequences according to their functionality and therefore creating standard biological parts which can be used to create large systems. What is needed now are flexible tools which not only permit access and modification to that data but also allow one to perform meaningful manipulation and use of that information in an intelligent and efficient way. These tools need to be useful to biologists working in a laboratory environment while leveraging the experience of the larger CAD community.
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</p><p>A Platform-Based Design (PBD) approach looks at how genetic information can be viewed as having a particular functionality and what is now needed is to assemble platforms (collections of DNA elements) to perform this functionality. This work attempts to leverage the same methodology employed by PBD for embedded systems to the design of synthetic biological systems. This work places synthetic biology in a PBD framework, discusses required EDA concepts in biological terms, and describes a toolset (<a href="/wiki/index.php/Clotho_Tool" title="Clotho Tool">Clotho</a>) which will implement the ideas outlined here.
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<a name="News"></a><h2> <span class="mw-headline">News</span></h2>
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<a name="7.2F15.2F08_-__Clotho_Alpha_Release_Coming.21"></a><h3> <span class="mw-headline"><b>7/15/08</b> - <a href="/wiki/index.php/Clotho_Development" title="Clotho Development"> Clotho Alpha Release Coming!</a></span></h3>
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<p>Based on the work of the <a href="https://2008.igem.org/Team:UC_Berkeley_Tools" class="external text" title="https://2008.igem.org/Team:UC_Berkeley_Tools" rel="nofollow">Berkeley computational iGEM team</a>, the alpha version of Clotho is currently under development. It should be released by August 1st, 2008. Naturally this is a very preliminary release and is intended to get feedback, test deployment issues, and chase down bugs. It lacks functional and architectural views which are planned as well as a connection to <a href="http://www.pobol.org" class="external text" title="http://www.pobol.org" rel="nofollow">Pobol</a> based repositories. These features should be present in a Beta release in the fall of 2008. More information on this can be found <a href="/wiki/index.php/Clotho_Development" title="Clotho Development"> here</a>.
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</p>
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<a name="7.2F26.2F08_-_Clotho_Alpha_Release"></a><h3> <span class="mw-headline"><b>7/26/08</b> - Clotho Alpha Release</span></h3>
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<div class="thumb tright"><div class="thumbinner" style="width:182px;"><a href="/wiki/index.php/Image:Clotho_logo1.png" class="image" title="Clotho Alpha"><img alt="Clotho Alpha" src="/wiki/images/e/ea/Clotho_logo1.png" width="180" height="69" border="0" class="thumbimage" /></a>  <div class="thumbcaption"><div class="magnify" style="float:right"><a href="/wiki/index.php/Image:Clotho_logo1.png" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div>Clotho Alpha</div></div></div>
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<p>We are pleased to announce that the Clotho alpha release is available!! You can get it <a href="http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development#Alpha_Version" class="external text" title="http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development#Alpha_Version" rel="nofollow">here</a>. The executable jar file and java docs are available now and source code should be released within a week (if not sooner). Enjoy! Keep those bug reports coming in:)
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</p>
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<a name="7.2F27.2F08_-_Clotho_Alpha_Release_1.1"></a><h3> <span class="mw-headline"><b>7/27/08</b> - Clotho Alpha Release 1.1</span></h3>
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<p>A bug slipped into the alpha release which rendered parts navigation useless. It has been fixed and now is available for download. The .jar file and the README file in the .zip indicate that you are using 1.1. This was available as of 7:15pm PST on 7/27/08. Sorry for any inconvenience.
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</p>
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<a name="7.2F28.2F08_-_iGEM_Blog"></a><h3> <span class="mw-headline"><b>7/28/08</b> - iGEM Blog</span></h3>
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<p>Clotho is part of a Berkeley College of Engineering blog. Check out <a href="http://blogs.coe.berkeley.edu/igem/" class="external free" title="http://blogs.coe.berkeley.edu/igem/" rel="nofollow">http://blogs.coe.berkeley.edu/igem/</a>
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</p>
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<a name="7.2F29.2F08_-_Clotho_Alpha_Source_Code_Available"></a><h3> <span class="mw-headline"><b>7/29/08</b> - Clotho Alpha Source Code Available</span></h3>
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<p>The Clotho Alpha source code is now available <a href="/wiki/index.php/Clotho_Development" title="Clotho Development"> here</a>. In addition, the required libraries are also available. These are publicly available elsewhere but are included here for convenience and compatibility. A README file is in the works which will provide instructions for those unfamiliar with building java programs.
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</p>
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<a name="People"></a><h2> <span class="mw-headline">People</span></h2>
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<div class="floatright"><span><a href="/wiki/index.php/Image:Berkeleylogo.jpg" class="image" title="Berkeleylogo.jpg"><img alt="" src="/wiki/images/9/90/Berkeleylogo.jpg" width="180" height="136" border="0" /></a></span></div>
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<p><b>UC Berkeley EECS Leads</b>
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</p>
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<ul><li> <a href="http://ddensmore.net" class="external text" title="http://ddensmore.net" rel="nofollow">Dr. Douglas Densmore</a> 
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</li><li> <a href="http://www.eecs.berkeley.edu/~alberto" class="external text" title="http://www.eecs.berkeley.edu/~alberto" rel="nofollow">Prof. Alberto Sangiovanni-Vincentelli</a>
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</li></ul>
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<p><b>UC Berkeley EECS Design Team</b>
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</p>
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<ul><li> Anne Van Devender (visiting student)
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</li><li> Jonathan Whiteaker
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</li><li> Ben Sussman
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</li></ul>
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<p><br clear="all" />
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<div class="floatright"><span><a href="/wiki/index.php/Image:Synberc.jpg" class="image" title="Synberc.jpg"><img alt="" src="/wiki/images/2/27/Synberc.jpg" width="397" height="110" border="0" /></a></span></div>
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<p><b>UC Berkeley Synthetic Biology Lead</b>
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</p>
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<ul><li> <a href="https://andersonlab.qb3.berkeley.edu" class="external text" title="https://andersonlab.qb3.berkeley.edu" rel="nofollow">Prof. J.Christopher Anderson</a>
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</li></ul>
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<p><b>UC Berkeley BioEngineering Design Team</b>
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</p>
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<ul><li> Nade Sritanyaratana
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</li><li> Matthew Johnson
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</li></ul>
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<p><b>UC Berkeley Synthetic Biology Consultant</b>
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</p>
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<ul><li> Jonathan Goler
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</li></ul>
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<div class="floatright"><span><a href="/wiki/index.php/Image:Ucsflogo.jpg" class="image" title="Ucsflogo.jpg"><img alt="" src="/wiki/images/4/4e/Ucsflogo.jpg" width="120" height="61" border="0" /></a></span></div>
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<p><b>UCSF Team Lead</b>
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</p>
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<ul><li> <a href="http://www.voigtlab.ucsf.edu" class="external text" title="http://www.voigtlab.ucsf.edu" rel="nofollow">Prof. Christopher Voigt</a>
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</li></ul>
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<p><b>UCSF Consultants</b>
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</p>
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<ul><li> Dr. Howard Salis
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</li><li> Karsten Temme
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</li><li> Ethan Mirsky 
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<div class="floatright"><span><a href="/wiki/index.php/Image:Stanfordlogo.gif" class="image" title="Stanfordlogo.gif"><img alt="" src="/wiki/images/0/05/Stanfordlogo.gif" width="100" height="100" border="0" /></a></span></div>
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<p><b>Stanford Consultant</b>
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</p>
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<ul><li> Dr. Ryan Owen
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</li></ul>
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<a name="More_Information"></a><h2> <span class="mw-headline">More Information</span></h2>
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<p>For information about the project:
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</p>
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<ul><li> <a href="/wiki/index.php/Introduction" title="Introduction">Introduction</a> 
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</li><li> <a href="/wiki/index.php/Platform_Based_Design" title="Platform Based Design">Platform Based Design</a> 
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</li><li> <a href="/wiki/index.php/Design_Concepts" title="Design Concepts">Design Concepts</a> 
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</li><li> <a href="/wiki/index.php/Related_Work" title="Related Work">Related Work</a> 
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</li><li> <a href="/wiki/index.php/Clotho_Tool" title="Clotho Tool">Clotho Tool</a> 
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</li><li> <a href="/wiki/index.php/Future_Work" title="Future Work">Future Work</a> 
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</li><li> <a href="/wiki/index.php/More_Material" title="More Material">More Material</a>
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Retrieved from "<a href="http://biocad-server.eecs.berkeley.edu/wiki/index.php/BioCad">http://biocad-server.eecs.berkeley.edu/wiki/index.php/BioCad</a>"</div>
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<center>[http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development#Downloads_and_Information <b>The Alpha release is here</b>]! Be the first to try it out! </center>
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<b>Team:</b> iGEM 2008 UC Berkeley Tools. a.k.a., UC Berkeley Dry Team (why'd <b>we</b> have to be the dry ones?)
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<b>Members:</b> Nade Sritanyaratana, Matthew Johnson, Anne Van Devender
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<li id="lastmod"> This page was last modified 00:04, 31 July 2008.</li>
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==The Project==
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[[Image:DayShot_Campanile.png|thumb|The Campanile, UC Berkeley]]
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Genomics has reached the stage at which the amount of DNA sequence information in existing databases is quite large. Synthetic biology now is using these databases to catalog sequences according to their functionality and therefore creating standard biological parts which can be used to create large systems.
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As these databases grow, the need for integrated tools that perform complex operations, organize information, and automate regular processes is becoming increasingly obvious. The synthetic biology community could be better-served with the development of flexible tools which not only permit access and modification to that data but also allow one to perform meaningful manipulation and use of that information in an intelligent and efficient way. These tools need to be useful to biologists working in a laboratory environment while leveraging the experience of the larger CAD community.
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This project develops a toolset called "Clotho" which provides a variety of design views and tools to aid biologists to modify existing synthetic biological systems as well as create new ones. These tools differ from current offerings in this area in that they not only provide the needed tools to manipulate designs in one complete system but also provide unique ways in which to visualize the design as well as a number of connections to both local and global part repositories.
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For any inquiries or comments, please prefix emails with [iGEM 2008 Cal Comp Team]. So, if the preferred subject of the email were "Clotho Question", then please subject the email as "[iGEM 2008 Cal Comp Team]Clotho Question". Thanks!
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Revision as of 11:55, 31 July 2008

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> BioCad - PBD of Synthetic Biological Tools

BioCad

From PBD of Synthetic Biological Tools

Jump to: navigation, search

Welcome to the "Platform-Based Design of Synthetic Biological Tools" Wiki

This website provides information and tools for the design of synthetic biological systems using the notions of Platform-based design from the EDA community in electrical engineering and computer science. The work is based at UC Berkeley but includes participants from a number of universities and organizations.


Contents

Overview

Genomics has reached the stage at which the amount of DNA sequence information in existing databases is quite large. Moreover, synthetic biology now is using these databases to catalog sequences according to their functionality and therefore creating standard biological parts which can be used to create large systems. What is needed now are flexible tools which not only permit access and modification to that data but also allow one to perform meaningful manipulation and use of that information in an intelligent and efficient way. These tools need to be useful to biologists working in a laboratory environment while leveraging the experience of the larger CAD community.

A Platform-Based Design (PBD) approach looks at how genetic information can be viewed as having a particular functionality and what is now needed is to assemble platforms (collections of DNA elements) to perform this functionality. This work attempts to leverage the same methodology employed by PBD for embedded systems to the design of synthetic biological systems. This work places synthetic biology in a PBD framework, discusses required EDA concepts in biological terms, and describes a toolset (Clotho) which will implement the ideas outlined here.


News

7/15/08 - Clotho Alpha Release Coming!

Based on the work of the Berkeley computational iGEM team, the alpha version of Clotho is currently under development. It should be released by August 1st, 2008. Naturally this is a very preliminary release and is intended to get feedback, test deployment issues, and chase down bugs. It lacks functional and architectural views which are planned as well as a connection to Pobol based repositories. These features should be present in a Beta release in the fall of 2008. More information on this can be found here.

7/26/08 - Clotho Alpha Release

Clotho Alpha
Clotho Alpha

We are pleased to announce that the Clotho alpha release is available!! You can get it here. The executable jar file and java docs are available now and source code should be released within a week (if not sooner). Enjoy! Keep those bug reports coming in:)

7/27/08 - Clotho Alpha Release 1.1

A bug slipped into the alpha release which rendered parts navigation useless. It has been fixed and now is available for download. The .jar file and the README file in the .zip indicate that you are using 1.1. This was available as of 7:15pm PST on 7/27/08. Sorry for any inconvenience.

7/28/08 - iGEM Blog

Clotho is part of a Berkeley College of Engineering blog. Check out http://blogs.coe.berkeley.edu/igem/

7/29/08 - Clotho Alpha Source Code Available

The Clotho Alpha source code is now available here. In addition, the required libraries are also available. These are publicly available elsewhere but are included here for convenience and compatibility. A README file is in the works which will provide instructions for those unfamiliar with building java programs.

People

UC Berkeley EECS Leads

UC Berkeley EECS Design Team

  • Anne Van Devender (visiting student)
  • Jonathan Whiteaker
  • Ben Sussman


UC Berkeley Synthetic Biology Lead

UC Berkeley BioEngineering Design Team

  • Nade Sritanyaratana
  • Matthew Johnson

UC Berkeley Synthetic Biology Consultant

  • Jonathan Goler


UCSF Team Lead

UCSF Consultants

  • Dr. Howard Salis
  • Karsten Temme
  • Ethan Mirsky


Stanford Consultant

  • Dr. Ryan Owen


More Information

For information about the project:

Retrieved from "http://biocad-server.eecs.berkeley.edu/wiki/index.php/BioCad"

Retrieved from "http://2008.igem.org/Team:UC_Berkeley_Tools"