http://2008.igem.org/wiki/index.php?title=Special:Contributions/Trichard&feed=atom&limit=50&target=Trichard&year=&month=2008.igem.org - User contributions [en]2024-03-29T06:58:36ZFrom 2008.igem.orgMediaWiki 1.16.5http://2008.igem.org/Team:PennStateTeam:PennState2008-10-30T03:25:15Z<p>Trichard: </p>
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<td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState" title="Welcome!">Home</a> </td><br />
<td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState/Team" >The Team</a> </td><br />
<td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState/Project" title="Full Abstracts.">The Project</a> </td><br />
<td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState/Parts">Parts</a> </td><br />
<td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState/Notebook" title="Day to day lab activity">Notebook</a> </td><br />
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<br />
<!-- <br />
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<h4>Diauxie Elimination</h4><br />
<dl id="hbnav"><br />
<dd><a href="https://2008.igem.org/Team:PennState/diauxie/intro">Introduction</a></dd><br />
<dd><a href="https://2008.igem.org/Team:PennState/diauxie/TheSystem">The System</a></dd><br />
<dd><a href="https://2008.igem.org/Team:PennState/diauxie/Strategies">Strategies</a></dd><br />
<dd><a href="https://2008.igem.org/Team:PennState/diauxie/progress">Progress</a></dd><br />
<dd><a href="https://2008.igem.org/Team:PennState/diauxie/conclusions">Conclusions</a></dd><br />
<dd><a href="https://2008.igem.org/Team:PennState/diauxie/parts" title="Parts submitted to the registry for diauxie">Parts</a></dd><br />
<dd><a href="https://2008.igem.org/Team:PennState/diauxie/references">References</a></dd><br />
</dl><br />
<h4><acronym title="Nuclear Hormone Receptor">NHR Biosensors</acronym><br/></h4><br />
<dl id="denav"><br />
<dd><a href="https://2008.igem.org/Team:PennState/NHR/introduction">NHR Introduction</a></dd><br />
<br />
<dd><a href="https://2008.igem.org/Team:PennState/smartfold/overview">Phthalate Biosensor</a></dd><br />
<br />
<dd><a href="https://2008.igem.org/Team:PennState/fusion/overview">BPA Biosensor</a></dd><br />
</dl><br />
</td><br />
<!-- Main content area --><br />
<td valign="top" id="pagecontent" width="80%"><span style="font-size: 16pt">Welcome to Penn State iGEM 2008</span><br />
<hr /><br />
<p class="start"><a href="http://www.psu.edu" title="Pennsylvania State University" target="_blank">Penn State University</a> has participated in the International Genetically Engineered Machines (iGEM) competition for four years as of 2008, and we are excited to participate once more. Our team consists of 5 undergraduate students, one visiting undergrad and one high school student who work independently, coordinated through weekly meetings with our advisers. Check out our <a href="https://2008.igem.org/Team:PennState/Team" title="Penn State's 2008 iGEM team">Team Page</a> to meet us!</p><br />
<p><strong>Our main focus for 2008 was the elimination of <a href="https://2008.igem.org/Team:PennState/diauxie/intro">diauxie</a> in <em>E. coli</em> to create a xylose inducible system independent of glucose regulation.</strong> This system could be used for creating more efficient bioproduction by altering the utilization of 5 and 6 carbon sugars. Please check out the links on the left to navigate through our work.</p><br />
<p>Two other projects begun this year focus on creating <a href="https://2008.igem.org/Team:PennState/NHR/introduction"What kind of 'Biosensors' are we talking about?">biosensors</a> that use human nuclear hormone receptors to recognize potentially harmful compounds. These receptor systems occur naturally in the human body, but our goal is to retain and utilize their functions in <em>E. coli</em>. The links on the left should introduce you to our thought process and progress on each of these projects, and provide a fuller introduction to the topic.</p><br />
<p> Please explore our website to find out more about us and our projects! If there are any questions or comments about the information on this site please feel free to contact us at <a href="mailto:gjt5001@psu.edu" title="email us">gjt5001@psu.edu</a>. </p><br />
<br />
<span style="font-size: 14pt"><a href="https://2008.igem.org/Team:PennState/MedalChecklist">Medal Checklist</a></span><br />
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<table><br />
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<td style="padding-top:30px; padding-right:30px" valign="top" width="45%"><br />
<h3>Related Links</h3><br />
<hr /><br />
<ul><br />
<li><a href="http://partsregistry.org/Main_Page" title="Parts Registry">Parts Registry</a></li><br />
<br />
<li><a href="http://www.che.psu.edu/Faculty/Cirino/" title="Prof. Pat Cirino's Lab website" target="_blank">Prof. Pat Cirino's Lab website</a></li><br />
<li><a href="http://www.abe.psu.edu/fac/Richard/Overview.htm" title="Prof. Tom Richard's Lab website" target="_blank">Prof. Tom Richard's Lab website</a></li><br />
<li><a href="http://openwetware.org/wiki/IGEM:PennState" title="Penn State iGEM OpenWetWare" target="_blank">Penn State iGEM OpenWetWare</a></li><br />
<br />
<br />
<li><a href="http://www.princeton.edu/che/people/faculty/wood/" title="David Wood" target="_blank">David Wood</a></li><br />
<li><a href="http://www.cmtc.psu.edu/" title="Center for Molecular Toxicology and Carcinogenesis" target="_blank">PennState Center for Molecular Toxicology and Carcinogenesis</a></li><br />
</ul><br />
</td><br />
<td style="padding-top:30px; padding-right:30px" valign="top" width="45%"><br />
<h3>Drew Endy On Synthetic Biology</h3><br />
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<h3>Garrett Tobin On Diauxie Elimination</h3><br />
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<h4 style="font-size: 14pt;">Sponsors for our team! Thanks so much!</h4><br />
<hr /><br />
<img src="http://ntp.neuroscience.wisc.edu/gwis/gifs/Invitrogen.jpg" alt="invitrogen" style="float:left; clear: left; margin-right: 4%; margin-top: 40px; width: 48%;"/><br />
<img src="http://www.x-cd.com/wepan06/Dupont.gif" alt="Dupont" style="float:left; clear: right; width: 48%;"/><br />
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</html></div>Trichardhttp://2008.igem.org/Team:PennStateTeam:PennState2008-10-30T03:20:32Z<p>Trichard: </p>
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</div><br />
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<!-- Table displaying top row of links --><br />
<table class="links" ><br />
<tr><br />
<td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState" title="Welcome!">Home</a> </td><br />
<td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState/Team" >The Team</a> </td><br />
<td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState/Project" title="Full Abstracts.">The Project</a> </td><br />
<td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState/Parts">Parts</a> </td><br />
<td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState/Notebook" title="Day to day lab activity">Notebook</a> </td><br />
</tr><br />
</table><br />
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<table> <!-- Table for content area --><br />
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<br />
<!-- <br />
Navigation menu for the projects<br />
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<td valign="top" width="20%" id="projectnav"><br />
<h4>Diauxie Elimination</h4><br />
<dl id="hbnav"><br />
<dd><a href="https://2008.igem.org/Team:PennState/diauxie/intro">Introduction</a></dd><br />
<dd><a href="https://2008.igem.org/Team:PennState/diauxie/TheSystem">The System</a></dd><br />
<dd><a href="https://2008.igem.org/Team:PennState/diauxie/Strategies">Strategies</a></dd><br />
<dd><a href="https://2008.igem.org/Team:PennState/diauxie/progress">Progress</a></dd><br />
<dd><a href="https://2008.igem.org/Team:PennState/diauxie/conclusions">Conclusions</a></dd><br />
<dd><a href="https://2008.igem.org/Team:PennState/diauxie/parts" title="Parts submitted to the registry for diauxie">Parts</a></dd><br />
<dd><a href="https://2008.igem.org/Team:PennState/diauxie/references">References</a></dd><br />
</dl><br />
<h4><acronym title="Nuclear Hormone Receptor">NHR Biosensors</acronym><br/></h4><br />
<dl id="denav"><br />
<dd><a href="https://2008.igem.org/Team:PennState/NHR/introduction">NHR Introduction</a></dd><br />
<br />
<dd><a href="https://2008.igem.org/Team:PennState/smartfold/overview">Phthalate Biosensor</a></dd><br />
<br />
<dd><a href="https://2008.igem.org/Team:PennState/fusion/overview">BPA Biosensor</a></dd><br />
</dl><br />
</td><br />
<!-- Main content area --><br />
<td valign="top" id="pagecontent" width="80%"><span style="font-size: 16pt">Welcome to Penn State iGEM 2008</span><br />
<hr /><br />
<p class="start"><a href="http://www.psu.edu" title="Pennsylvania State University" target="_blank">Penn State University</a> has participated in the International Genetically Engineered Machines (iGEM) competition for four years as of 2008, and we are excited to participate once more. Our team consists of 5 undergraduate students, one visiting undergrad and one high school student who work independently, coordinated through weekly meetings with our advisers. Check out our <a href="https://2008.igem.org/Team:PennState/Team" title="Penn State's 2008 iGEM team">Team Page</a> to meet us!</p><br />
<p><strong>Our main focus for 2008 was the elimination of <a href="https://2008.igem.org/Team:PennState/diauxie/intro">diauxie</a> in <em>E. coli</em> to create a xylose inducible system independent of glucose regulation.</strong> This system could be used for creating more efficient bioproduction by altering the utilization of 5 and 6 carbon sugars. Please check out the links on the left to navigate through our work.</p><br />
<p>Two other projects begun this year focus on creating <a href="https://2008.igem.org/Team:PennState/NHR/introduction"What kind of 'Biosensors' are we talking about?">biosensors</a> that use human nuclear hormone receptors to recognize potentially harmful compounds. These receptor systems occur naturally in the human body, but our goal is to retain and utilize their functions in <em>E. coli</em>. The links on the left should introduce you to our thought process and progress on each of these projects, and provide a fuller introduction to the topic.</p><br />
<p> Please explore our website to find out more about us and our projects! If there are any questions or comments about the information on this site please feel free to contact us at <a href="mailto:gjt5001@psu.edu" title="email us">gjt5001@psu.edu</a>. </p><br />
<span style="font-size: 14pt"><a href="https://2008.igem.org/Team:PennState/MedalChecklist">Medal Checklist</a></span><br />
<br />
<table><br />
<tr><br />
<td style="padding-top:30px; padding-right:30px" valign="top" width="45%"><br />
<h3>Related Links</h3><br />
<hr /><br />
<ul><br />
<li><a href="http://partsregistry.org/Main_Page" title="Parts Registry">Parts Registry</a></li><br />
<br />
<li><a href="http://www.che.psu.edu/Faculty/Cirino/" title="Prof. Pat Cirino's Lab website" target="_blank">Prof. Pat Cirino's Lab website</a></li><br />
<li><a href="http://www.abe.psu.edu/fac/Richard/Overview.htm" title="Prof. Tom Richard's Lab website" target="_blank">Prof. Tom Richard's Lab website</a></li><br />
<li><a href="http://openwetware.org/wiki/IGEM:PennState" title="Penn State iGEM OpenWetWare" target="_blank">Penn State iGEM OpenWetWare</a></li><br />
<br />
<br />
<li><a href="http://www.princeton.edu/che/people/faculty/wood/" title="David Wood" target="_blank">David Wood</a></li><br />
<li><a href="http://www.cmtc.psu.edu/" title="Center for Molecular Toxicology and Carcinogenesis" target="_blank">PennState Center for Molecular Toxicology and Carcinogenesis</a></li><br />
</ul><br />
</td><br />
<td style="padding-top:30px; padding-right:30px" valign="top" width="45%"><br />
<h3>Drew Endy On Synthetic Biology</h3><br />
<hr /><br />
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<h3>Garrett Tobin On Diauxie Elimination</h3><br />
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<h4 style="font-size: 14pt;">Sponsors for our team! Thanks so much!</h4><br />
<hr /><br />
<img src="http://ntp.neuroscience.wisc.edu/gwis/gifs/Invitrogen.jpg" alt="invitrogen" style="float:left; clear: left; margin-right: 4%; margin-top: 40px; width: 48%;"/><br />
<img src="http://www.x-cd.com/wepan06/Dupont.gif" alt="Dupont" style="float:left; clear: right; width: 48%;"/><br />
<br />
</body><br />
</html></div>Trichardhttp://2008.igem.org/Judging/Variance/WarsawJudging/Variance/Warsaw2008-10-12T14:59:31Z<p>Trichard: </p>
<hr />
<div>===Request===<br />
Dear iGEM Judges, <br />
<br />
During this year's iGEM competition our team is building a system of biological machines allowing to investigate protein interactions and simultaneously change sequence of one of them in order to achieve the strongest possible interaction. The character of our project requires stable single or low copy number vector carrying part of our system which we call 'one-armed bandit'. Low copy number vector is a template for random mutagenesis which is crucial part of this system. For this reason we would like to use pACYC177 and pMPM-T5 derivatives as a backbones for our parts. We have tried to use vector BBa_I739204 (derivative of pACYC177) , but we weren't able to recover it from DNA Kit of Parts. <br />
<br />
Another thing is as our pACYC177 already contained RBS and lactose promoter, constructing such vector from the beginning would be redundant. In the case of pACYC177 backbone we've had also to use cloning sites different from standard because it doesn't contain standard restriction sites and changing multicloning site would be time-consuming. Another simple reason is that in few cases our parts contain standard sites inside their sequence . We tried to put our tools into parts with standard cloning sites, but we are already sure that for a few of them it will be impossible.<br />
<br />
We also used some non-standard vectors in the section of our system which requires purification of recombinant fusion (protein A + part of beta-lactamase) proteins. Sequences of mentioned fusions were cloned into pet15b vector from Novagen, giving us an opportunity to purify his-tagged proteins easily. We want to mention here that prepared parts will be sent on standard BioBrick vectors unless it will be impossible because of different restriction sites. <br />
<br />
All mentioned variances are required for our system to work. In our set-up of vectors and strains everything has to be fully adjusted and change or removal of any part will cause damage of the whole system. That's why we are requesting permission to submit non-biobrick parts to the registry. <br />
<br />
We will make sure that our parts can be easily extracted from the plasmid either through digestion with commercially available enzymes or through PCR (and we will also make sure that all non-standard parts are fully described and documented to ensure that they are useful for the community. <br />
<br />
Thanks for your time and consideration <br />
<br />
Pawel Krawczyk<br />
<br />
University of Warsaw iGEM'08 team<br />
<br />
===Response===<br />
Dear Pawel:<br />
<br />
We fully appreciate the challenges you describe, and are pleased to see that you will be submitting prepared parts on standard BioBrick vectors whenever possible. Please do clearly explain the reasons in those cases that you feel are impossible, and submit those parts clearly identified as being on a different vector. While we regret that you were unable to extract BBa_I739204, it would have been good to try the pSB3 series which has the copy number range and hopefully stability you need. <br />
<br />
It seems like you are also asking for a variance to submit your assembled device on a non-standard plasmid. This would be fine if you are willing to propose and document a new assembly standard and submit the vector in that format. Please look at the existing documentation of existing standard biobrick assembly plasmids in the registry to see what would be expected.<br />
<br />
The Novagen vector presumably has restrictions on distribution, in which case you also need to avoid submission on that vector.<br />
<br />
Sincerely,<br />
<br />
iGEM judging team<br />
<br />
===Response^2===<br />
Dear iGEM Judges,<br />
<br />
Thank you for your quick reply to our request. We hope to answer all the questions you asked us.<br />
For the moment we have put 7 out of 13 of our parts into BioBrick standard. We're working hard to finish the remaining 6, but we feel that given all other requirements we have to fulfill (and regular student duties) we might be unable to do it in time. One of the reasons is complexity of these parts, i.e. several XbaI, EcoRI or NotI sites, all of which should be removed. Discussed parts are located either on pMPM vector, or on our derivative of pACYC177. <br />
We are now working on the documentation of our new assembly standard and we will make sure that it will help the Community to use our device and a new standard. Briefly writing – our standard uses NdeI or NcoI as a beginning of part. Sequences recognized by these enzymes include ATG start codon, which allows to easily exchange ORFs in a given part. This is very useful in devices generating proteins on a high-throughput scale (which is the case of our device). For protein fusions we use BamHI or SacI restriction sites because they allow to introduce linkers between fused proteins, containing only glycine and serine. Gly-Ser linkers are in our opinion the best general-purpose protein linkers, but their introduction is impossible with currently available standards. We want to point out that available standard didn't suit our parts because it introduces 'scars' (TACTAG sequences) between each two parts. That would disrupt reading frame of our fusions or introduce wrong amino acids to the linker and all our parts need to be 'scarless'.<br />
<br />
We are aware that this promise cannot have any influence on your decision concerning our request nor on the final judgment, but if you feel it is desirable for the community that we submit all the remaining parts, we will commit ourselves to do it after the Jamboree. We'd rather use the little time that is left to test and document our device since we believe it is worth putting it to work in the first place. <br />
I hope I've answered all of your doubts.<br />
<br />
Sincerely<br />
<br />
Pawel Krawczyk<br />
<br />
University of Warsaw iGEM team</div>Trichardhttp://2008.igem.org/Judging/Variance/BrownJudging/Variance/Brown2008-10-10T03:17:24Z<p>Trichard: /* Response */</p>
<hr />
<div>===Request===<br />
<br />
Dear Judges,<br />
<br />
At Brown, we are building a regulatory gene network in ''Saccharomyces cerevisiae'', and are excited to contribute to the growing collection of yeast parts in the Registry. We are building our constructs using the Silver Lab Biofusion standard for the fusion of protein domains, and the Biobrick standard for the addition of regulatory regions. Construction takes place on Biobrick vectors, while the final constructs are cloned onto integrative yeast shuttle vectors from the pRS30x family. (http://www.genetics.org/cgi/reprint/122/1/19.pdf) The pRS vectors are not suitable for Biobrick construction, but their multiple cloning sites provide for the convenient cloning of a complete Biobrick construct onto the vector. (http://openwetware.org/wiki/Silver:_BB_Strategy) Our parts on pRS vectors are useful as complete constructs for integration into the yeast genome, and in that way would be a valuable addition to the registry. Some final constructs could be useful as construction intermediates as well- in these cases we would like to submit them on both pRS vectors for yeast integration as-is, and on standard Biobrick vectors for use in construction.<br />
<br />
Thank you,<br />
<br />
John Szymanski<br><br />
Brown iGEM<br><br />
Team Limiter<br />
<br />
===Response===<br />
<br />
Hi John:<br />
<br />
Thank you for your inquiry. First, we absolutely welcome your basic parts as standard BioBrick alpha parts. For the pRS vectors, we would like your team to document how you are moving the BB alpha parts onto a yeast shuttle vector, and further explain how and why this is useful. We expect that this second aspect of the work could be recognized as a new BB assembly technique (for moving BBa parts onto yeast chromosomes), and approve your request contingent on further documentation. <br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/HeidelbergJudging/Variance/Heidelberg2008-10-10T03:12:36Z<p>Trichard: New page: ===Request=== Dear Judges, the Heidelberg iGEM team has been focusing on the shuttling of DNA via conjugation. The conjugation origin of replication (oriT) is inserted into a plasmid or g...</p>
<hr />
<div>===Request===<br />
Dear Judges,<br />
<br />
the Heidelberg iGEM team has been focusing on the shuttling of DNA via conjugation. The conjugation origin of replication (oriT) is inserted into a plasmid or genome of interest; in the presence of a (non-modifiable) conjugation plasmid as a chassis the DNA of interest is transfered to cells of a second E. coli strain.<br />
<br />
1) We would like to add this conjugation plasmid to the Registry as a chassis system. The diverse genes are essential for effective conjugation and are not supposed to be modified. However, in the Registry there are only chassis systems for bacterial strains and cell-free systems yet. Where should we best place this 60 kb helper plasmid? We think it would be suitable to introduce a category for "Chassis Plasmids"!<br />
<br />
2) We have inserted the oriT into the lambda phage genome and used the above mentioned conjugation/oriT system to transfer the phage via conjugation. Since the phage genome is not a standard vector, we have been deliberating over an appropriate standard, but we had to conclude that - in terms of time and money - this is out of our scope:<br />
<br />
The oriT fragment in the lambda phage genome cannot be exchanged via standard prefix and suffix sites, since the corresponding restriction sites occur too frequently in the >40 kb lambda phage genome to be eliminated; indeed, we were lucky to even find few single-cutting restriction sites to make an insertion of the oriT fragment possible! There is still no simple cloning strategy yet to exchange the oriT in the phage genome, because the smallest embracing fragment that is flanked by single-cutting restriction sites contains genes essential for the phage (e.g. GAM). Since mutagenesis would be inefficient due to the large size, the introduction of standard sites would be possible only in a synthesis approach with costs of estimated 25,000 USD - and this is not affordable from our team budget.<br />
<br />
The phage, however, is an essential part for the dynamics of our overall population system (hunter/prey), and we are convinced of its value for the Registry: The system will provide a novel approach to effectively eradicate a specific target strain. A category for T7 phages - containing only few constructs yet - already exists in the Registry, and we suggest to declare it as a more general category for "bacteriophages"; our modified lambda phage could then be placed there. To account for consistency with Registry standards, however, we will in addition provide the oriT with standard restriction sites in a standard vector. <br />
<br />
We would therefore like to ask, if you consider the introduction of the two categories as appropriate. <br />
<br />
We sincerely look forward to your judgement!<br />
<br />
Faithfully yours,<br />
<br />
Jens Keienburg<br />
<br />
the Heidelberg iGEM team.<br />
<br />
<br />
____________________________________<br />
Jens Keienburg, M. Sc.<br />
Bioquant, AG Eils<br />
Ruperto-Carola University<br />
INF 267 (R. 355), 69120 Heidelberg, Germany<br />
Office: +49 (0) 6221 54 51 305<br />
Mobile: +49 (0) 0176 6201 0563<br />
Fax: + 49 (0) 6221 54 51 488</div>Trichardhttp://2008.igem.org/JudgingJudging2008-10-10T03:11:50Z<p>Trichard: /* BioBrick standard variance requests */</p>
<hr />
<div><span style="color:red;">'''Note:''' </span> All Awards & Judging Criteria for iGEM 2008 are currently in draft form. The Awards & Judging details will be finalized in a few weeks. Please send any comments or suggestions for awards and judging by email to the judging committee at judging AT igem DOT org. For example, if you anticipate that your team will do something amazing or important, but that such a project would not be recognized via any of the mechanisms or awards below, let us know as soon as possible.<br />
<br />
<br />
<br />
===[[Judging/Judging_Criteria | Judging criteria]]===<br />
<br />
<br />
===[[Judging/Awards | Awards]]===<br />
<br />
<br />
===Important Dates===<br />
<br />
Be sure to study the official iGEM [[Calendar_of_Events | calendar]] to find out the final dates for different judging requirements.<br />
<br />
<br />
===BioBrick standard variance requests===<br />
One of the [[Requirements | requirements]] for iGEM is that teams are required to provide their parts to the Registry as standard biological parts in standard BioBrick plasmids. If a team wishes to use a different plasmid or different assembly method, they must document the new standard, explain their decision, and receive approval from iGEM Headquarters by the stated [[Calendar_of_Events | deadline]]. Please send your requests to judging AT igem DOT org.<br />
<br />
Here is a list of variance requests:<br />
# [[Judging/Variance/UCSF | UCSF]] ''(approved)''<br />
# [[Judging/Variance/Wisconsin | Wisconsin]] ''(denied)''<br />
# [[Judging/Variance/Cambridge| Cambridge]] ''(approved)''<br />
# [[Judging/Variance/LCG-UNAM Mexico | LCG-UNAM Mexico]] ''(under evaluation)''<br />
# [[Judging/Variance/Brown | Brown]] ''(approved)''<br />
# [[Judging/Variance/Guelph | Guelph]] ''(under evaluation)''<br />
# [[Judging/Variance/BNU | Bejing Normal University]] ''(under evaluation)''<br />
# [[Judging/Variance/Lethbridge_CCS | Lethbridge CCS]] ''(under evaluation)''<br />
# [[Judging/Variance/Warsaw| Warsaw]] ''(under evaluation)''<br />
# [[Judging/Variance/Peking| Peking University]] ''(under evaluation)''<br />
# [[Judging/Variance/Freiburg| Freiburg]] ''(approved)''<br />
# [[Judging/Variance/UC Berkeley| UC Berkeley]] ''(approved)''<br />
# [[Judging/Variance/U. Michigan| U. Michigan]] ''(approved)''<br />
# [[Judging/Variance/Heidelberg| Heidelberg]] ''(under evaluation)''<br />
<br />
Click on an individual team to see their request.<br />
<br />
Those variance requests will be "denied" that ask to submit non-biobricked parts or non-standard plasmids to the registry, but do not propose and document a new standard. The relevant guidance is provided by item 6 of the iGEM 2008 [https://2008.igem.org/Requirements Requirements] page. <br />
<br />
The standard plasmid backbones that should be used for part submission are the pSB series in the Registry. These plasmid backbones can be found on the [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid plasmid page] on the Registry (partsregistry.org)<br />
<br />
The judges recognize that many parts will require different vectors for specific devices or applications. However, one of the fundamental principles of iGEM is that we are all making parts to share. Submitting parts on a standard vector allows for easy replication and distribution as well as use. While it is a bit more work to move a biobrick part from a dedicated device plasmid to a standard biobrick plasmid, that extra effort will facilitate sharing and interoperability and will be greatly appreciated by both your peers and those that come after you. We do encourage the development of new standard vectors, but want to see complete documentation and evidence that they work before allowing their use for parts submission to the registry.<br />
<br />
===Complaints===<br />
<br />
To file an official complaint regarding iGEM 2008 judging you must send an email to complaints AT igem DOT org. Your email should include your real name, the real name of your school and team, and the real name and email address of your faculty advisor. Your email must also be copied to your faculty advisor. In your email please clearly state your complaint and what you hope will happen as a result of filing your official complaint. The iGEM judging committee will work diligently to respond to all complaints as quickly as possible. Complaints that are sent to other email addresses, or that do not include the requested information will be ignored. All decisions by the judges regarding complaints are final.</div>Trichardhttp://2008.igem.org/Judging/Variance/WarsawJudging/Variance/Warsaw2008-10-10T03:06:00Z<p>Trichard: /* Response */</p>
<hr />
<div>===Request===<br />
Dear iGEM Judges, <br />
<br />
During this year's iGEM competition our team is building a system of biological machines allowing to investigate protein interactions and simultaneously change sequence of one of them in order to achieve the strongest possible interaction. The character of our project requires stable single or low copy number vector carrying part of our system which we call 'one-armed bandit'. Low copy number vector is a template for random mutagenesis which is crucial part of this system. For this reason we would like to use pACYC177 and pMPM-T5 derivatives as a backbones for our parts. We have tried to use vector BBa_I739204 (derivative of pACYC177) , but we weren't able to recover it from DNA Kit of Parts. <br />
<br />
Another thing is as our pACYC177 already contained RBS and lactose promoter, constructing such vector from the beginning would be redundant. In the case of pACYC177 backbone we've had also to use cloning sites different from standard because it doesn't contain standard restriction sites and changing multicloning site would be time-consuming. Another simple reason is that in few cases our parts contain standard sites inside their sequence . We tried to put our tools into parts with standard cloning sites, but we are already sure that for a few of them it will be impossible.<br />
<br />
We also used some non-standard vectors in the section of our system which requires purification of recombinant fusion (protein A + part of beta-lactamase) proteins. Sequences of mentioned fusions were cloned into pet15b vector from Novagen, giving us an opportunity to purify his-tagged proteins easily. We want to mention here that prepared parts will be sent on standard BioBrick vectors unless it will be impossible because of different restriction sites. <br />
<br />
All mentioned variances are required for our system to work. In our set-up of vectors and strains everything has to be fully adjusted and change or removal of any part will cause damage of the whole system. That's why we are requesting permission to submit non-biobrick parts to the registry. <br />
<br />
We will make sure that our parts can be easily extracted from the plasmid either through digestion with commercially available enzymes or through PCR (and we will also make sure that all non-standard parts are fully described and documented to ensure that they are useful for the community. <br />
<br />
Thanks for your time and consideration <br />
<br />
Pawel Krawczyk<br />
<br />
University of Warsaw iGEM'08 team<br />
<br />
===Response===<br />
Dear Pawel:<br />
<br />
We fully appreciate the challenges you describe, and are pleased to see that you will be submitting prepared parts on standard BioBrick vectors whenever possible. Please do clearly explain the reasons in those cases that you feel are impossible, and submit those parts clearly identified as being on a different vector. While we regret that you were unable to extract BBa_I739204, it would have been good to try the pSB3 series which has the copy number range and hopefully stability you need. <br />
<br />
It seems like you are also asking for a variance to submit your assembled device on a non-standard plasmid. This would be fine if you are willing to propose and document a new assembly standard and submit the vector in that format. Please look at the existing documentation of existing standard biobrick assembly plasmids in the registry to see what would be expected.<br />
<br />
The Novagen vector presumably has restrictions on distribution, in which case you also need to avoid submission on that vector.<br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/WarsawJudging/Variance/Warsaw2008-10-10T03:04:25Z<p>Trichard: /* Response */</p>
<hr />
<div>===Request===<br />
Dear iGEM Judges, <br />
<br />
During this year's iGEM competition our team is building a system of biological machines allowing to investigate protein interactions and simultaneously change sequence of one of them in order to achieve the strongest possible interaction. The character of our project requires stable single or low copy number vector carrying part of our system which we call 'one-armed bandit'. Low copy number vector is a template for random mutagenesis which is crucial part of this system. For this reason we would like to use pACYC177 and pMPM-T5 derivatives as a backbones for our parts. We have tried to use vector BBa_I739204 (derivative of pACYC177) , but we weren't able to recover it from DNA Kit of Parts. <br />
<br />
Another thing is as our pACYC177 already contained RBS and lactose promoter, constructing such vector from the beginning would be redundant. In the case of pACYC177 backbone we've had also to use cloning sites different from standard because it doesn't contain standard restriction sites and changing multicloning site would be time-consuming. Another simple reason is that in few cases our parts contain standard sites inside their sequence . We tried to put our tools into parts with standard cloning sites, but we are already sure that for a few of them it will be impossible.<br />
<br />
We also used some non-standard vectors in the section of our system which requires purification of recombinant fusion (protein A + part of beta-lactamase) proteins. Sequences of mentioned fusions were cloned into pet15b vector from Novagen, giving us an opportunity to purify his-tagged proteins easily. We want to mention here that prepared parts will be sent on standard BioBrick vectors unless it will be impossible because of different restriction sites. <br />
<br />
All mentioned variances are required for our system to work. In our set-up of vectors and strains everything has to be fully adjusted and change or removal of any part will cause damage of the whole system. That's why we are requesting permission to submit non-biobrick parts to the registry. <br />
<br />
We will make sure that our parts can be easily extracted from the plasmid either through digestion with commercially available enzymes or through PCR (and we will also make sure that all non-standard parts are fully described and documented to ensure that they are useful for the community. <br />
<br />
Thanks for your time and consideration <br />
<br />
Pawel Krawczyk<br />
<br />
University of Warsaw iGEM'08 team<br />
<br />
===Response===<br />
Dear Pawel:<br />
<br />
We fully appreciate the challenges you describe, and are pleased to see that you will be submitting prepared parts on standard BioBrick vectors whenever possible. Please do clearly explain the reasons in those cases that you feel are impossible, and submit those parts clearly identified as being on a different vector. While we regret that you were unable to extract BBa_I739204, it would have been good to try the pSB3 series which has the copy number range and hopefully stability you need. <br />
<br />
It seems like you are also asking for a varience to submit your assembled device on a non-standard plasmid. This would be fine if you are willing to propose and document a new assembly standard and submit the vector in that format. Please look at the existing documentation of existing standard biobrick assembly plasmids in the registry to see what would be expected.<br />
<br />
The Novagen vector presumably has restrictions on distribution, in which case you also need to avoid submission on that vector.<br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/WarsawJudging/Variance/Warsaw2008-10-10T03:01:27Z<p>Trichard: /* Response */</p>
<hr />
<div>===Request===<br />
Dear iGEM Judges, <br />
<br />
During this year's iGEM competition our team is building a system of biological machines allowing to investigate protein interactions and simultaneously change sequence of one of them in order to achieve the strongest possible interaction. The character of our project requires stable single or low copy number vector carrying part of our system which we call 'one-armed bandit'. Low copy number vector is a template for random mutagenesis which is crucial part of this system. For this reason we would like to use pACYC177 and pMPM-T5 derivatives as a backbones for our parts. We have tried to use vector BBa_I739204 (derivative of pACYC177) , but we weren't able to recover it from DNA Kit of Parts. <br />
<br />
Another thing is as our pACYC177 already contained RBS and lactose promoter, constructing such vector from the beginning would be redundant. In the case of pACYC177 backbone we've had also to use cloning sites different from standard because it doesn't contain standard restriction sites and changing multicloning site would be time-consuming. Another simple reason is that in few cases our parts contain standard sites inside their sequence . We tried to put our tools into parts with standard cloning sites, but we are already sure that for a few of them it will be impossible.<br />
<br />
We also used some non-standard vectors in the section of our system which requires purification of recombinant fusion (protein A + part of beta-lactamase) proteins. Sequences of mentioned fusions were cloned into pet15b vector from Novagen, giving us an opportunity to purify his-tagged proteins easily. We want to mention here that prepared parts will be sent on standard BioBrick vectors unless it will be impossible because of different restriction sites. <br />
<br />
All mentioned variances are required for our system to work. In our set-up of vectors and strains everything has to be fully adjusted and change or removal of any part will cause damage of the whole system. That's why we are requesting permission to submit non-biobrick parts to the registry. <br />
<br />
We will make sure that our parts can be easily extracted from the plasmid either through digestion with commercially available enzymes or through PCR (and we will also make sure that all non-standard parts are fully described and documented to ensure that they are useful for the community. <br />
<br />
Thanks for your time and consideration <br />
<br />
Pawel Krawczyk<br />
<br />
University of Warsaw iGEM'08 team<br />
<br />
===Response===<br />
Dear Pawel:<br />
<br />
We fully appreciate the challenges you describe, and are pleased to see that you will be submitting prepared parts on standard BioBrick vectors whenever possible. Please do clearly explain the reasons in those cases that you feel are impossible, and submit those parts clearly identified as being on a different vector. While we regret that you were unable to extract BBa_I739204, it would have been good to try the pSB3 series which has the copy number range and hopefully stability you need. <br />
<br />
It seems like you are also asking for a varience to submit your assembled device on a non-. This would be fine if you are willing to propose and document a new assembly standard. Please look at the existing documentation of existing standard biobrick assembly plasmids in the registry to see what would be expected.<br />
<br />
The Novagen vector presumably has restrictions on distribution, in which case you also need to avoid submission on that vector.<br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/JudgingJudging2008-10-10T02:58:33Z<p>Trichard: /* BioBrick standard variance requests */</p>
<hr />
<div><span style="color:red;">'''Note:''' </span> All Awards & Judging Criteria for iGEM 2008 are currently in draft form. The Awards & Judging details will be finalized in a few weeks. Please send any comments or suggestions for awards and judging by email to the judging committee at judging AT igem DOT org. For example, if you anticipate that your team will do something amazing or important, but that such a project would not be recognized via any of the mechanisms or awards below, let us know as soon as possible.<br />
<br />
<br />
<br />
===[[Judging/Judging_Criteria | Judging criteria]]===<br />
<br />
<br />
===[[Judging/Awards | Awards]]===<br />
<br />
<br />
===Important Dates===<br />
<br />
Be sure to study the official iGEM [[Calendar_of_Events | calendar]] to find out the final dates for different judging requirements.<br />
<br />
<br />
===BioBrick standard variance requests===<br />
One of the [[Requirements | requirements]] for iGEM is that teams are required to provide their parts to the Registry as standard biological parts in standard BioBrick plasmids. If a team wishes to use a different plasmid or different assembly method, they must document the new standard, explain their decision, and receive approval from iGEM Headquarters by the stated [[Calendar_of_Events | deadline]]. Please send your requests to judging AT igem DOT org.<br />
<br />
Here is a list of variance requests:<br />
# [[Judging/Variance/UCSF | UCSF]] ''(approved)''<br />
# [[Judging/Variance/Wisconsin | Wisconsin]] ''(denied)''<br />
# [[Judging/Variance/Cambridge| Cambridge]] ''(approved)''<br />
# [[Judging/Variance/LCG-UNAM Mexico | LCG-UNAM Mexico]] ''(under evaluation)''<br />
# [[Judging/Variance/Brown | Brown]] ''(approved)''<br />
# [[Judging/Variance/Guelph | Guelph]] ''(under evaluation)''<br />
# [[Judging/Variance/BNU | Bejing Normal University]] ''(under evaluation)''<br />
# [[Judging/Variance/Lethbridge_CCS | Lethbridge CCS]] ''(under evaluation)''<br />
# [[Judging/Variance/Warsaw| Warsaw]] ''(under evaluation)''<br />
# [[Judging/Variance/Peking| Peking University]] ''(under evaluation)''<br />
# [[Judging/Variance/Freiburg| Freiburg]] ''(approved)''<br />
# [[Judging/Variance/UC Berkeley| UC Berkeley]] ''(approved)''<br />
# [[Judging/Variance/U. Michigan| U. Michigan]] ''(approved)''<br />
<br />
Click on an individual team to see their request.<br />
<br />
Those variance requests will be "denied" that ask to submit non-biobricked parts or non-standard plasmids to the registry, but do not propose and document a new standard. The relevant guidance is provided by item 6 of the iGEM 2008 [https://2008.igem.org/Requirements Requirements] page. <br />
<br />
The standard plasmid backbones that should be used for part submission are the pSB series in the Registry. These plasmid backbones can be found on the [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid plasmid page] on the Registry (partsregistry.org)<br />
<br />
The judges recognize that many parts will require different vectors for specific devices or applications. However, one of the fundamental principles of iGEM is that we are all making parts to share. Submitting parts on a standard vector allows for easy replication and distribution as well as use. While it is a bit more work to move a biobrick part from a dedicated device plasmid to a standard biobrick plasmid, that extra effort will facilitate sharing and interoperability and will be greatly appreciated by both your peers and those that come after you. We do encourage the development of new standard vectors, but want to see complete documentation and evidence that they work before allowing their use for parts submission to the registry.<br />
<br />
===Complaints===<br />
<br />
To file an official complaint regarding iGEM 2008 judging you must send an email to complaints AT igem DOT org. Your email should include your real name, the real name of your school and team, and the real name and email address of your faculty advisor. Your email must also be copied to your faculty advisor. In your email please clearly state your complaint and what you hope will happen as a result of filing your official complaint. The iGEM judging committee will work diligently to respond to all complaints as quickly as possible. Complaints that are sent to other email addresses, or that do not include the requested information will be ignored. All decisions by the judges regarding complaints are final.</div>Trichardhttp://2008.igem.org/Judging/Variance/BrownJudging/Variance/Brown2008-10-10T02:57:21Z<p>Trichard: /* Response */</p>
<hr />
<div>===Request===<br />
<br />
Dear Judges,<br />
<br />
At Brown, we are building a regulatory gene network in ''Saccharomyces cerevisiae'', and are excited to contribute to the growing collection of yeast parts in the Registry. We are building our constructs using the Silver Lab Biofusion standard for the fusion of protein domains, and the Biobrick standard for the addition of regulatory regions. Construction takes place on Biobrick vectors, while the final constructs are cloned onto integrative yeast shuttle vectors from the pRS30x family. (http://www.genetics.org/cgi/reprint/122/1/19.pdf) The pRS vectors are not suitable for Biobrick construction, but their multiple cloning sites provide for the convenient cloning of a complete Biobrick construct onto the vector. (http://openwetware.org/wiki/Silver:_BB_Strategy) Our parts on pRS vectors are useful as complete constructs for integration into the yeast genome, and in that way would be a valuable addition to the registry. Some final constructs could be useful as construction intermediates as well- in these cases we would like to submit them on both pRS vectors for yeast integration as-is, and on standard Biobrick vectors for use in construction.<br />
<br />
Thank you,<br />
<br />
John Szymanski<br><br />
Brown iGEM<br><br />
Team Limiter<br />
<br />
===Response===<br />
<br />
Hi John:<br />
<br />
Thank you for your inquiry. First, we absolutely welcome your basic parts as standard BioBrick alpha parts. For the pRS vectors, we would like your team to document how you are moving the BB alpha parts onto a yeast shuttle vector, and further explain how and why this is useful. We expect that this second aspect of the work could be recognized as a new BB assembly technique (for moving BBa parts onto yeast chromosomes), and with adequate documentation would be more than welcome.<br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/LCG-UNAM_MexicoJudging/Variance/LCG-UNAM Mexico2008-10-10T02:30:58Z<p>Trichard: </p>
<hr />
<div>===Request===<br />
<br />
Dear iGEM judges,<br />
<br />
The team LCG-UNAM-MEXICO is participating this year for the first <br />
time, and I'm writing on behalf of the team to request permission <br />
for submitting our Biobricks in non-standard vectors.<br />
<br />
Our project requires very tight regulation of E. coli nickel <br />
extrusion pump (RcnA) through several regulatory upstream proteins. <br />
Our Analysis suggest that we need to control very accurately the <br />
production of several molecules and a crucial part of this requires <br />
stable low copy-number vectors. For this reason we would like to use <br />
pRK415 and pBBIMCS-5 derivatives as our plasmid backbones. We will <br />
be adding Biobrick prefix and suffix to both of them. We will also <br />
make sure that our parts are easily extracted from the plasmid <br />
either through digestion with commercially available enzymes or <br />
through PCR.<br />
<br />
All this information will be shared to ensure that our Biobricks are <br />
useful for the community.<br />
<br />
Thanks for your time and consideration<br />
<br />
Sur Herrera Paredes<br />
<br />
LCG-UNAM-MEXICO<br />
Licenciatura en Ciencias Genómicas<br />
Universidad Nacional Autónoma de México<br />
<br />
===Response===<br />
<br />
Dear Sur:<br />
<br />
We need some additional information about this request. It appears you are developing some new BioBrick alpha compatible vectors derived from PRK415 and pBBIMCS-5, which could be very useful in and of themselves (i.e., new parts). We like this idea, but do require complete documentation about these vectors so they can be used by others in the future. Examples of the documentation required of standard biobrick vectors are at: http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid<br />
<br />
If you are able to provide adequate documentation of these new vectors, then we would be pleased to evaluate them as standard vectors and hopefully allow submission of your new parts as proposed. Otherwise, you should submit your parts on an existing standard plasmid, specifically the pSB series in the biobricks registry. <br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/U._MichiganJudging/Variance/U. Michigan2008-10-09T12:13:53Z<p>Trichard: /* Request */</p>
<hr />
<div>===Request===<br />
Dear iGEM Judges,<br />
<br />
I am writing on behalf of the University of Michigan Synthetic Biology <br />
team to request your permission to submit non-BioBrick parts to the <br />
registry.<br />
<br />
For iGEM 2008, our team is trying to build a synthetic clock in E.coli <br />
that is an alteration of one found in mammals. However, upon review <br />
of clock literature, we realized that our clock has more potential to <br />
oscillate if we reduce the noise in the system. Hence, we want to <br />
incorporate our genetic operons into the E.coli chromosome. Our tool <br />
for doing this are landing pads.<br />
<br />
The two landing pads we are using for the project will replace the <br />
arabinose and leucine operons. The leucine landing pad is a construct <br />
that Dong Eun Chang, a former member of the Ninfa lab created, and the <br />
arabinose landing pad was one of the projects we presented at iGEM <br />
last year. These landing pads are BioBrick compatible, so standard <br />
BioBrick assembly can be used to construct into these plasmids. We <br />
are in the process of writing up and uploading the documentation for <br />
these parts on our wiki.<br />
<br />
<br />
Thank you for your time and consideration,<br />
Amrit Misra<br />
<br />
===Response===<br />
<br />
Amit,<br />
<br />
Thanks for your email. Request approved. Please carefully document <br />
how others can use your landing pads and provide the <br />
parts to the Registry in a format that will support ready reuse by <br />
others. Please also make sure to enter descriptions and instruction <br />
for using the parts directly into the Parts pages too.<br />
<br />
Best,<br />
Drew and the iGEM Judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/U._MichiganJudging/Variance/U. Michigan2008-10-09T12:12:39Z<p>Trichard: /* Request */</p>
<hr />
<div>===Request===<br />
Dear iGEM Judges,<br />
<br />
I'm writing on behalf of 2008 Peking University iGEM Team to ask for permission to send non-biobrick parts to the registry for the jamboree. <br />
<br />
As we can not find effective vectors for yeast expression in the registry, our team has been using the pGREG series of plasmids for yeast protein expression. We have to use the promoter which is sensitive to lacI or Gal4, so those yeast plasmids in the registry can not serve this function. For the same reason our parts can not flank the four standard restriction sites since our vector contains these four or at least some of these four. Of course, we are trying to standardize the parts we have constructed but it seems the time is limited. We wonder if we can send those plasmids based on PGREG backbone. <br />
<br />
Moreover, since our project has something to do the precise spot mutation of gal4, those plasmids contain gal4 or gal4 delta gene can not be standardized. As gal4 gene also contain some of the four restriction sites. <br />
<br />
Another thing that should be mentioned is that our gene hAIDsc is a codon optimized gene kindly offered by Pro. Youri. I am not sure whether he permits us to send this part to open source. <br />
<br />
Thank you very much!<br />
<br />
Zhou Zhou<br />
College of Life Sciences, Peking University<br />
Beijing, 100871<br />
P.R.China<br />
mikezzchina@gmail.com<br />
<br />
===Response===<br />
<br />
Amit,<br />
<br />
Thanks for your email. Request approved. Please carefully document <br />
how others can use your landing pads and provide the <br />
parts to the Registry in a format that will support ready reuse by <br />
others. Please also make sure to enter descriptions and instruction <br />
for using the parts directly into the Parts pages too.<br />
<br />
Best,<br />
Drew and the iGEM Judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/U._MichiganJudging/Variance/U. Michigan2008-10-09T12:12:12Z<p>Trichard: </p>
<hr />
<div>===Request===<br />
Dear iGEM Judges,<br />
I'm writing on behalf of 2008 Peking University iGEM Team to ask for permission to send non-biobrick parts to the registry for the jamboree. <br />
As we can not find effective vectors for yeast expression in the registry, our team has been using the pGREG series of plasmids for yeast protein expression. We have to use the promoter which is sensitive to lacI or Gal4, so those yeast plasmids in the registry can not serve this function. For the same reason our parts can not flank the four standard restriction sites since our vector contains these four or at least some of these four. Of course, we are trying to standardize the parts we have constructed but it seems the time is limited. We wonder if we can send those plasmids based on PGREG backbone. <br />
Moreover, since our project has something to do the precise spot mutation of gal4, those plasmids contain gal4 or gal4 delta gene can not be standardized. As gal4 gene also contain some of the four restriction sites. <br />
Another thing that should be mentioned is that our gene hAIDsc is a codon optimized gene kindly offered by Pro. Youri. I am not sure whether he permits us to send this part to open source. <br />
Thank you very much!<br />
<br />
Zhou Zhou<br />
College of Life Sciences, Peking University<br />
Beijing, 100871<br />
P.R.China<br />
mikezzchina@gmail.com<br />
===Response===<br />
<br />
Amit,<br />
<br />
Thanks for your email. Request approved. Please carefully document <br />
how others can use your landing pads and provide the <br />
parts to the Registry in a format that will support ready reuse by <br />
others. Please also make sure to enter descriptions and instruction <br />
for using the parts directly into the Parts pages too.<br />
<br />
Best,<br />
Drew and the iGEM Judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/PekingJudging/Variance/Peking2008-10-09T12:08:24Z<p>Trichard: /* Response */</p>
<hr />
<div>===Request===<br />
<br />
Dear iGEM Judges,<br />
I'm writing on behalf of 2008 Peking University iGEM Team to ask for permission to send non-biobrick parts to the registry for the jamboree. <br />
<br />
As we can not find effective vectors for yeast expression in the registry, our team has been using the pGREG series of plasmids for yeast protein expression. We have to use the promoter which is sensitive to lacI or Gal4, so those yeast plasmids in the registry can not serve this function. For the same reason our parts can not flank the four standard restriction sites since our vector contains these four or at least some of these four. Of course, we are trying to standardize the parts we have constructed but it seems the time is limited. We wonder if we can send those plasmids based on PGREG backbone. <br />
<br />
<br />
Moreover, since our project has something to do the precise spot mutation of gal4, those plasmids contain gal4 or gal4 delta gene can not be standardized. As gal4 gene also contain some of the four restriction sites. <br />
<br />
<br />
Another thing that should be mentioned is that our gene hAIDsc is a codon optimized gene kindly offered by Pro. Youri. I am not sure whether he permits us to send this part to open source. <br />
<br />
Thank you very much!<br />
<br />
Zhou Zhou<br />
College of Life Sciences, Peking University<br />
Beijing, 100871<br />
P.R.China<br />
mikezzchina@gmail.com<br />
<br />
===Responses===<br />
Dear Zhou,<br />
<br />
It seems like there are three separate issues you are inquiring about. <br />
<br />
The first issue is a problem with the limited number of yeast vectors in the registry, and the need for one that is compatible with your lacI and Gal4 sensitive promotor. The best solution to that would be to add a new vector to the registry, which we would welcome with appropriate documentation. You chose the pGREG series of plasmids, but this series contains the standard restriction sites for biobricks, which makes it incompatible with standard registry parts and thus not a great candidate for addition to the registry. There are two solutions to this problem: 1) make the pGREG vector compatible with biobrick parts, possibly (and with luck) by deleting the current biobrick restriction sites from the vector; or 2) create and document a new assembly standard. The Silver lab has done the later, which you might consider: http://openwetware.org/wiki/Silver:_BB_Strategy . The Silver lab approach, with a twist, is being adopted by the iGEM team from Brown University, as described on our judging variance request website:<br />
https://2008.igem.org/Judging/Variance/Brown<br />
<br />
The second issue, which at least partially derives from the first, is that your parts do not have biobricked ends. If you are proposing a new biobrick part standard, then you will need to carefully document that standard and propose it to the registry. In that absence of a new standard proposal, you should move your parts to a standard biobrick vector for submission. While we recognize that time is now short, this is not a new issue for your team, and should have been obvious as soon as you began working on your design.<br />
<br />
Finally, please do try to obtain permission to submit hAIDsc to the registry as an open source part. If permission is not provided, then you should not submit that part. A core principle of iGEM is that we all gain by sharing, and the registry cannot maintain or distribute parts that are not open source/open access.<br />
<br />
Please provide additional information about issues 1) and 2) if you plan to propose new assembly or part standards. While this will be a challenge, it is also a great opportunity to make a contribution to the community.<br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/U._MichiganJudging/Variance/U. Michigan2008-10-09T12:06:21Z<p>Trichard: New page: ===Request=== ===Response=== On Oct 8, 2008, at 11:18 PM, Zhou Zhou wrote: Dear iGEM Judges, I'm writing on behalf of 2008 Peking University iGEM Team to ask for permission to...</p>
<hr />
<div>===Request===<br />
<br />
===Response===<br />
<br />
<br />
<br />
<br />
<br />
On Oct 8, 2008, at 11:18 PM, Zhou Zhou wrote:<br />
<br />
Dear iGEM Judges,<br />
I'm writing on behalf of 2008 Peking University iGEM Team to ask for permission to send non-biobrick parts to the registry for the jamboree. <br />
As we can not find effective vectors for yeast expression in the registry, our team has been using the pGREG series of plasmids for yeast protein expression. We have to use the promoter which is sensitive to lacI or Gal4, so those yeast plasmids in the registry can not serve this function. For the same reason our parts can not flank the four standard restriction sites since our vector contains these four or at least some of these four. Of course, we are trying to standardize the parts we have constructed but it seems the time is limited. We wonder if we can send those plasmids based on PGREG backbone. <br />
Moreover, since our project has something to do the precise spot mutation of gal4, those plasmids contain gal4 or gal4 delta gene can not be standardized. As gal4 gene also contain some of the four restriction sites. <br />
Another thing that should be mentioned is that our gene hAIDsc is a codon optimized gene kindly offered by Pro. Youri. I am not sure whether he permits us to send this part to open source. <br />
Thank you very much!<br />
<br />
Zhou Zhou<br />
College of Life Sciences, Peking University<br />
Beijing, 100871<br />
P.R.China<br />
mikezzchina@gmail.com</div>Trichardhttp://2008.igem.org/JudgingJudging2008-10-09T12:05:38Z<p>Trichard: /* BioBrick standard variance requests */</p>
<hr />
<div><span style="color:red;">'''Note:''' </span> All Awards & Judging Criteria for iGEM 2008 are currently in draft form. The Awards & Judging details will be finalized in a few weeks. Please send any comments or suggestions for awards and judging by email to the judging committee at judging AT igem DOT org. For example, if you anticipate that your team will do something amazing or important, but that such a project would not be recognized via any of the mechanisms or awards below, let us know as soon as possible.<br />
<br />
<br />
<br />
===[[Judging/Judging_Criteria | Judging criteria]]===<br />
<br />
<br />
===[[Judging/Awards | Awards]]===<br />
<br />
<br />
===Important Dates===<br />
<br />
Be sure to study the official iGEM [[Calendar_of_Events | calendar]] to find out the final dates for different judging requirements.<br />
<br />
<br />
===BioBrick standard variance requests===<br />
One of the [[Requirements | requirements]] for iGEM is that teams are required to provide their parts to the Registry as standard biological parts in standard BioBrick plasmids. If a team wishes to use a different plasmid or different assembly method, they must document the new standard, explain their decision, and receive approval from iGEM Headquarters by the stated [[Calendar_of_Events | deadline]]. Please send your requests to judging AT igem DOT org.<br />
<br />
Here is a list of variance requests:<br />
# [[Judging/Variance/UCSF | UCSF]] ''(approved)''<br />
# [[Judging/Variance/Wisconsin | Wisconsin]] ''(denied)''<br />
# [[Judging/Variance/Cambridge| Cambridge]] ''(approved)''<br />
# [[Judging/Variance/LCG-UNAM Mexico | LCG-UNAM Mexico]] ''(under evaluation)''<br />
# [[Judging/Variance/Brown | Brown]] ''(under evaluation)''<br />
# [[Judging/Variance/Guelph | Guelph]] ''(under evaluation)''<br />
# [[Judging/Variance/BNU | Bejing Normal University]] ''(under evaluation)''<br />
# [[Judging/Variance/Lethbridge_CCS | Lethbridge CCS]] ''(under evaluation)''<br />
# [[Judging/Variance/Warsaw| Warsaw]] ''(under evaluation)''<br />
# [[Judging/Variance/Peking| Peking University]] ''(under evaluation)''<br />
# [[Judging/Variance/Freiburg| Freiburg]] ''(approved)''<br />
# [[Judging/Variance/UC Berkeley| UC Berkeley]] ''(approved)''<br />
# [[Judging/Variance/U. Michigan| U. Michigan]] ''(approved)''<br />
<br />
Click on an individual team to see their request.<br />
<br />
Those variance requests will be "denied" that ask to submit non-biobricked parts or non-standard plasmids to the registry, but do not propose and document a new standard. The relevant guidance is provided by item 6 of the iGEM 2008 [https://2008.igem.org/Requirements Requirements] page. <br />
<br />
The standard plasmid backbones that should be used for part submission are the pSB series in the Registry. These plasmid backbones can be found on the [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid plasmid page] on the Registry (partsregistry.org)<br />
<br />
The judges recognize that many parts will require different vectors for specific devices or applications. However, one of the fundamental principles of iGEM is that we are all making parts to share. Submitting parts on a standard vector allows for easy replication and distribution as well as use. While it is a bit more work to move a biobrick part from a dedicated device plasmid to a standard biobrick plasmid, that extra effort will facilitate sharing and interoperability and will be greatly appreciated by both your peers and those that come after you. We do encourage the development of new standard vectors, but want to see complete documentation and evidence that they work before allowing their use for parts submission to the registry.<br />
<br />
===Complaints===<br />
<br />
To file an official complaint regarding iGEM 2008 judging you must send an email to complaints AT igem DOT org. Your email should include your real name, the real name of your school and team, and the real name and email address of your faculty advisor. Your email must also be copied to your faculty advisor. In your email please clearly state your complaint and what you hope will happen as a result of filing your official complaint. The iGEM judging committee will work diligently to respond to all complaints as quickly as possible. Complaints that are sent to other email addresses, or that do not include the requested information will be ignored. All decisions by the judges regarding complaints are final.</div>Trichardhttp://2008.igem.org/Judging/Variance/UC_BerkeleyJudging/Variance/UC Berkeley2008-10-09T02:43:32Z<p>Trichard: New page: ===Request=== Dear iGEM Judges, I'm writing on behalf of the 2008 UC Berkeley iGEM Team to request permission to submit parts in the BBb standard of Biobricks to the registry for this ye...</p>
<hr />
<div>===Request===<br />
Dear iGEM Judges, <br />
<br />
I'm writing on behalf of the 2008 UC Berkeley iGEM Team to request permission to submit parts in the BBb standard of Biobricks to the registry for this year's Jamboree. <br />
<br />
For the second year in a row, the UC Berkeley iGEM team is using the BBb standard of Biobricks, where parts are flanked by BglII and BamHI sites rather than XbaI and SpeI sites. Over 1,000 parts have been developed in this standard and the BBb standard has been described and discussed in the BioBricks community. More information about this standard is described at http://openwetware.org/wiki/Arking:JCATutorialIntro1<br />
In the spirit of iGEM, we hope to share these parts with the community, and we are constructing them using biobricks, but with a variation on the original version. Given the strengths the BBb Biobrick standards, we hope you will accept our constructs for this year's competition.<br />
<br />
<br />
Thank you for your consideration, <br />
<br />
<br />
<br />
Madhvi Venkatesh (Anderson Lab)<br />
<br />
UC Berkeley iGEM Team <br />
===Response===<br />
Madhvi,<br />
<br />
Thanks for your email. Terrific / request approved!<br />
<br />
We would be grateful if you could please refer to the assembly standard that you are using as "BioBricks beta option 1" or "BBb1" for short. <br />
<br />
Several "BBb" standards have been proposed, developed, or are in use, and we are working to provide clarity across the world-wide BioBricks community. More information is online here: http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical/Formats<br />
<br />
Also, please coordinate with the Registry staff regarding how you will be preparing any submitted DNA so that they can prepare to handle any necessary BBb1 plasmids, et cetera.<br />
<br />
All best,<br />
Drew</div>Trichardhttp://2008.igem.org/JudgingJudging2008-10-09T02:41:38Z<p>Trichard: /* BioBrick standard variance requests */</p>
<hr />
<div><span style="color:red;">'''Note:''' </span> All Awards & Judging Criteria for iGEM 2008 are currently in draft form. The Awards & Judging details will be finalized in a few weeks. Please send any comments or suggestions for awards and judging by email to the judging committee at judging AT igem DOT org. For example, if you anticipate that your team will do something amazing or important, but that such a project would not be recognized via any of the mechanisms or awards below, let us know as soon as possible.<br />
<br />
<br />
<br />
===[[Judging/Judging_Criteria | Judging criteria]]===<br />
<br />
<br />
===[[Judging/Awards | Awards]]===<br />
<br />
<br />
===Important Dates===<br />
<br />
Be sure to study the official iGEM [[Calendar_of_Events | calendar]] to find out the final dates for different judging requirements.<br />
<br />
<br />
===BioBrick standard variance requests===<br />
One of the [[Requirements | requirements]] for iGEM is that teams are required to provide their parts to the Registry as standard biological parts in standard BioBrick plasmids. If a team wishes to use a different plasmid or different assembly method, they must document the new standard, explain their decision, and receive approval from iGEM Headquarters by the stated [[Calendar_of_Events | deadline]]. Please send your requests to judging AT igem DOT org.<br />
<br />
Here is a list of variance requests:<br />
# [[Judging/Variance/UCSF | UCSF]] ''(approved)''<br />
# [[Judging/Variance/Wisconsin | Wisconsin]] ''(denied)''<br />
# [[Judging/Variance/Cambridge| Cambridge]] ''(approved)''<br />
# [[Judging/Variance/LCG-UNAM Mexico | LCG-UNAM Mexico]] ''(under evaluation)''<br />
# [[Judging/Variance/Brown | Brown]] ''(under evaluation)''<br />
# [[Judging/Variance/Guelph | Guelph]] ''(under evaluation)''<br />
# [[Judging/Variance/BNU | Bejing Normal University]] ''(under evaluation)''<br />
# [[Judging/Variance/Lethbridge_CCS | Lethbridge CCS]] ''(under evaluation)''<br />
# [[Judging/Variance/Warsaw| Warsaw]] ''(under evaluation)''<br />
# [[Judging/Variance/Peking| Peking University]] ''(under evaluation)''<br />
# [[Judging/Variance/Freiburg| Freiburg]] ''(approved)''<br />
# [[Judging/Variance/UC Berkeley| UC Berkeley]] ''(approved)''<br />
<br />
Click on an individual team to see their request.<br />
<br />
Those variance requests will be "denied" that ask to submit non-biobricked parts or non-standard plasmids to the registry, but do not propose and document a new standard. The relevant guidance is provided by item 6 of the iGEM 2008 [https://2008.igem.org/Requirements Requirements] page. <br />
<br />
The standard plasmid backbones that should be used for part submission are the pSB series in the Registry. These plasmid backbones can be found on the [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid plasmid page] on the Registry (partsregistry.org)<br />
<br />
The judges recognize that many parts will require different vectors for specific devices or applications. However, one of the fundamental principles of iGEM is that we are all making parts to share. Submitting parts on a standard vector allows for easy replication and distribution as well as use. While it is a bit more work to move a biobrick part from a dedicated device plasmid to a standard biobrick plasmid, that extra effort will facilitate sharing and interoperability and will be greatly appreciated by both your peers and those that come after you. We do encourage the development of new standard vectors, but want to see complete documentation and evidence that they work before allowing their use for parts submission to the registry.<br />
<br />
===Complaints===<br />
<br />
To file an official complaint regarding iGEM 2008 judging you must send an email to complaints AT igem DOT org. Your email should include your real name, the real name of your school and team, and the real name and email address of your faculty advisor. Your email must also be copied to your faculty advisor. In your email please clearly state your complaint and what you hope will happen as a result of filing your official complaint. The iGEM judging committee will work diligently to respond to all complaints as quickly as possible. Complaints that are sent to other email addresses, or that do not include the requested information will be ignored. All decisions by the judges regarding complaints are final.</div>Trichardhttp://2008.igem.org/JudgingJudging2008-10-09T02:40:19Z<p>Trichard: /* BioBrick standard variance requests */</p>
<hr />
<div><span style="color:red;">'''Note:''' </span> All Awards & Judging Criteria for iGEM 2008 are currently in draft form. The Awards & Judging details will be finalized in a few weeks. Please send any comments or suggestions for awards and judging by email to the judging committee at judging AT igem DOT org. For example, if you anticipate that your team will do something amazing or important, but that such a project would not be recognized via any of the mechanisms or awards below, let us know as soon as possible.<br />
<br />
<br />
<br />
===[[Judging/Judging_Criteria | Judging criteria]]===<br />
<br />
<br />
===[[Judging/Awards | Awards]]===<br />
<br />
<br />
===Important Dates===<br />
<br />
Be sure to study the official iGEM [[Calendar_of_Events | calendar]] to find out the final dates for different judging requirements.<br />
<br />
<br />
===BioBrick standard variance requests===<br />
One of the [[Requirements | requirements]] for iGEM is that teams are required to provide their parts to the Registry as standard biological parts in standard BioBrick plasmids. If a team wishes to use a different plasmid or different assembly method, they must document the new standard, explain their decision, and receive approval from iGEM Headquarters by the stated [[Calendar_of_Events | deadline]]. Please send your requests to judging AT igem DOT org.<br />
<br />
Here is a list of variance requests:<br />
# [[Judging/Variance/UCSF | UCSF]] ''(approved)''<br />
# [[Judging/Variance/Wisconsin | Wisconsin]] ''(denied)''<br />
# [[Judging/Variance/Cambridge| Cambridge]] ''(approved)''<br />
# [[Judging/Variance/LCG-UNAM Mexico | LCG-UNAM Mexico]] ''(under evaluation)''<br />
# [[Judging/Variance/Brown | Brown]] ''(under evaluation)''<br />
# [[Judging/Variance/Guelph | Guelph]] ''(under evaluation)''<br />
# [[Judging/Variance/BNU | Bejing Normal University]] ''(under evaluation)''<br />
# [[Judging/Variance/Lethbridge_CCS | Lethbridge CCS]] ''(under evaluation)''<br />
# [[Judging/Variance/Warsaw| Warsaw]] ''(under evaluation)''<br />
# [[Judging/Variance/Peking| Peking University]] ''(under evaluation)''<br />
# [[Judging/Variance/Freiburg| Freiburg]] ''(approved)''<br />
<br />
Click on an individual team to see their request.<br />
<br />
Those variance requests will be "denied" that ask to submit non-biobricked parts or non-standard plasmids to the registry, but do not propose and document a new standard. The relevant guidance is provided by item 6 of the iGEM 2008 [https://2008.igem.org/Requirements Requirements] page. <br />
<br />
The standard plasmid backbones that should be used for part submission are the pSB series in the Registry. These plasmid backbones can be found on the [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid plasmid page] on the Registry (partsregistry.org)<br />
<br />
The judges recognize that many parts will require different vectors for specific devices or applications. However, one of the fundamental principles of iGEM is that we are all making parts to share. Submitting parts on a standard vector allows for easy replication and distribution as well as use. While it is a bit more work to move a biobrick part from a dedicated device plasmid to a standard biobrick plasmid, that extra effort will facilitate sharing and interoperability and will be greatly appreciated by both your peers and those that come after you. We do encourage the development of new standard vectors, but want to see complete documentation and evidence that they work before allowing their use for parts submission to the registry.<br />
<br />
===Complaints===<br />
<br />
To file an official complaint regarding iGEM 2008 judging you must send an email to complaints AT igem DOT org. Your email should include your real name, the real name of your school and team, and the real name and email address of your faculty advisor. Your email must also be copied to your faculty advisor. In your email please clearly state your complaint and what you hope will happen as a result of filing your official complaint. The iGEM judging committee will work diligently to respond to all complaints as quickly as possible. Complaints that are sent to other email addresses, or that do not include the requested information will be ignored. All decisions by the judges regarding complaints are final.</div>Trichardhttp://2008.igem.org/Judging/Variance/FreiburgJudging/Variance/Freiburg2008-10-09T02:39:47Z<p>Trichard: /* Response */</p>
<hr />
<div>===Request===<br />
Dear iGEM-judging team,<br />
<br />
representing 2008Žs team of the Albert-Ludwigs-Universität Freiburg, I am<br />
asking for permission to submit our parts in a non-standard vector, which is<br />
fully compatible to the standard cloning scheme (none of the<br />
Biobrick-restriction sites -except for pre- and suffix of the parts- occur<br />
in the vector), and which is in addition compatible with our extended<br />
restriction-site-system for fusion-proteins from last yearŽs proposal<br />
(details: <br />
https://2007.igem.org/Freiburg07/report_fusion_parts ).<br />
<br />
This is necessary, because we have to avoid the stop-codons generated by the<br />
Biobrick-scars. Unfortunately, the standard vector contains the additional<br />
restriction sites we use for our parts.<br />
<br />
As said, the vector ('pMA' from Geneart used for iGEM orders) would feature<br />
full compatibility, and the parts we want to submit fulfill all criteria of<br />
the Biobrick-standard. If you give us permission and need further<br />
information about the vector (sequence?), please let me know.<br />
<br />
Sincerely,<br />
<br />
Philipp<br />
<br />
===Response===<br />
Philipp,<br />
<br />
Request approved. Please coordinate with the Registry staff so that <br />
they are prepared to handle your plasmid. Also, please enter and <br />
describe the pMA vector as a new vector in the Registry database if it <br />
is not already so described.<br />
<br />
Thank you for providing the reference and documentation in your inquiry. The documentation was very helpful, and should be provided in the registry description for the pMA vector.<br />
<br />
Best,<br />
Drew and the iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/FreiburgJudging/Variance/Freiburg2008-10-09T02:36:44Z<p>Trichard: /* Response */</p>
<hr />
<div>===Request===<br />
Dear iGEM-judging team,<br />
<br />
representing 2008Žs team of the Albert-Ludwigs-Universität Freiburg, I am<br />
asking for permission to submit our parts in a non-standard vector, which is<br />
fully compatible to the standard cloning scheme (none of the<br />
Biobrick-restriction sites -except for pre- and suffix of the parts- occur<br />
in the vector), and which is in addition compatible with our extended<br />
restriction-site-system for fusion-proteins from last yearŽs proposal<br />
(details: <br />
http://parts.mit.edu/igem07/index.php/Freiburg07/report_fusion_parts ).<br />
<br />
This is necessary, because we have to avoid the stop-codons generated by the<br />
Biobrick-scars. Unfortunately, the standard vector contains the additional<br />
restriction sites we use for our parts.<br />
<br />
As said, the vector ('pMA' from Geneart used for iGEM orders) would feature<br />
full compatibility, and the parts we want to submit fulfill all criteria of<br />
the Biobrick-standard. If you give us permission and need further<br />
information about the vector (sequence?), please let me know.<br />
<br />
Sincerely,<br />
<br />
Philipp<br />
<br />
===Response===<br />
Dear Philipp,<br />
<br />
Your approach sounds reasonable. Just to be clear, is the vector that you would be submitting your parts open source, and available for free distribution? If so, then please submit your vector as a new part (including documentation), so that the registry has a standard, freely available plasmid that is compatible with your system for fusion-proteins. With the new vector in the registry, it would be appropriate to use that vector to submit your parts.<br />
<br />
Thanks you for writing and referencing the documentation, which was quite helpful.<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/FreiburgJudging/Variance/Freiburg2008-10-09T02:36:13Z<p>Trichard: /* Response */</p>
<hr />
<div>===Request===<br />
Dear iGEM-judging team,<br />
<br />
representing 2008Žs team of the Albert-Ludwigs-Universität Freiburg, I am<br />
asking for permission to submit our parts in a non-standard vector, which is<br />
fully compatible to the standard cloning scheme (none of the<br />
Biobrick-restriction sites -except for pre- and suffix of the parts- occur<br />
in the vector), and which is in addition compatible with our extended<br />
restriction-site-system for fusion-proteins from last yearŽs proposal<br />
(details: <br />
http://parts.mit.edu/igem07/index.php/Freiburg07/report_fusion_parts ).<br />
<br />
This is necessary, because we have to avoid the stop-codons generated by the<br />
Biobrick-scars. Unfortunately, the standard vector contains the additional<br />
restriction sites we use for our parts.<br />
<br />
As said, the vector ('pMA' from Geneart used for iGEM orders) would feature<br />
full compatibility, and the parts we want to submit fulfill all criteria of<br />
the Biobrick-standard. If you give us permission and need further<br />
information about the vector (sequence?), please let me know.<br />
<br />
Sincerely,<br />
<br />
Philipp<br />
<br />
===Response===<br />
Dear Philipp,<br />
<br />
Your approach sounds reasonable. Just to be clear, is the vector that you would be submitting your parts open source, and available for free distribution? If so, then please submit your vector as a new part (including documentation), so that the registry has a standard, freely available plasmid that is compatible with your system for fusion-proteins. With the new vector in the registry, it would be appropriate to use that vector to submit your parts.<br />
<br />
Thanks you for referencing the documentation.<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/FreiburgJudging/Variance/Freiburg2008-10-09T02:34:24Z<p>Trichard: New page: ===Request=== Dear iGEM-judging team, representing 2008Žs team of the Albert-Ludwigs-Universität Freiburg, I am asking for permission to submit our parts in a non-standard vector, which...</p>
<hr />
<div>===Request===<br />
Dear iGEM-judging team,<br />
<br />
representing 2008Žs team of the Albert-Ludwigs-Universität Freiburg, I am<br />
asking for permission to submit our parts in a non-standard vector, which is<br />
fully compatible to the standard cloning scheme (none of the<br />
Biobrick-restriction sites -except for pre- and suffix of the parts- occur<br />
in the vector), and which is in addition compatible with our extended<br />
restriction-site-system for fusion-proteins from last yearŽs proposal<br />
(details: <br />
http://parts.mit.edu/igem07/index.php/Freiburg07/report_fusion_parts ).<br />
<br />
This is necessary, because we have to avoid the stop-codons generated by the<br />
Biobrick-scars. Unfortunately, the standard vector contains the additional<br />
restriction sites we use for our parts.<br />
<br />
As said, the vector ('pMA' from Geneart used for iGEM orders) would feature<br />
full compatibility, and the parts we want to submit fulfill all criteria of<br />
the Biobrick-standard. If you give us permission and need further<br />
information about the vector (sequence?), please let me know.<br />
<br />
Sincerely,<br />
<br />
Philipp<br />
<br />
===Response===<br />
Dear Philipp,<br />
<br />
Your approach sounds reasonable. Just to be clear, is the vector that you would be submitting your parts on open source? If so, then please submit that vector as a part so that the registry has a standard, freely available plasmid that is compatible with your system for fusion-proteins. With the vector in the registry, it would be perfectly appropriate to use that vector to submit your parts.<br />
<br />
Thanks you for referencing the documentation.<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/JudgingJudging2008-10-09T02:26:37Z<p>Trichard: /* BioBrick standard variance requests */</p>
<hr />
<div><span style="color:red;">'''Note:''' </span> All Awards & Judging Criteria for iGEM 2008 are currently in draft form. The Awards & Judging details will be finalized in a few weeks. Please send any comments or suggestions for awards and judging by email to the judging committee at judging AT igem DOT org. For example, if you anticipate that your team will do something amazing or important, but that such a project would not be recognized via any of the mechanisms or awards below, let us know as soon as possible.<br />
<br />
<br />
<br />
===[[Judging/Judging_Criteria | Judging criteria]]===<br />
<br />
<br />
===[[Judging/Awards | Awards]]===<br />
<br />
<br />
===Important Dates===<br />
<br />
Be sure to study the official iGEM [[Calendar_of_Events | calendar]] to find out the final dates for different judging requirements.<br />
<br />
<br />
===BioBrick standard variance requests===<br />
One of the [[Requirements | requirements]] for iGEM is that teams are required to provide their parts to the Registry as standard biological parts in standard BioBrick plasmids. If a team wishes to use a different plasmid or different assembly method, they must document the new standard, explain their decision, and receive approval from iGEM Headquarters by the stated [[Calendar_of_Events | deadline]]. Please send your requests to judging AT igem DOT org.<br />
<br />
Here is a list of variance requests:<br />
# [[Judging/Variance/UCSF | UCSF]] ''(approved)''<br />
# [[Judging/Variance/Wisconsin | Wisconsin]] ''(denied)''<br />
# [[Judging/Variance/Cambridge| Cambridge]] ''(approved)''<br />
# [[Judging/Variance/LCG-UNAM Mexico | LCG-UNAM Mexico]] ''(under evaluation)''<br />
# [[Judging/Variance/Brown | Brown]] ''(under evaluation)''<br />
# [[Judging/Variance/Guelph | Guelph]] ''(under evaluation)''<br />
# [[Judging/Variance/BNU | Bejing Normal University]] ''(under evaluation)''<br />
# [[Judging/Variance/Lethbridge_CCS | Lethbridge CCS]] ''(under evaluation)''<br />
# [[Judging/Variance/Warsaw| Warsaw]] ''(under evaluation)''<br />
# [[Judging/Variance/Peking| Peking University]] ''(under evaluation)''<br />
# [[Judging/Variance/Freiburg| Freiburg]] ''(under evaluation)''<br />
<br />
Click on an individual team to see their request.<br />
<br />
Those variance requests will be "denied" that ask to submit non-biobricked parts or non-standard plasmids to the registry, but do not propose and document a new standard. The relevant guidance is provided by item 6 of the iGEM 2008 [https://2008.igem.org/Requirements Requirements] page. <br />
<br />
The standard plasmid backbones that should be used for part submission are the pSB series in the Registry. These plasmid backbones can be found on the [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid plasmid page] on the Registry (partsregistry.org)<br />
<br />
The judges recognize that many parts will require different vectors for specific devices or applications. However, one of the fundamental principles of iGEM is that we are all making parts to share. Submitting parts on a standard vector allows for easy replication and distribution as well as use. While it is a bit more work to move a biobrick part from a dedicated device plasmid to a standard biobrick plasmid, that extra effort will facilitate sharing and interoperability and will be greatly appreciated by both your peers and those that come after you. We do encourage the development of new standard vectors, but want to see complete documentation and evidence that they work before allowing their use for parts submission to the registry.<br />
<br />
===Complaints===<br />
<br />
To file an official complaint regarding iGEM 2008 judging you must send an email to complaints AT igem DOT org. Your email should include your real name, the real name of your school and team, and the real name and email address of your faculty advisor. Your email must also be copied to your faculty advisor. In your email please clearly state your complaint and what you hope will happen as a result of filing your official complaint. The iGEM judging committee will work diligently to respond to all complaints as quickly as possible. Complaints that are sent to other email addresses, or that do not include the requested information will be ignored. All decisions by the judges regarding complaints are final.</div>Trichardhttp://2008.igem.org/Judging/Variance/CambridgeJudging/Variance/Cambridge2008-10-08T17:38:50Z<p>Trichard: /* Request */</p>
<hr />
<div>===Request===<br />
Dear iGEM Judges,<br />
<br />
I'm writing on behalf of the 2008 Cambridge iGEM team. Much of our<br />
work this summer involves investigating the use Bacillus subtilis as<br />
an iGEM chassis. In order to do so, we are creating a new set of<br />
Bacillus-compatible ectopic and integrational BioBrick plasmids. These<br />
plasmids combine ORFs from various sources, including homology regions<br />
to facilitate chromosomal insertion, a gram-positive replication<br />
origin, a BioBrick backbone, and standard PCR sites. They will<br />
contain appropriate Biobrick cut sites and scars, and the sequences<br />
are therefore indistinguishable from the existing standard.<br />
<br />
However, to efficiently assemble these 'Frankenstein' vectors we<br />
utilized the In-Fusion method from ClonTech [1]. In-Fusion uses 15<br />
base pair regions of homology between the ends of linear DNA fragments<br />
to join them together. This approach has many advantages over<br />
traditional digestion/ligation, including the ability to assemble as<br />
many as 4 or 5 pieces together in a single step. You can see a<br />
schematic of the approach on our wiki [2].<br />
<br />
The In-Fusion method only complements the BioBrick standard, and the<br />
majority of our constructs this year were generated using traditional<br />
ligation. However, the ability to rapidly and easily assemble multiple<br />
fragments at once has been invaluable, and as the cost of oligos<br />
continues to fall, we believe this new assembly method will become<br />
increasingly attractive to Synthetic Biology.<br />
<br />
While this method is currently proprietary and somewhat<br />
cost-prohibitive, one of our long-term focuses is to create an<br />
Open-Source version that can be widely adopted for future iGEM teams.<br />
<br />
We look forward to sharing these vectors with the iGEM community and<br />
speaking about their assembly during our presentation at the Jamboree.<br />
We hope you will accept these new vectors for the competition this<br />
year.<br />
<br />
Thank you,<br />
<br />
Daniel Goodman and the University of Cambridge iGEM Team<br />
<br />
[1] http://www.clontech.com/products/detail.asp?product_id=162275&tabno=2<br />
<br />
[2] http://openwetware.org/wiki/IGEM:Cambridge/2008/Notebook/Bacillus<br />
<br />
===Response===<br />
Daniel,<br />
<br />
Thank you for your detailed email. Request approved. Please <br />
carefully document all differences from the BBa standard in your <br />
submissions and online materials, and how the two methods are <br />
related / compatible (and when they are not).<br />
<br />
Also, we would be grateful if you could provide a brief written <br />
summary in some distributable format for how the team believes an open <br />
version of the method you described should be structured (i.e., <br />
standardized) so that we can begin to develop support for such an <br />
approach.<br />
<br />
Best,<br />
Drew</div>Trichardhttp://2008.igem.org/Judging/Variance/CambridgeJudging/Variance/Cambridge2008-10-08T17:38:33Z<p>Trichard: </p>
<hr />
<div>===Request===<br />
Dear iGEM Judges,<br />
<br />
I'm writing on behalf of the 2008 Cambridge iGEM team. Much of our<br />
work this summer involves investigating the use Bacillus subtilis as<br />
an iGEM chassis. In order to do so, we are creating a new set of<br />
Bacillus-compatible ectopic and integrational BioBrick plasmids. These<br />
plasmids combine ORFs from various sources, including homology regions<br />
to facilitate chromosomal insertion, a gram-positive replication<br />
origin, a BioBrick backbone, and standard PCR sites. They will<br />
contain appropriate Biobrick cut sites and scars, and the sequences<br />
are therefore indistinguishable from the existing standard.<br />
<br />
However, to efficiently assemble these 'Frankenstein' vectors we<br />
utilized the In-Fusion method from ClonTech [1]. In-Fusion uses 15<br />
base pair regions of homology between the ends of linear DNA fragments<br />
to join them together. This approach has many advantages over<br />
traditional digestion/ligation, including the ability to assemble as<br />
many as 4 or 5 pieces together in a single step. You can see a<br />
schematic of the approach on our wiki [2].<br />
<br />
The In-Fusion method only complements the BioBrick standard, and the<br />
majority of our constructs this year were generated using traditional<br />
ligation. However, the ability to rapidly and easily assemble multiple<br />
fragments at once has been invaluable, and as the cost of oligos<br />
continues to fall, we believe this new assembly method will become<br />
increasingly attractive to Synthetic Biology.<br />
<br />
While this method is currently proprietary and somewhat<br />
cost-prohibitive, one of our long-term focuses is to create an<br />
Open-Source version that can be widely adopted for future iGEM teams.<br />
<br />
We look forward to sharing these vectors with the iGEM community and<br />
speaking about their assembly during our presentation at the Jamboree.<br />
We hope you will accept these new vectors for the competition this<br />
year.<br />
<br />
Thank you,<br />
<br />
Daniel Goodman and the University of Cambridge iGEM Team<br />
<br />
[1] http://www.clontech.com/products/detail.asp?product_id=162275&tabno=2<br />
[2] http://openwetware.org/wiki/IGEM:Cambridge/2008/Notebook/Bacillus<br />
<br />
===Response===<br />
Daniel,<br />
<br />
Thank you for your detailed email. Request approved. Please <br />
carefully document all differences from the BBa standard in your <br />
submissions and online materials, and how the two methods are <br />
related / compatible (and when they are not).<br />
<br />
Also, we would be grateful if you could provide a brief written <br />
summary in some distributable format for how the team believes an open <br />
version of the method you described should be structured (i.e., <br />
standardized) so that we can begin to develop support for such an <br />
approach.<br />
<br />
Best,<br />
Drew</div>Trichardhttp://2008.igem.org/Judging/Variance/CambridgeJudging/Variance/Cambridge2008-10-08T17:38:05Z<p>Trichard: New page: ===Request=== Dear iGEM Judges, I'm writing on behalf of the 2008 Cambridge iGEM team. Much of our work this summer involves investigating the use Bacillus subtilis as an iGEM chassis. ...</p>
<hr />
<div>===Request===<br />
Dear iGEM Judges,<br />
<br />
I'm writing on behalf of the 2008 Cambridge iGEM team. Much of our<br />
work this summer involves investigating the use Bacillus subtilis as<br />
an iGEM chassis. In order to do so, we are creating a new set of<br />
Bacillus-compatible ectopic and integrational BioBrick plasmids. These<br />
plasmids combine ORFs from various sources, including homology regions<br />
to facilitate chromosomal insertion, a gram-positive replication<br />
origin, a BioBrick backbone, and standard PCR sites. They will<br />
contain appropriate Biobrick cut sites and scars, and the sequences<br />
are therefore indistinguishable from the existing standard.<br />
<br />
However, to efficiently assemble these 'Frankenstein' vectors we<br />
utilized the In-Fusion method from ClonTech [1]. In-Fusion uses 15<br />
base pair regions of homology between the ends of linear DNA fragments<br />
to join them together. This approach has many advantages over<br />
traditional digestion/ligation, including the ability to assemble as<br />
many as 4 or 5 pieces together in a single step. You can see a<br />
schematic of the approach on our wiki [2].<br />
<br />
The In-Fusion method only complements the BioBrick standard, and the<br />
majority of our constructs this year were generated using traditional<br />
ligation. However, the ability to rapidly and easily assemble multiple<br />
fragments at once has been invaluable, and as the cost of oligos<br />
continues to fall, we believe this new assembly method will become<br />
increasingly attractive to Synthetic Biology.<br />
<br />
While this method is currently proprietary and somewhat<br />
cost-prohibitive, one of our long-term focuses is to create an<br />
Open-Source version that can be widely adopted for future iGEM teams.<br />
<br />
We look forward to sharing these vectors with the iGEM community and<br />
speaking about their assembly during our presentation at the Jamboree.<br />
We hope you will accept these new vectors for the competition this<br />
year.<br />
<br />
Thank you,<br />
Daniel Goodman and the University of Cambridge iGEM Team<br />
<br />
[1] http://www.clontech.com/products/detail.asp?product_id=162275&tabno=2<br />
[2] http://openwetware.org/wiki/IGEM:Cambridge/2008/Notebook/Bacillus<br />
<br />
===Response===<br />
Daniel,<br />
<br />
Thank you for your detailed email. Request approved. Please <br />
carefully document all differences from the BBa standard in your <br />
submissions and online materials, and how the two methods are <br />
related / compatible (and when they are not).<br />
<br />
Also, we would be grateful if you could provide a brief written <br />
summary in some distributable format for how the team believes an open <br />
version of the method you described should be structured (i.e., <br />
standardized) so that we can begin to develop support for such an <br />
approach.<br />
<br />
Best,<br />
Drew</div>Trichardhttp://2008.igem.org/JudgingJudging2008-10-08T17:36:37Z<p>Trichard: /* BioBrick standard variance requests */</p>
<hr />
<div><span style="color:red;">'''Note:''' </span> All Awards & Judging Criteria for iGEM 2008 are currently in draft form. The Awards & Judging details will be finalized in a few weeks. Please send any comments or suggestions for awards and judging by email to the judging committee at judging AT igem DOT org. For example, if you anticipate that your team will do something amazing or important, but that such a project would not be recognized via any of the mechanisms or awards below, let us know as soon as possible.<br />
<br />
<br />
<br />
===[[Judging/Judging_Criteria | Judging criteria]]===<br />
<br />
<br />
===[[Judging/Awards | Awards]]===<br />
<br />
<br />
===Important Dates===<br />
<br />
Be sure to study the official iGEM [[Calendar_of_Events | calendar]] to find out the final dates for different judging requirements.<br />
<br />
<br />
===BioBrick standard variance requests===<br />
One of the [[Requirements | requirements]] for iGEM is that teams are required to provide their parts to the Registry as standard biological parts in standard BioBrick plasmids. If a team wishes to use a different plasmid or different assembly method, they must document the new standard, explain their decision, and receive approval from iGEM Headquarters by the stated [[Calendar_of_Events | deadline]]. Please send your requests to judging AT igem DOT org.<br />
<br />
Here is a list of variance requests:<br />
# [[Judging/Variance/UCSF | UCSF]] ''(approved)''<br />
# [[Judging/Variance/Wisconsin | Wisconsin]] ''(denied)''<br />
# [[Judging/Variance/Cambridge| Cambridge]] ''(approved)''<br />
# [[Judging/Variance/LCG-UNAM Mexico | LCG-UNAM Mexico]] ''(under evaluation)''<br />
# [[Judging/Variance/Brown | Brown]] ''(under evaluation)''<br />
# [[Judging/Variance/Guelph | Guelph]] ''(under evaluation)''<br />
# [[Judging/Variance/BNU | Bejing Normal University]] ''(under evaluation)''<br />
# [[Judging/Variance/Lethbridge_CCS | Lethbridge CCS]] ''(under evaluation)''<br />
# [[Judging/Variance/Warsaw| Warsaw]] ''(under evaluation)''<br />
# [[Judging/Variance/Peking| Peking University]] ''(under evaluation)''<br />
<br />
Click on an individual team to see their request.<br />
<br />
Those variance requests will be "denied" that ask to submit non-biobricked parts or non-standard plasmids to the registry, but do not propose and document a new standard. The relevant guidance is provided by item 6 of the iGEM 2008 [https://2008.igem.org/Requirements Requirements] page. <br />
<br />
The standard plasmid backbones that should be used for part submission are the pSB series in the Registry. These plasmid backbones can be found on the [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid plasmid page] on the Registry (partsregistry.org)<br />
<br />
The judges recognize that many parts will require different vectors for specific devices or applications. However, one of the fundamental principles of iGEM is that we are all making parts to share. Submitting parts on a standard vector allows for easy replication and distribution as well as use. While it is a bit more work to move a biobrick part from a dedicated device plasmid to a standard biobrick plasmid, that extra effort will facilitate sharing and interoperability and will be greatly appreciated by both your peers and those that come after you. We do encourage the development of new standard vectors, but want to see complete documentation and evidence that they work before allowing their use for parts submission to the registry.<br />
<br />
===Complaints===<br />
<br />
To file an official complaint regarding iGEM 2008 judging you must send an email to complaints AT igem DOT org. Your email should include your real name, the real name of your school and team, and the real name and email address of your faculty advisor. Your email must also be copied to your faculty advisor. In your email please clearly state your complaint and what you hope will happen as a result of filing your official complaint. The iGEM judging committee will work diligently to respond to all complaints as quickly as possible. Complaints that are sent to other email addresses, or that do not include the requested information will be ignored. All decisions by the judges regarding complaints are final.</div>Trichardhttp://2008.igem.org/Judging/Variance/PekingJudging/Variance/Peking2008-10-08T17:22:50Z<p>Trichard: /* Response */</p>
<hr />
<div>===Request===<br />
<br />
Dear iGEM Judges,<br />
I'm writing on behalf of 2008 Peking University iGEM Team to ask for permission to send non-biobrick parts to the registry for the jamboree. <br />
<br />
As we can not find effective vectors for yeast expression in the registry, our team has been using the pGREG series of plasmids for yeast protein expression. We have to use the promoter which is sensitive to lacI or Gal4, so those yeast plasmids in the registry can not serve this function. For the same reason our parts can not flank the four standard restriction sites since our vector contains these four or at least some of these four. Of course, we are trying to standardize the parts we have constructed but it seems the time is limited. We wonder if we can send those plasmids based on PGREG backbone. <br />
<br />
<br />
Moreover, since our project has something to do the precise spot mutation of gal4, those plasmids contain gal4 or gal4 delta gene can not be standardized. As gal4 gene also contain some of the four restriction sites. <br />
<br />
<br />
Another thing that should be mentioned is that our gene hAIDsc is a codon optimized gene kindly offered by Pro. Youri. I am not sure whether he permits us to send this part to open source. <br />
<br />
Thank you very much!<br />
<br />
Zhou Zhou<br />
College of Life Sciences, Peking University<br />
Beijing, 100871<br />
P.R.China<br />
mikezzchina@gmail.com<br />
<br />
===Response===<br />
Dear Zhou,<br />
<br />
It seems like there are three separate issues you are inquiring about. <br />
<br />
The first issue is a problem with the limited number of yeast vectors in the registry, and the need for one that is compatible with your lacI and Gal4 sensitive promotor. The best solution to that would be to add a new vector to the registry, which we would welcome with appropriate documentation. You chose the pGREG series of plasmids, but this series contains the standard restriction sites for biobricks, which makes it incompatible with standard registry parts and thus not a great candidate for addition to the registry. There are two solutions to this problem: 1) make the pGREG vector compatible with biobrick parts, possibly (and with luck) by deleting the current biobrick restriction sites from the vector; or 2) create and document a new assembly standard. The Silver lab has done the later, which you might consider: http://openwetware.org/wiki/Silver:_BB_Strategy . The Silver lab approach, with a twist, is being adopted by the iGEM team from Brown University, as described on our judging variance request website:<br />
https://2008.igem.org/Judging/Variance/Brown<br />
<br />
The second issue, which at least partially derives from the first, is that your parts do not have biobricked ends. If you are proposing a new biobrick part standard, then you will need to carefully document that standard and propose it to the registry. In that absence of a new standard proposal, you should move your parts to a standard biobrick vector for submission. While we recognize that time is now short, this is not a new issue for your team, and should have been obvious as soon as you began working on your design.<br />
<br />
<br />
Finally, please do try to obtain permission to submit hAIDsc to the registry as an open source part. If permission is not provided, then you should not submit that part. A core principle of iGEM is that we all gain by sharing, and the registry cannot maintain or distribute parts that are not open source/open access.<br />
<br />
Please provide additional information about issues 1) and 2) if you plan to propose new assembly or part standards. While this will be a challenge, it is also a great opportunity to make a contribution to the community.<br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/PekingJudging/Variance/Peking2008-10-08T17:15:32Z<p>Trichard: /* Request */</p>
<hr />
<div>===Request===<br />
<br />
Dear iGEM Judges,<br />
<br />
I'm writing on behalf of 2008 Peking University iGEM Team to ask for permission to send non-biobrick parts to the registry for the jamboree. <br />
<br />
As we can not find effective vectors for yeast expression in the registry, our team has been using the pGREG series of plasmids for yeast protein expression. We have to use the promoter which is sensitive to lacI or Gal4, so those yeast plasmids in the registry can not serve this function. For the same reason our parts can not flank the four standard restriction sites since our vector contains these four or at least some of these four. Of course, we are trying to standardize the parts we have constructed but it seems the time is limited. We wonder if we can send those plasmids based on PGREG backbone. <br />
<br />
<br />
Moreover, since our project has something to do the precise spot mutation of gal4, those plasmids contain gal4 or gal4 delta gene can not be standardized. As gal4 gene also contain some of the four restriction sites. <br />
<br />
<br />
Another thing that should be mentioned is that our gene hAIDsc is a codon optimized gene kindly offered by Pro. Youri. I am not sure whether he permits us to send this part to open source. <br />
<br />
Thank you very much!<br />
<br />
Zhou Zhou<br />
College of Life Sciences, Peking University<br />
Beijing, 100871<br />
P.R.China<br />
mikezzchina@gmail.com<br />
<br />
===Response===<br />
Dear Zhou,<br />
<br />
It seems like there are three separate issues you are inquiring about. <br />
<br />
The first issue is a problem with the limited number of yeast vectors in the registry, and the need for one that is compatible with your lacI and Gal4 sensitive promotor. The appropriate solution to that would be to add a new vector to the registry, which we would welcome. You chose the pGREG series of plasmids, but this series contains the standard restriction sites for biobricks, which makes it incompatible with standard registry parts. There are two solutions to this problem: 1) make the pGREG vector compatible with biobricking, possibly (and with luck) by deleting those biobrick restriction sites from the vector; or 2) create and document a new assembly standard. The Silver lab has done the later, which you might consider: http://openwetware.org/wiki/Silver:_BB_Strategy . The Silver lab approach, with a twist, is being adopted by the iGEM team from Brown University, as described on our judging variance request website:<br />
https://2008.igem.org/Judging/Variance/Brown<br />
<br />
The second issue, which at least partially derives from the first, is that your parts do not have biobricked ends. If you are proposing a new biobrick part standard, then you will need to carefully document that standard and propose it to the registry. In that absence of a new standard proposal, submitting parts that are not in biobrick format will not be useful to the registry. <br />
<br />
<br />
Finally, please try to obtain permission to submit hAIDsc to the registry as an open source part. If permission is not provided, then you should not submit that part.<br />
<br />
Please provide additional information about issues 1) and 2) if you plan to propose new assembly or part standards. While this will be a challenge, it is also a great opportunity to make a contribution to the community.<br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/PekingJudging/Variance/Peking2008-10-08T17:15:13Z<p>Trichard: </p>
<hr />
<div>===Request===<br />
<br />
Dear iGEM Judges,<br />
I'm writing on behalf of 2008 Peking University iGEM Team to ask for permission to send non-biobrick parts to the registry for the jamboree. <br />
<br />
As we can not find effective vectors for yeast expression in the registry, our team has been using the pGREG series of plasmids for yeast protein expression. We have to use the promoter which is sensitive to lacI or Gal4, so those yeast plasmids in the registry can not serve this function. For the same reason our parts can not flank the four standard restriction sites since our vector contains these four or at least some of these four. Of course, we are trying to standardize the parts we have constructed but it seems the time is limited. We wonder if we can send those plasmids based on PGREG backbone. <br />
<br />
<br />
Moreover, since our project has something to do the precise spot mutation of gal4, those plasmids contain gal4 or gal4 delta gene can not be standardized. As gal4 gene also contain some of the four restriction sites. <br />
<br />
<br />
Another thing that should be mentioned is that our gene hAIDsc is a codon optimized gene kindly offered by Pro. Youri. I am not sure whether he permits us to send this part to open source. <br />
<br />
Thank you very much!<br />
<br />
Zhou Zhou<br />
College of Life Sciences, Peking University<br />
Beijing, 100871<br />
P.R.China<br />
mikezzchina@gmail.com<br />
<br />
===Response===<br />
Dear Zhou,<br />
<br />
It seems like there are three separate issues you are inquiring about. <br />
<br />
The first issue is a problem with the limited number of yeast vectors in the registry, and the need for one that is compatible with your lacI and Gal4 sensitive promotor. The appropriate solution to that would be to add a new vector to the registry, which we would welcome. You chose the pGREG series of plasmids, but this series contains the standard restriction sites for biobricks, which makes it incompatible with standard registry parts. There are two solutions to this problem: 1) make the pGREG vector compatible with biobricking, possibly (and with luck) by deleting those biobrick restriction sites from the vector; or 2) create and document a new assembly standard. The Silver lab has done the later, which you might consider: http://openwetware.org/wiki/Silver:_BB_Strategy . The Silver lab approach, with a twist, is being adopted by the iGEM team from Brown University, as described on our judging variance request website:<br />
https://2008.igem.org/Judging/Variance/Brown<br />
<br />
The second issue, which at least partially derives from the first, is that your parts do not have biobricked ends. If you are proposing a new biobrick part standard, then you will need to carefully document that standard and propose it to the registry. In that absence of a new standard proposal, submitting parts that are not in biobrick format will not be useful to the registry. <br />
<br />
<br />
Finally, please try to obtain permission to submit hAIDsc to the registry as an open source part. If permission is not provided, then you should not submit that part.<br />
<br />
Please provide additional information about issues 1) and 2) if you plan to propose new assembly or part standards. While this will be a challenge, it is also a great opportunity to make a contribution to the community.<br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/PekingJudging/Variance/Peking2008-10-08T16:47:59Z<p>Trichard: /* Request */</p>
<hr />
<div>===Request===<br />
<br />
Dear iGEM Judges,<br />
I'm writing on behalf of 2008 Peking University iGEM Team to ask for permission to send non-biobrick parts to the registry for the jamboree. <br />
As we can not find effective vectors for yeast expression in the registry, our team has been using the pGREG series of plasmids for yeast protein expression. We have to use the promoter which is sensitive to lacI or Gal4, so those yeast plasmids in the registry can not serve this function. For the same reason our parts can not flank the four standard restriction sites since our vector contains these four or at least some of these four. Of course, we are trying to standardize the parts we have constructed but it seems the time is limited. We wonder if we can send those plasmids based on PGREG backbone. <br />
Moreover, since our project has something to do the precise spot mutation of gal4, those plasmids contain gal4 or gal4 delta gene can not be standardized. As gal4 gene also contain some of the four restriction sites. <br />
Another thing that should be mentioned is that our gene hAIDsc is a codon optimized gene kindly offered by Pro. Youri. I am not sure whether he permits us to send this part to open source. <br />
Thank you very much!<br />
<br />
Zhou Zhou<br />
College of Life Sciences, Peking University<br />
Beijing, 100871<br />
P.R.China<br />
mikezzchina@gmail.com<br />
<br />
===Response===<br />
Dear Zhou,<br />
<br />
It seems like there are three separate issues you are inquiring about. <br />
<br />
The first issue is a problem with the limited number of yeast vectors in the registry, and the need for one that is compatible with your lacI and Gal4 sensitive promotor. The appropriate solution to that would be to add a new vector to the registry, which we would welcome. You chose the pGREG series of plasmids, but this series contains the standard restriction sites for biobricks, which makes it incompatible with standard registry parts. There are two solutions to this problem: 1) make the pGREG vector compatible with biobricking, possibly (and with luck) by deleting those biobrick restriction sites from the vector; or 2) create and document a new assembly standard. The Silver lab has done the later, which you might consider: http://openwetware.org/wiki/Silver:_BB_Strategy . The Silver lab approach, with a twist, is being adopted by the iGEM team from Brown University, as described on our judging variance request website:<br />
https://2008.igem.org/Judging/Variance/Brown<br />
<br />
The second issue, which at least partially derives from the first, is that your parts do not have biobricked ends. If you are proposing a new biobrick part standard, then you will need to carefully document that standard and propose it to the registry. In that absence of a new standard proposal, submitting parts that are not in biobrick format will not be useful to the registry. <br />
<br />
<br />
Finally, please try to obtain permission to submit hAIDsc to the registry as an open source part. If permission is not provided, then you should not submit that part.<br />
<br />
Please provide additional information about issues 1) and 2) if you plan to propose new assembly or part standards. While this will be a challenge, it is also a great opportunity to make a contribution to the community.<br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/PekingJudging/Variance/Peking2008-10-08T16:47:39Z<p>Trichard: New page: ===Request=== Dear iGEM Judges, I'm writing on behalf of 2008 Peking University iGEM Team to ask for permission to send non-biobrick parts to the registry for the jamboree. As...</p>
<hr />
<div>===Request===<br />
Dear iGEM Judges,<br />
I'm writing on behalf of 2008 Peking University iGEM Team to ask for permission to send non-biobrick parts to the registry for the jamboree. <br />
As we can not find effective vectors for yeast expression in the registry, our team has been using the pGREG series of plasmids for yeast protein expression. We have to use the promoter which is sensitive to lacI or Gal4, so those yeast plasmids in the registry can not serve this function. For the same reason our parts can not flank the four standard restriction sites since our vector contains these four or at least some of these four. Of course, we are trying to standardize the parts we have constructed but it seems the time is limited. We wonder if we can send those plasmids based on PGREG backbone. <br />
Moreover, since our project has something to do the precise spot mutation of gal4, those plasmids contain gal4 or gal4 delta gene can not be standardized. As gal4 gene also contain some of the four restriction sites. <br />
Another thing that should be mentioned is that our gene hAIDsc is a codon optimized gene kindly offered by Pro. Youri. I am not sure whether he permits us to send this part to open source. <br />
Thank you very much!<br />
<br />
Zhou Zhou<br />
College of Life Sciences, Peking University<br />
Beijing, 100871<br />
P.R.China<br />
mikezzchina@gmail.com<br />
<br />
===Response===<br />
Dear Zhou,<br />
<br />
It seems like there are three separate issues you are inquiring about. <br />
<br />
The first issue is a problem with the limited number of yeast vectors in the registry, and the need for one that is compatible with your lacI and Gal4 sensitive promotor. The appropriate solution to that would be to add a new vector to the registry, which we would welcome. You chose the pGREG series of plasmids, but this series contains the standard restriction sites for biobricks, which makes it incompatible with standard registry parts. There are two solutions to this problem: 1) make the pGREG vector compatible with biobricking, possibly (and with luck) by deleting those biobrick restriction sites from the vector; or 2) create and document a new assembly standard. The Silver lab has done the later, which you might consider: http://openwetware.org/wiki/Silver:_BB_Strategy . The Silver lab approach, with a twist, is being adopted by the iGEM team from Brown University, as described on our judging variance request website:<br />
https://2008.igem.org/Judging/Variance/Brown<br />
<br />
The second issue, which at least partially derives from the first, is that your parts do not have biobricked ends. If you are proposing a new biobrick part standard, then you will need to carefully document that standard and propose it to the registry. In that absence of a new standard proposal, submitting parts that are not in biobrick format will not be useful to the registry. <br />
<br />
<br />
Finally, please try to obtain permission to submit hAIDsc to the registry as an open source part. If permission is not provided, then you should not submit that part.<br />
<br />
Please provide additional information about issues 1) and 2) if you plan to propose new assembly or part standards. While this will be a challenge, it is also a great opportunity to make a contribution to the community.<br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/JudgingJudging2008-10-08T16:36:09Z<p>Trichard: /* BioBrick standard variance requests */</p>
<hr />
<div><span style="color:red;">'''Note:''' </span> All Awards & Judging Criteria for iGEM 2008 are currently in draft form. The Awards & Judging details will be finalized in a few weeks. Please send any comments or suggestions for awards and judging by email to the judging committee at judging AT igem DOT org. For example, if you anticipate that your team will do something amazing or important, but that such a project would not be recognized via any of the mechanisms or awards below, let us know as soon as possible.<br />
<br />
<br />
<br />
===[[Judging/Judging_Criteria | Judging criteria]]===<br />
<br />
<br />
===[[Judging/Awards | Awards]]===<br />
<br />
<br />
===Important Dates===<br />
<br />
Be sure to study the official iGEM [[Calendar_of_Events | calendar]] to find out the final dates for different judging requirements.<br />
<br />
<br />
===BioBrick standard variance requests===<br />
One of the [[Requirements | requirements]] for iGEM is that teams are required to provide their parts to the Registry as standard biological parts in standard BioBrick plasmids. If a team wishes to use a different plasmid or different assembly method, they must document the new standard, explain their decision, and receive approval from iGEM Headquarters by the stated [[Calendar_of_Events | deadline]]. Please send your requests to judging AT igem DOT org.<br />
<br />
Here is a list of variance requests:<br />
# [[Judging/Variance/UCSF | UCSF]] ''(approved)''<br />
# [[Judging/Variance/Wisconsin | Wisconsin]] ''(denied)''<br />
# [[Judging/Variance/LCG-UNAM Mexico | LCG-UNAM Mexico]] ''(under evaluation)''<br />
# [[Judging/Variance/Brown | Brown]] ''(under evaluation)''<br />
# [[Judging/Variance/Guelph | Guelph]] ''(under evaluation)''<br />
# [[Judging/Variance/BNU | Bejing Normal University]] ''(under evaluation)''<br />
# [[Judging/Variance/Lethbridge_CCS | Lethbridge CCS]] ''(under evaluation)''<br />
# [[Judging/Variance/Warsaw| Warsaw]] ''(under evaluation)''<br />
# [[Judging/Variance/Peking| Peking University]] ''(under evaluation)''<br />
<br />
Click on an individual team to see their request.<br />
<br />
Those variance requests will be "denied" that ask to submit non-biobricked parts or non-standard plasmids to the registry, but do not propose and document a new standard. The relevant guidance is provided by item 6 of the iGEM 2008 [https://2008.igem.org/Requirements Requirements] page. <br />
<br />
The standard plasmid backbones that should be used for part submission are the pSB series in the Registry. These plasmid backbones can be found on the [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid plasmid page] on the Registry (partsregistry.org)<br />
<br />
The judges recognize that many parts will require different vectors for specific devices or applications. However, one of the fundamental principles of iGEM is that we are all making parts to share. Submitting parts on a standard vector allows for easy replication and distribution as well as use. While it is a bit more work to move a biobrick part from a dedicated device plasmid to a standard biobrick plasmid, that extra effort will facilitate sharing and interoperability and will be greatly appreciated by both your peers and those that come after you. We do encourage the development of new standard vectors, but want to see complete documentation and evidence that they work before allowing their use for parts submission to the registry.<br />
<br />
===Complaints===<br />
<br />
To file an official complaint regarding iGEM 2008 judging you must send an email to complaints AT igem DOT org. Your email should include your real name, the real name of your school and team, and the real name and email address of your faculty advisor. Your email must also be copied to your faculty advisor. In your email please clearly state your complaint and what you hope will happen as a result of filing your official complaint. The iGEM judging committee will work diligently to respond to all complaints as quickly as possible. Complaints that are sent to other email addresses, or that do not include the requested information will be ignored. All decisions by the judges regarding complaints are final.</div>Trichardhttp://2008.igem.org/JudgingJudging2008-10-08T15:38:16Z<p>Trichard: /* BioBrick standard variance requests */</p>
<hr />
<div><span style="color:red;">'''Note:''' </span> All Awards & Judging Criteria for iGEM 2008 are currently in draft form. The Awards & Judging details will be finalized in a few weeks. Please send any comments or suggestions for awards and judging by email to the judging committee at judging AT igem DOT org. For example, if you anticipate that your team will do something amazing or important, but that such a project would not be recognized via any of the mechanisms or awards below, let us know as soon as possible.<br />
<br />
<br />
<br />
===[[Judging/Judging_Criteria | Judging criteria]]===<br />
<br />
<br />
===[[Judging/Awards | Awards]]===<br />
<br />
<br />
===Important Dates===<br />
<br />
Be sure to study the official iGEM [[Calendar_of_Events | calendar]] to find out the final dates for different judging requirements.<br />
<br />
<br />
===BioBrick standard variance requests===<br />
One of the [[Requirements | requirements]] for iGEM is that teams are required to provide their parts to the Registry as standard biological parts in standard BioBrick plasmids. If a team wishes to use a different plasmid or different assembly method, they must document the new standard, explain their decision, and receive approval from iGEM Headquarters by the stated [[Calendar_of_Events | deadline]]. Please send your requests to judging AT igem DOT org.<br />
<br />
Here is a list of variance requests:<br />
# [[Judging/Variance/UCSF | UCSF]] ''(approved)''<br />
# [[Judging/Variance/Wisconsin | Wisconsin]] ''(denied)''<br />
# [[Judging/Variance/LCG-UNAM Mexico | LCG-UNAM Mexico]] ''(under evaluation)''<br />
# [[Judging/Variance/Brown | Brown]] ''(under evaluation)''<br />
# [[Judging/Variance/Guelph | Guelph]] ''(under evaluation)''<br />
# [[Judging/Variance/BNU | Bejing Normal University]] ''(under evaluation)''<br />
# [[Judging/Variance/Lethbridge_CCS | Lethbridge CCS]] ''(under evaluation)''<br />
# [[Judging/Variance/Warsaw| Warsaw]] ''(under evaluation)''<br />
# [[Judging/Variance/Peking| Peking University]] ''(under evaluation)''<br />
<br />
Click on an individual team to see their request.<br />
<br />
Those variance requests will be "denied" that ask to submit non-biobricked parts or non-standard plasmids to the registry, but do not propose and document a new standard. The relevant guidance is provided by item 6 of the iGEM 2008 [https://2008.igem.org/Requirements Requirements] page. The standard plasmid backbones that should be used for part submission are the pSB series in the Registry. These plasmid backbones can be found on the [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid plasmid page] on the Registry (partsregistry.org)<br />
<br />
The judges recognize that many parts will require different vectors for specific devices or applications. However, one of the fundamental principles of iGEM is that we are all making parts to share. Submitting parts on a standard vector allows for easy replication and distribution as well as use. While it is a bit more work to move a biobrick part from a dedicated device plasmid to a standard biobrick plasmid, that extra effort will facilitate sharing and interoperability and will be greatly appreciated by both your peers and those that come after you. We do encourage the development of new standard vectors, but want to see complete documentation and evidence that they work before allowing their use for parts submission to the registry.<br />
<br />
===Complaints===<br />
<br />
To file an official complaint regarding iGEM 2008 judging you must send an email to complaints AT igem DOT org. Your email should include your real name, the real name of your school and team, and the real name and email address of your faculty advisor. Your email must also be copied to your faculty advisor. In your email please clearly state your complaint and what you hope will happen as a result of filing your official complaint. The iGEM judging committee will work diligently to respond to all complaints as quickly as possible. Complaints that are sent to other email addresses, or that do not include the requested information will be ignored. All decisions by the judges regarding complaints are final.</div>Trichardhttp://2008.igem.org/Judging/Variance/WarsawJudging/Variance/Warsaw2008-10-08T14:51:20Z<p>Trichard: New page: ===Request=== Dear iGEM Judges, During this year's iGEM competition our team is building a system of biological machines allowing to investigate protein interactions and simultaneously c...</p>
<hr />
<div>===Request===<br />
Dear iGEM Judges, <br />
<br />
During this year's iGEM competition our team is building a system of biological machines allowing to investigate protein interactions and simultaneously change sequence of one of them in order to achieve the strongest possible interaction. The character of our project requires stable single or low copy number vector carrying part of our system which we call 'one-armed bandit'. Low copy number vector is a template for random mutagenesis which is crucial part of this system. For this reason we would like to use pACYC177 and pMPM-T5 derivatives as a backbones for our parts. We have tried to use vector BBa_I739204 (derivative of pACYC177) , but we weren't able to recover it from DNA Kit of Parts. <br />
<br />
Another thing is as our pACYC177 already contained RBS and lactose promoter, constructing such vector from the beginning would be redundant. In the case of pACYC177 backbone we've had also to use cloning sites different from standard because it doesn't contain standard restriction sites and changing multicloning site would be time-consuming. Another simple reason is that in few cases our parts contain standard sites inside their sequence . We tried to put our tools into parts with standard cloning sites, but we are already sure that for a few of them it will be impossible.<br />
<br />
We also used some non-standard vectors in the section of our system which requires purification of recombinant fusion (protein A + part of beta-lactamase) proteins. Sequences of mentioned fusions were cloned into pet15b vector from Novagen, giving us an opportunity to purify his-tagged proteins easily. We want to mention here that prepared parts will be sent on standard BioBrick vectors unless it will be impossible because of different restriction sites. <br />
<br />
All mentioned variances are required for our system to work. In our set-up of vectors and strains everything has to be fully adjusted and change or removal of any part will cause damage of the whole system. That's why we are requesting permission to submit non-biobrick parts to the registry. <br />
<br />
We will make sure that our parts can be easily extracted from the plasmid either through digestion with commercially available enzymes or through PCR (and we will also make sure that all non-standard parts are fully described and documented to ensure that they are useful for the community. <br />
<br />
Thanks for your time and consideration <br />
<br />
Pawel Krawczyk<br />
<br />
University of Warsaw iGEM'08 team<br />
<br />
===Response===<br />
Dear Paul:<br />
<br />
We fully appreciate the challenges you describe, and are pleased to see that you will be submitting prepared parts on standard BioBrick vectors whenever possible. Please do clearly explain the reasons in those cases that you feel are impossible, and submit those parts clearly identified as being on a different vector. While we regret that you were unable to extract BBa_I739204, it would have been good to try the pSB3 series which has the copy number range and hopefully stability you need. <br />
<br />
It seems like you are also asking for a varience to submit your assembled device on a non-. This would be fine if you are willing to propose and document a new assembly standard. Please look at the existing documentation of existing standard biobrick assembly plasmids in the registry to see what would be expected.<br />
<br />
The Novagen vector presumably has restrictions on distribution, in which case you also need to avoid submission on that vector.<br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/JudgingJudging2008-10-08T14:34:11Z<p>Trichard: /* BioBrick standard variance requests */</p>
<hr />
<div><span style="color:red;">'''Note:''' </span> All Awards & Judging Criteria for iGEM 2008 are currently in draft form. The Awards & Judging details will be finalized in a few weeks. Please send any comments or suggestions for awards and judging by email to the judging committee at judging AT igem DOT org. For example, if you anticipate that your team will do something amazing or important, but that such a project would not be recognized via any of the mechanisms or awards below, let us know as soon as possible.<br />
<br />
<br />
<br />
===[[Judging/Judging_Criteria | Judging criteria]]===<br />
<br />
<br />
===[[Judging/Awards | Awards]]===<br />
<br />
<br />
===Important Dates===<br />
<br />
Be sure to study the official iGEM [[Calendar_of_Events | calendar]] to find out the final dates for different judging requirements.<br />
<br />
<br />
===BioBrick standard variance requests===<br />
One of the [[Requirements | requirements]] for iGEM is that teams are required to provide their parts to the Registry as standard biological parts in standard BioBrick plasmids. If a team wishes to use a different plasmid or different assembly method, they must document the new standard, explain their decision, and receive approval from iGEM Headquarters by the stated [[Calendar_of_Events | deadline]]. Please send your requests to judging AT igem DOT org.<br />
<br />
Here is a list of variance requests:<br />
# [[Judging/Variance/UCSF | UCSF]] ''(approved)''<br />
# [[Judging/Variance/Wisconsin | Wisconsin]] ''(denied)''<br />
# [[Judging/Variance/LCG-UNAM Mexico | LCG-UNAM Mexico]] ''(under evaluation)''<br />
# [[Judging/Variance/Brown | Brown]] ''(under evaluation)''<br />
# [[Judging/Variance/Guelph | Guelph]] ''(under evaluation)''<br />
# [[Judging/Variance/BNU | Bejing Normal University]] ''(under evaluation)''<br />
# [[Judging/Variance/Lethbridge_CCS | Lethbridge CCS]] ''(under evaluation)''<br />
# [[Judging/Variance/Warsaw| Warsaw]] ''(under evaluation)''<br />
<br />
Click on an individual team to see their request.<br />
<br />
Those variance requests will be "denied" that ask to submit non-biobricked parts or non-standard plasmids to the registry, but do not propose and document a new standard. The relevant guidance is provided by item 6 of the iGEM 2008 [https://2008.igem.org/Requirements Requirements] page. The standard plasmid backbones that should be used for part submission are the pSB series in the Registry. These plasmid backbones can be found on the [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid plasmid page] on the Registry (partsregistry.org)<br />
<br />
The judges recognize that many parts will require different vectors for specific devices or applications. However, one of the fundamental principles of iGEM is that we are all making parts to share. Submitting parts on a standard vector allows for easy replication and distribution as well as use. While it is a bit more work to move a biobrick part from a dedicated device plasmid to a standard biobrick plasmid, that extra effort will facilitate sharing and interoperability and will be greatly appreciated by both your peers and those that come after you. We do encourage the development of new standard vectors, but want to see complete documentation and evidence that they work before allowing their use for parts submission to the registry.<br />
<br />
===Complaints===<br />
<br />
To file an official complaint regarding iGEM 2008 judging you must send an email to complaints AT igem DOT org. Your email should include your real name, the real name of your school and team, and the real name and email address of your faculty advisor. Your email must also be copied to your faculty advisor. In your email please clearly state your complaint and what you hope will happen as a result of filing your official complaint. The iGEM judging committee will work diligently to respond to all complaints as quickly as possible. Complaints that are sent to other email addresses, or that do not include the requested information will be ignored. All decisions by the judges regarding complaints are final.</div>Trichardhttp://2008.igem.org/Judging/Variance/Lethbridge_CCSJudging/Variance/Lethbridge CCS2008-10-08T14:32:26Z<p>Trichard: /* Response */</p>
<hr />
<div>====Request====<br />
Dear iGEM judges,<br />
I am writing on behalf of the Lethbridge CCS team to request permission to submit non-BioBrick parts to the registry.<br />
<br />
We are a high school team, investigating the possibility of ligase-independent cloning (LIC) as a standard method for preparing new BioBricks. The LIC method uses a non-BioBrick plasmid as a starting point; in this plasmid, the standard MCS is replaced by a LIC-specific overhang sequence. In order to prepare a new BioBrick, the standard prefix & suffix are included in the primers used to amplify a gene of interest, which is then inserted into the LIC plasmid.<br />
<br />
Thus, BioBricks are generated by our technique (and we hope to submit several), but a non-BioBrick plasmid is required as an initial step. We believe that the LIC method has great potential as an easily adopted, readily automated method of BioBrick preparation, and ask your permission to submit our non-standard plasmid to the Registry. In the spirit of iGEM, we will of course be sharing our experiences and protocols for use of this plasmid.<br />
<br />
Thanks very much for your consideration.<br />
<br />
Marc Slingerland<br />
Lethbridge CCS team<br />
<br />
====Response====<br />
Dear Marc,<br />
<br />
It seems like your non-BioBrick plasmid could be added to the registry with sufficient documentation, and that the needed testing and evaluation are integral to your team's project. This would be a special function plasmid, and might evolve to a new standard, which sounds like it is your goal. So it would be perfectly appropriate to submit that part. However, just in case their are unanticipated problems with that new plasmid, we recommend that you also submit the individual components of your device (the LIC-specific overhang sequence and any other components) on standard biobrick vectors as separate parts for the registry. <br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/Lethbridge_CCSJudging/Variance/Lethbridge CCS2008-10-08T14:30:32Z<p>Trichard: </p>
<hr />
<div>====Request====<br />
Dear iGEM judges,<br />
I am writing on behalf of the Lethbridge CCS team to request permission to submit non-BioBrick parts to the registry.<br />
<br />
We are a high school team, investigating the possibility of ligase-independent cloning (LIC) as a standard method for preparing new BioBricks. The LIC method uses a non-BioBrick plasmid as a starting point; in this plasmid, the standard MCS is replaced by a LIC-specific overhang sequence. In order to prepare a new BioBrick, the standard prefix & suffix are included in the primers used to amplify a gene of interest, which is then inserted into the LIC plasmid.<br />
<br />
Thus, BioBricks are generated by our technique (and we hope to submit several), but a non-BioBrick plasmid is required as an initial step. We believe that the LIC method has great potential as an easily adopted, readily automated method of BioBrick preparation, and ask your permission to submit our non-standard plasmid to the Registry. In the spirit of iGEM, we will of course be sharing our experiences and protocols for use of this plasmid.<br />
<br />
Thanks very much for your consideration.<br />
<br />
Marc Slingerland<br />
Lethbridge CCS team<br />
<br />
====Response====<br />
Dear Marc,<br />
<br />
It seems like your non-BioBrick plasmid could be added to the registry with sufficient documentation, and that the needed testing and evaluation are integral to your team's project. This would be a special function plasmid, and might evolve to a new standard, which sound like it is your goal. In the interim however, we recommend that you submit both the new plasmid AND the individual components of your device (the LIC-specific overhang sequence and any other components) on standard biobrick vectors as separate parts for the registry. <br />
<br />
Sincerely,<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/GuelphJudging/Variance/Guelph2008-10-08T14:21:12Z<p>Trichard: </p>
<hr />
<div>===Request===<br />
<br />
Dear iGEM Judges,<br />
<br />
I’m writing on behalf of the 2008 Guelph iGEM Team to request <br />
permission to submit non-biobrick parts to the registry for this year’s Jamboree.<br />
<br />
For the first year of our school's participation in the competition, <br />
the Guelph iGEM team is building a synthetic operon for co-expression of a<br />
large number of carotenoid metabolic genes necessitating a slightly<br />
divergent cloning technique for straigtforward, multipart sequential<br />
ligations. We generated biobrick parts with appropriate restriction<br />
sites in commercial cloning vectors, but have also included non <br />
standard<br />
biobrick REs to allow us to serially ligate several genes into a<br />
synthetic operon and RNAi conformations.<br />
<br />
Our strategy begins to generate a promoter with the start codon <br />
friendly restriction site Nde driving GFP expression in the promoter testing<br />
device, pSB1A3-E0240. The GFP is removed and the CrtE gene is inserted<br />
next to the promoter with the Nde while the Xba in the 3' end is fused<br />
to the vector's SpeI and nullified. This first gene included SpeI and<br />
XhoI sites in its 3' UTR, allowing the next gene to be inserted using<br />
Xba and Xho, while it carries SpeI and XhoI sites as well. And so on.<br />
Using this strategy we believe it possible to extend the synthetic<br />
operon to a large number of genes. Obviously if we had used a biobrick<br />
RE like Not1 instead of Xho, Biobrick parts we would've made would<br />
include the Xba or Spe sites inside the NotI sites flanking the <br />
Biobrick.<br />
<br />
Likewise, we have used a modified RE scheme for construction of our<br />
second project - an RNAi generating Biobrick for silencing plant genes<br />
using bacteria. In order to enable use of any pre-existing Biobrick in<br />
the registry, we ordered a construct with Biobrick RE in an altered<br />
orientation. Eco and Spe together on one side of the corn actin1 <br />
intron, and Not and Xba on the other side. To the 3' end we included a <br />
synthetic terminator followed by the PstI site, and the MfeI and NdeI sites at <br />
the 5' end which allowed us to non-conservatively insert the construct <br />
into the Biobrick vector pSB1A2, eliminating the MfeI site (compatible ends<br />
with EcoRI) and allowing us again to cut with the NdeI to fuse to the<br />
strong constitutive promoter we are using. Our target vector for this<br />
project has NdeI and PstI sites we plan to use to conveniently insert<br />
this RNAi constuct into. Part of our strategy is to use a broad host<br />
range plasmid which will accept a number of different inserts, and the<br />
NdeI and PstI sites are ideal for this.<br />
<br />
In the spirit of iGEM, we hope to share these parts with the <br />
community,<br />
and to facilitate this transfer, we have all our parts in two <br />
commercial<br />
cloning vectors, pJET from Fermentas, and pDRIVE from Quiagen. If<br />
requested of the committee, we can transfer these parts to Biobrick<br />
vectors but would also like to know if submission of these sequenced<br />
parts will be acceptable as is. Much of this is outlined on our wiki<br />
with diagrams. We hope you will accept our constructs for this year's<br />
competition and let us know what changes to our plan will be <br />
necessary.<br />
<br />
<br />
Thank you for your consideration,<br />
<br />
David Johnston<br />
<br />
Guelph iGEM Team<br />
<br />
===Response===<br />
<br />
Dear David:<br />
<br />
There are a number of issues here. First, you specifically request permission to submit your parts to the registry on the commercial cloning vectors pJET and pDRIVE that you are using in your constructs. The registry encourages the development of new standard plasmids, with two constraints: 1) they must be free of any commercial restrictions on further distribution and use; and 2) they must be thoroughly documented, similar to the documentation provided for existing plasmids. It does not appear that your proposal would satisfy those constraints, but we would welcome further information if we are wrong.<br />
<br />
It also appears that you are using a new assembly strategy for serial ligation that includes non-standard biobrick ends. However, it is not clear that you are proposing your serial ligation strategy as a new biobrick standard, or simply want to make your parts available in that form. If you are interested in an evaluation of that assembly strategy as a new standard, please let us know. Otherwise, to avoid confusion in the absence of a new standard, you should only submit the current biobrick standard versions of your parts.<br />
<br />
Assuming you choose not to develop new plasmid or assembly standards in the short term, then please submit your new parts as biobrick parts on an existing standard biobrick plasmid. These vectors can be found at http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid<br />
<br />
It would be helpful if you would indicate in the registry that you have these parts (both biobricked and with your alternate REs) available on those commercial vectors. If that generates frequent requests, then it would clearly be important to develop a new standard vector and/or cloning strategy for the registry.<br />
<br />
Sincerely,<br />
<br />
iGEM judging team<br />
<br />
===Response to your Response===<br />
<br />
Dear iGEM Judging Team, <br />
<br />
Thank you for your respopnse. We will get all our genes and constructs into pSB1A2. Since they do all conform to biobrick standards, it likely doesn't matter that our submissions will also contain NdeI and XhoI restriction sites. Right? <br />
<br />
One other thing: we are proud that the RNAi construct tool we designed (and put into pSB1A2) could allow ANY biobrick part (with the sites EcoRI, NotI, XbaI, and SpeI) to be made into an RNAi construct. It uses the Biobrick RE but not in your standard Biobrick conformationa. An approximation of its structure follows: <br />
<br />
NdeI - EcoRI - XbaI - Intron - NotI - SpeI - Terminator - PstI <br />
<br />
Please tell me if this posses a problem. <br />
<br />
Oh, and one more thing. The broad host range plasmid we are using was released to us for use in this competition after our signing of an MTA. We are allowed to use it in this competition, but there are clauses in the document preventing the spread of this plasmid outside of our direct use so I don't know if we can submit it as a biobrick (although I want to). Will this pose a problem for our entry?<br />
<br />
Sincerely, <br />
<br />
David Johnston <br />
iGEM Guelph<br />
<br />
===Response Cubed===<br />
<br />
Hi David:<br />
<br />
We are discussing the first two questions, but meanwhile want to be clear about the third. It sounds like you have lots of parts that you can submit on standard vectors, but are constrained regarding distribution of the broad host range assembly plasmid. While you can certainly use that commercial plasmid in the competition to demonstrate and test your device, it would not be appropriate to submit the assembled device on that plasmid to the registry. That constraint will not penalize your team in the competition as long as you submit the device components on pSB1A2 or another standard vector as you propose.<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/GuelphJudging/Variance/Guelph2008-10-08T14:00:56Z<p>Trichard: /* Response */</p>
<hr />
<div>===Request===<br />
<br />
Dear iGEM Judges,<br />
<br />
I’m writing on behalf of the 2008 Guelph iGEM Team to request <br />
permission to submit non-biobrick parts to the registry for this year’s Jamboree.<br />
<br />
For the first year of our school's participation in the competition, <br />
the Guelph iGEM team is building a synthetic operon for co-expression of a<br />
large number of carotenoid metabolic genes necessitating a slightly<br />
divergent cloning technique for straigtforward, multipart sequential<br />
ligations. We generated biobrick parts with appropriate restriction<br />
sites in commercial cloning vectors, but have also included non <br />
standard<br />
biobrick REs to allow us to serially ligate several genes into a<br />
synthetic operon and RNAi conformations.<br />
<br />
Our strategy begins to generate a promoter with the start codon <br />
friendly restriction site Nde driving GFP expression in the promoter testing<br />
device, pSB1A3-E0240. The GFP is removed and the CrtE gene is inserted<br />
next to the promoter with the Nde while the Xba in the 3' end is fused<br />
to the vector's SpeI and nullified. This first gene included SpeI and<br />
XhoI sites in its 3' UTR, allowing the next gene to be inserted using<br />
Xba and Xho, while it carries SpeI and XhoI sites as well. And so on.<br />
Using this strategy we believe it possible to extend the synthetic<br />
operon to a large number of genes. Obviously if we had used a biobrick<br />
RE like Not1 instead of Xho, Biobrick parts we would've made would<br />
include the Xba or Spe sites inside the NotI sites flanking the <br />
Biobrick.<br />
<br />
Likewise, we have used a modified RE scheme for construction of our<br />
second project - an RNAi generating Biobrick for silencing plant genes<br />
using bacteria. In order to enable use of any pre-existing Biobrick in<br />
the registry, we ordered a construct with Biobrick RE in an altered<br />
orientation. Eco and Spe together on one side of the corn actin1 <br />
intron, and Not and Xba on the other side. To the 3' end we included a <br />
synthetic terminator followed by the PstI site, and the MfeI and NdeI sites at <br />
the 5' end which allowed us to non-conservatively insert the construct <br />
into the Biobrick vector pSB1A2, eliminating the MfeI site (compatible ends<br />
with EcoRI) and allowing us again to cut with the NdeI to fuse to the<br />
strong constitutive promoter we are using. Our target vector for this<br />
project has NdeI and PstI sites we plan to use to conveniently insert<br />
this RNAi constuct into. Part of our strategy is to use a broad host<br />
range plasmid which will accept a number of different inserts, and the<br />
NdeI and PstI sites are ideal for this.<br />
<br />
In the spirit of iGEM, we hope to share these parts with the <br />
community,<br />
and to facilitate this transfer, we have all our parts in two <br />
commercial<br />
cloning vectors, pJET from Fermentas, and pDRIVE from Quiagen. If<br />
requested of the committee, we can transfer these parts to Biobrick<br />
vectors but would also like to know if submission of these sequenced<br />
parts will be acceptable as is. Much of this is outlined on our wiki<br />
with diagrams. We hope you will accept our constructs for this year's<br />
competition and let us know what changes to our plan will be <br />
necessary.<br />
<br />
<br />
Thank you for your consideration,<br />
<br />
David Johnston<br />
<br />
Guelph iGEM Team<br />
<br />
===Response===<br />
<br />
Dear David:<br />
<br />
There are a number of issues here. First, you specifically request permission to submit your parts to the registry on the commercial cloning vectors pJET and pDRIVE that you are using in your constructs. The registry encourages the development of new standard plasmids, with two constraints: 1) they must be free of any commercial restrictions on further distribution and use; and 2) they must be thoroughly documented, similar to the documentation provided for existing plasmids. It does not appear that your proposal would satisfy those constraints, but we would welcome further information if we are wrong.<br />
<br />
It also appears that you are using a new assembly strategy for serial ligation that includes non-standard biobrick ends. However, it is not clear that you are proposing your serial ligation strategy as a new biobrick standard, or simply want to make your parts available in that form. If you are interested in an evaluation of that assembly strategy as a new standard, please let us know. Otherwise, to avoid confusion in the absence of a new standard, you should only submit the current biobrick standard versions of your parts.<br />
<br />
Assuming you choose not to develop new plasmid or assembly standards in the short term, then please submit your new parts as biobrick parts on an existing standard biobrick plasmid. These vectors can be found at http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid<br />
<br />
It would be helpful if you would indicate in the registry that you have these parts (both biobricked and with your alternate REs) available on those commercial vectors. If that generates frequent requests, then it would clearly be important to develop a new standard vector and/or cloning strategy for the registry.<br />
<br />
Sincerely,<br />
<br />
iGEM judging team<br />
<br />
===Response to your Response===<br />
<br />
Dear iGEM Judging Team, <br />
<br />
Thank you for your respopnse. We will get all our genes and constructs into pSB1A2. Since they do all conform to biobrick standards, it likely doesn't matter that our submissions will also contain NdeI and XhoI restriction sites. Right? <br />
<br />
One other thing: we are proud that the RNAi construct tool we designed (and put into pSB1A2) could allow ANY biobrick part (with the sites EcoRI, NotI, XbaI, and SpeI) to be made into an RNAi construct. It uses the Biobrick RE but not in your standard Biobrick conformationa. An approximation of its structure follows: <br />
<br />
NdeI - EcoRI - XbaI - Intron - NotI - SpeI - Terminator - PstI <br />
<br />
Please tell me if this posses a problem. <br />
<br />
Oh, and one more thing. The broad host range plasmid we are using was released to us for use in this competition after our signing of an MTA. We are allowed to use it in this competition, but there are clauses in the document preventing the spread of this plasmid outside of our direct use so I don't know if we can submit it as a biobrick (although I want to). Will this pose a problem for our entry?<br />
<br />
Sincerely, <br />
<br />
David Johnston <br />
iGEM Guelph</div>Trichardhttp://2008.igem.org/Judging/Variance/LCG-UNAM_MexicoJudging/Variance/LCG-UNAM Mexico2008-10-08T13:59:45Z<p>Trichard: /* Response */</p>
<hr />
<div>===Request===<br />
<br />
Dear iGEM judges,<br />
<br />
The team LCG-UNAM-MEXICO is participating this year for the first <br />
time, and I'm writing on behalf of the team to request permission <br />
for submitting our Biobricks in non-standard vectors.<br />
<br />
Our project requires very tight regulation of E. coli nickel <br />
extrusion pump (RcnA) through several regulatory upstream proteins. <br />
Our Analysis suggest that we need to control very accurately the <br />
production of several molecules and a crucial part of this requires <br />
stable low copy-number vectors. For this reason we would like to use <br />
pRK415 and pBBIMCS-5 derivatives as our plasmid backbones. We will <br />
be adding Biobrick prefix and suffix to both of them. We will also <br />
make sure that our parts are easily extracted from the plasmid <br />
either through digestion with commercially available enzymes or <br />
through PCR.<br />
<br />
All this information will be shared to ensure that our Biobricks are <br />
useful for the community.<br />
<br />
Thanks for your time and consideration<br />
<br />
Sur Herrera Paredes<br />
<br />
LCG-UNAM-MEXICO<br />
Licenciatura en Ciencias Genómicas<br />
Universidad Nacional Autónoma de México<br />
<br />
===Response===<br />
<br />
Dear Sur:<br />
<br />
We need some additional information about this request. It appears you are developing some new BioBrick alpha compatible vectors, which could be very useful in and of themselves (i.e., new parts). We like this idea, but do require complete documentation about these vectors so they can be used by others in the future. Examples of the documentation required of standard biobrick vectors are at: http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid<br />
<br />
If you are able to provide adequate documentation of these new vectors, then we would be pleased to evaluate them as standard vectors and hopefully allow submission of your new parts as proposed. Otherwise, you should submit your parts on an existing standard plasmid, specifically the pSB series in the biobricks registry. <br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/WisconsinJudging/Variance/Wisconsin2008-10-08T13:57:56Z<p>Trichard: /* Response */</p>
<hr />
<div>===Request===<br />
<br />
To whom it may concern,<br />
<br />
I am a member of the Wisconsin iGEM team. We are unsure of whether or not we<br />
have to submit a notice and description of non-standard parts. We are<br />
planning to send in standard biobrick from parts for most aspects of our<br />
project. We have been using the pET28a vector from Novagen for multiple<br />
purposes and for a few reasons (T7-tag, his-tag, protease site, etc.). We<br />
are unsure if we are able to submit this plasmid with our genes in it due to<br />
it being a commerical product. We are also unsure of whether or not we need<br />
to submit it since we are planning on submitting standard biobrick plasmids<br />
with just our genes in them (none of the extra features such as the tags<br />
will be present). Also for one of our projects it was necessary to use the<br />
Rosetta-gami2(DE3)pLysS strain from Novagen for several different reasons.<br />
This strain has a fairly essential part in this project. I do not believe we<br />
can submit this strain to the registry. Should we still send in descriptions<br />
of these non standard parts even if we cannot actually submit them?<br />
<br />
Thanks,<br />
Andy<br />
<br />
===Response===<br />
<br />
Hi Andy,<br />
<br />
Please do not submit the commercial plasmids to the registry. However, when you submit your parts on standard biobrick plasmids, please do document that you have tags and other features available on your Novagen commercial plasmids so that others can contact you if needed. <br />
<br />
The standard vectors that should be used for part submission are the pSB series in the biobricks registry. These vectors can be found at http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid<br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/JudgingJudging2008-10-08T13:53:24Z<p>Trichard: /* BioBrick standard variance requests */</p>
<hr />
<div><span style="color:red;">'''Note:''' </span> All Awards & Judging Criteria for iGEM 2008 are currently in draft form. The Awards & Judging details will be finalized in a few weeks. Please send any comments or suggestions for awards and judging by email to the judging committee at judging AT igem DOT org. For example, if you anticipate that your team will do something amazing or important, but that such a project would not be recognized via any of the mechanisms or awards below, let us know as soon as possible.<br />
<br />
<br />
<br />
===[[Judging/Judging_Criteria | Judging criteria]]===<br />
<br />
<br />
===[[Judging/Awards | Awards]]===<br />
<br />
<br />
===Important Dates===<br />
<br />
Be sure to study the official iGEM [[Calendar_of_Events | calendar]] to find out the final dates for different judging requirements.<br />
<br />
<br />
===BioBrick standard variance requests===<br />
One of the [[Requirements | requirements]] for iGEM is that teams are required to provide their parts to the Registry as standard biological parts in standard BioBrick plasmids. If a team wishes to use a different plasmid or different assembly method, they must document the new standard, explain their decision, and receive approval from iGEM Headquarters by the stated [[Calendar_of_Events | deadline]]. Please send your requests to judging AT igem DOT org.<br />
<br />
Here is a list of variance requests:<br />
# [[Judging/Variance/UCSF | UCSF]] ''(approved)''<br />
# [[Judging/Variance/Wisconsin | Wisconsin]] ''(denied)''<br />
# [[Judging/Variance/LCG-UNAM Mexico | LCG-UNAM Mexico]] ''(under evaluation)''<br />
# [[Judging/Variance/Brown | Brown]] ''(under evaluation)''<br />
# [[Judging/Variance/Guelph | Guelph]] ''(under evaluation)''<br />
# [[Judging/Variance/BNU | Bejing Normal University]] ''(under evaluation)''<br />
# [[Judging/Variance/Lethbridge_CCS | Lethbridge CCS]] ''(under evaluation)''<br />
<br />
Click on an individual team to see their request.<br />
<br />
Those variance requests will be "denied" that ask to submit non-biobricked parts or non-standard plasmids to the registry, but do not propose and document a new standard. The relevant guidance is provided by item 6 of the iGEM 2008 [https://2008.igem.org/Requirements Requirements] page. The standard vectors that should be used for part submission are the pSB series in the biobricks registry. These vectors can be found at http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid<br />
<br />
The judges recognize that many parts will require different vectors for specific devices or applications. However, one of the fundamental principles of iGEM is that we are all making parts to share. Submitting parts on a standard vector allows for easy replication and distribution as well as use. While it is a bit more work to move a biobrick part from a dedicated device plasmid to a standard biobrick plasmid, that extra effort will facilitate sharing and interoperability and will be greatly appreciated by both your peers and those that come after you. We do encourage the development of new standard vectors, but want to see complete documentation and evidence that they work before allowing their use for parts submission to the registry.<br />
<br />
===Complaints===<br />
<br />
To file an official complaint regarding iGEM 2008 judging you must send an email to complaints AT igem DOT org. Your email should include your real name, the real name of your school and team, and the real name and email address of your faculty advisor. Your email must also be copied to your faculty advisor. In your email please clearly state your complaint and what you hope will happen as a result of filing your official complaint. The iGEM judging committee will work diligently to respond to all complaints as quickly as possible. Complaints that are sent to other email addresses, or that do not include the requested information will be ignored. All decisions by the judges regarding complaints are final.</div>Trichardhttp://2008.igem.org/JudgingJudging2008-10-05T19:54:59Z<p>Trichard: /* BioBrick standard variance requests */</p>
<hr />
<div><span style="color:red;">'''Note:''' </span> All Awards & Judging Criteria for iGEM 2008 are currently in draft form. The Awards & Judging details will be finalized in a few weeks. Please send any comments or suggestions for awards and judging by email to the judging committee at judging AT igem DOT org. For example, if you anticipate that your team will do something amazing or important, but that such a project would not be recognized via any of the mechanisms or awards below, let us know as soon as possible.<br />
<br />
<br />
<br />
===[[Judging/Judging_Criteria | Judging criteria]]===<br />
<br />
<br />
===[[Judging/Awards | Awards]]===<br />
<br />
<br />
===Important Dates===<br />
<br />
Be sure to study the official iGEM [[Calendar_of_Events | calendar]] to find out the final dates for different judging requirements.<br />
<br />
<br />
===BioBrick standard variance requests===<br />
One of the [[Requirements | requirements]] for iGEM is that teams are required to provide their parts to the Registry as standard biological parts in standard BioBrick plasmids. If a team wishes to use a different plasmid or different assembly method, they must document the new standard, explain their decision, and receive approval from iGEM Headquarters by the stated [[Calendar_of_Events | deadline]]. Please send your requests to judging AT igem DOT org.<br />
<br />
Here is a list of variance requests:<br />
# [[Judging/Variance/UCSF | UCSF]] ''(approved)''<br />
# [[Judging/Variance/Wisconsin | Wisconsin]] ''(denied)''<br />
# [[Judging/Variance/LCG-UNAM Mexico | LCG-UNAM Mexico]] ''(under evaluation)''<br />
# [[Judging/Variance/Brown | Brown]] ''(under evaluation)''<br />
# [[Judging/Variance/Guelph | Guelph]] ''(under evaluation)''<br />
# [[Judging/Variance/BNU | Bejing Normal University]] ''(under evaluation)''<br />
<br />
Click on an individual team to see their request.<br />
<br />
Those variance requests will be "denied" that ask to submit non-biobricked parts or non-standard plasmids to the registry, but do not propose and document a new standard. The relevant guidance is provided by item 6 of the iGEM 2008 [https://2008.igem.org/Requirements Requirements] page.<br />
<br />
The judges recognize that many parts will require different vectors for specific devices or applications. However, one of the fundamental principles of iGEM is that we are all making parts to share. Submitting parts on a standard vector allows for easy replication and distribution as well as use. While it is a bit more work to move a biobrick part from a dedicated device plasmid to a standard biobrick plasmid, that extra effort will facilitate sharing and interoperability and will be greatly appreciated by both your peers and those that come after you. We do encourage the development of new standard vectors, but want to see complete documentation and evidence that they work before allowing their use for parts submission to the registry.<br />
<br />
===Complaints===<br />
<br />
To file an official complaint regarding iGEM 2008 judging you must send an email to complaints AT igem DOT org. Your email should include your real name, the real name of your school and team, and the real name and email address of your faculty advisor. Your email must also be copied to your faculty advisor. In your email please clearly state your complaint and what you hope will happen as a result of filing your official complaint. The iGEM judging committee will work diligently to respond to all complaints as quickly as possible. Complaints that are sent to other email addresses, or that do not include the requested information will be ignored. All decisions by the judges regarding complaints are final.</div>Trichardhttp://2008.igem.org/Judging/Variance/WisconsinJudging/Variance/Wisconsin2008-10-05T19:51:42Z<p>Trichard: /* Response */</p>
<hr />
<div>===Request===<br />
<br />
To whom it may concern,<br />
<br />
I am a member of the Wisconsin iGEM team. We are unsure of whether or not we<br />
have to submit a notice and description of non-standard parts. We are<br />
planning to send in standard biobrick from parts for most aspects of our<br />
project. We have been using the pET28a vector from Novagen for multiple<br />
purposes and for a few reasons (T7-tag, his-tag, protease site, etc.). We<br />
are unsure if we are able to submit this plasmid with our genes in it due to<br />
it being a commerical product. We are also unsure of whether or not we need<br />
to submit it since we are planning on submitting standard biobrick plasmids<br />
with just our genes in them (none of the extra features such as the tags<br />
will be present). Also for one of our projects it was necessary to use the<br />
Rosetta-gami2(DE3)pLysS strain from Novagen for several different reasons.<br />
This strain has a fairly essential part in this project. I do not believe we<br />
can submit this strain to the registry. Should we still send in descriptions<br />
of these non standard parts even if we cannot actually submit them?<br />
<br />
Thanks,<br />
Andy<br />
<br />
===Response===<br />
<br />
Hi Andy,<br />
<br />
Please do not submit the commercial plasmids to the registry. However, when you submit your parts on standard biobrick plasmids, please do document that you have tags and other features available on your Novagen commercial plasmids so that others can contact you if needed.<br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/LCG-UNAM_MexicoJudging/Variance/LCG-UNAM Mexico2008-10-05T19:51:08Z<p>Trichard: /* Response */</p>
<hr />
<div>===Request===<br />
<br />
Dear iGEM judges,<br />
<br />
The team LCG-UNAM-MEXICO is participating this year for the first <br />
time, and I'm writing on behalf of the team to request permission <br />
for submitting our Biobricks in non-standard vectors.<br />
<br />
Our project requires very tight regulation of E. coli nickel <br />
extrusion pump (RcnA) through several regulatory upstream proteins. <br />
Our Analysis suggest that we need to control very accurately the <br />
production of several molecules and a crucial part of this requires <br />
stable low copy-number vectors. For this reason we would like to use <br />
pRK415 and pBBIMCS-5 derivatives as our plasmid backbones. We will <br />
be adding Biobrick prefix and suffix to both of them. We will also <br />
make sure that our parts are easily extracted from the plasmid <br />
either through digestion with commercially available enzymes or <br />
through PCR.<br />
<br />
All this information will be shared to ensure that our Biobricks are <br />
useful for the community.<br />
<br />
Thanks for your time and consideration<br />
<br />
Sur Herrera Paredes<br />
<br />
LCG-UNAM-MEXICO<br />
Licenciatura en Ciencias Genómicas<br />
Universidad Nacional Autónoma de México<br />
<br />
===Response===<br />
<br />
Dear Sur:<br />
<br />
We need some additional information about this request. It appears you are developing some new BioBrick alpha compatible vectors, which could be very useful in and of themselves (i.e., new parts). We like this idea, but do require complete documentation about these vectors so they can be used by others in the future. Examples of the documentation required of standard biobrick vectors are at: http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid<br />
<br />
If you are able to provide adequate documentation of these new vectors, then we would be pleased to evaluate them as standard vectors and hopefully allow submission of your new parts as proposed. Otherwise, you should submit your parts on an existing standard plasmid.<br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/LCG-UNAM_MexicoJudging/Variance/LCG-UNAM Mexico2008-10-05T19:50:54Z<p>Trichard: /* Response */</p>
<hr />
<div>===Request===<br />
<br />
Dear iGEM judges,<br />
<br />
The team LCG-UNAM-MEXICO is participating this year for the first <br />
time, and I'm writing on behalf of the team to request permission <br />
for submitting our Biobricks in non-standard vectors.<br />
<br />
Our project requires very tight regulation of E. coli nickel <br />
extrusion pump (RcnA) through several regulatory upstream proteins. <br />
Our Analysis suggest that we need to control very accurately the <br />
production of several molecules and a crucial part of this requires <br />
stable low copy-number vectors. For this reason we would like to use <br />
pRK415 and pBBIMCS-5 derivatives as our plasmid backbones. We will <br />
be adding Biobrick prefix and suffix to both of them. We will also <br />
make sure that our parts are easily extracted from the plasmid <br />
either through digestion with commercially available enzymes or <br />
through PCR.<br />
<br />
All this information will be shared to ensure that our Biobricks are <br />
useful for the community.<br />
<br />
Thanks for your time and consideration<br />
<br />
Sur Herrera Paredes<br />
<br />
LCG-UNAM-MEXICO<br />
Licenciatura en Ciencias Genómicas<br />
Universidad Nacional Autónoma de México<br />
<br />
===Response===<br />
<br />
Dear Sur:<br />
<br />
We need some additional information about this request. It appears you are developing some new BioBrick alpha compatible vectors, which could be very useful in and of themselves (i.e., new parts). We like this idea, but do require complete documentation about these vectors so they can be used by others in the future. Examples of the documentation required of standard biobrick vectors are at: http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid<br />
<br />
If you are able to provide adequate documentation of these new vectors, then we would be pleased to evaluate them as standard vectors and hopefully allow submission of your new parts as proposed. Otherwise, you should submit your parts on an existing standard plasmid.<br />
<br />
Sincerely, <br />
iGEM judging team</div>Trichardhttp://2008.igem.org/Judging/Variance/BrownJudging/Variance/Brown2008-10-05T19:49:50Z<p>Trichard: /* Request */</p>
<hr />
<div>===Request===<br />
<br />
Dear Judges,<br />
<br />
At Brown, we are building a regulatory gene network in ''Saccharomyces cerevisiae'', and are excited to contribute to the growing collection of yeast parts in the Registry. We are building our constructs using the Silver Lab Biofusion standard for the fusion of protein domains, and the Biobrick standard for the addition of regulatory regions. Construction takes place on Biobrick vectors, while the final constructs are cloned onto integrative yeast shuttle vectors from the pRS30x family. (http://www.genetics.org/cgi/reprint/122/1/19.pdf) The pRS vectors are not suitable for Biobrick construction, but their multiple cloning sites provide for the convenient cloning of a complete Biobrick construct onto the vector. (http://openwetware.org/wiki/Silver:_BB_Strategy) Our parts on pRS vectors are useful as complete constructs for integration into the yeast genome, and in that way would be a valuable addition to the registry. Some final constructs could be useful as construction intermediates as well- in these cases we would like to submit them on both pRS vectors for yeast integration as-is, and on standard Biobrick vectors for use in construction.<br />
<br />
Thank you,<br />
<br />
John Szymanski<br><br />
Brown iGEM<br><br />
Team Limiter<br />
<br />
===Response===<br />
<br />
Hi John:<br />
<br />
Thank you for your inquiry. First, we absolutely welcome your basic parts as standard BioBrick alpha parts. For the pRS vectors, we would like your team to document how you are moving the BB alpha parts onto a yeast shuttle vector, and further explain how and why this is useful. We expect that this second aspect of the work could be recognized as a new BB assembly technique (for moving BBa parts onto yeast chromosomes), but need further documentation.<br />
<br />
Sincerely,<br />
<br />
iGEM judging team</div>Trichard