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Team:Berkeley/Judging
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| + | In brief, this year's Berkeley 2010 iGEM team accomplished the following: | ||
| + | * A foundational advance in protein and DNA payload delivery to lower metazoans, opening the door to genetic modification of potentially very useful and previously intractable organisms using synthetic biology. | ||
| + | * An automated, user-friendly, forward-thinking approach to biosafety implemented in the software program Clotho, improving human practice in synthetic biology. | ||
| + | * Developed and deployed the new core of Clotho 2.0 as an App platform for synthetic biology tools | ||
| + | |||
| + | |||
==Requirements== | ==Requirements== | ||
===Bronze Medal=== | ===Bronze Medal=== | ||
| - | * Register the team, have a [https://2010.igem.org/Team:Berkeley/Team | + | * Register the team, have a [https://2010.igem.org/Team:Berkeley/Team great summer], and have fun attending the Jamboree. |
| - | * Create and share a [https://2010.igem.org/Team:Berkeley/Overview Description] of the team's project via the iGEM wiki. | + | * Create and share a [https://2010.igem.org/Team:Berkeley/Project/Overview Description] of the team's project via the iGEM wiki. |
* Present a Poster and Talk at the iGEM Jamboree. | * Present a Poster and Talk at the iGEM Jamboree. | ||
| - | * Enter information detailing at least one new standard BioBrick Part or Device in the Registry of Parts | + | * Enter information detailing at least one new standard BioBrick [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2010&group=Berkeley Part or Device] in the Registry of Parts |
===Silver Medal=== | ===Silver Medal=== | ||
| - | * Demonstrate that at least one [https://2010.igem.org/Team:Berkeley/ | + | * Demonstrate that at least one Part or Device of your own design and construction [https://2010.igem.org/Team:Berkeley/Results works] as expected. (See [https://2010.igem.org/Team:Berkeley/Self-Lysis Self-Lysis] and [https://2010.igem.org/Team:Berkeley/Vesicle-Buster Vesicle-Buster]) |
| - | * Characterize the operation of at least one new BioBrick Part or Device and enter this information on the Parts or Device page via the Registry of Parts | + | * Characterize the operation of at least one new BioBrick [http://partsregistry.org/wiki/index.php?title=Part:BBa_K426020 Part or Device] and enter this information on the Parts or Device page via the Registry of Parts. |
=== Gold Medal=== | === Gold Medal=== | ||
| - | * Characterize or improve an existing BioBrick Part or Device and enter this information back on the Registry | + | * Characterize or [http://partsregistry.org/wiki/index.php?title=Part:BBa_K426020 improve] an [http://partsregistry.org/wiki/index.php?title=Part:BBa_K112808 existing] BioBrick Part or Device and enter this information back on the Registry. |
| - | + | ||
| - | + | ||
* Outline and detail a new approach to an issue of [https://2010.igem.org/Team:Berkeley/Human_Practices Human Practice] in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation. | * Outline and detail a new approach to an issue of [https://2010.igem.org/Team:Berkeley/Human_Practices Human Practice] in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation. | ||
| + | |||
| + | === Bronze Mousepad === | ||
| + | * Registered the team, had a great summer, and had fun attending the Jamboree. | ||
| + | * Created and share a Description of the team's project via the iGEM wiki. | ||
| + | * Present a Poster and Talk at the iGEM Jamboree. | ||
| + | * Develop and make available via the Registry an open source software tool that supports synthetic biology based on BioBrick standard biological parts. Source code available from sourceforge (http://sourceforge.net/projects/clothocad/). Though we highly recommend downloading one of the more user-friendly distributables from the clothocad.org website or the source using subversion from sourceforge, a zip file containing the source code can also be downloaded [[Media:Team:Berkeley/ClothoSource.zip | here]]. | ||
| + | |||
| + | === Silver Mousepad === | ||
| + | * Provided a detailed, draft specification for the next version of your software tool, or a second, distinct software tools project | ||
| + | |||
| + | === Gold Mousepad === | ||
| + | * Outlined and detailed a new technical standard for managing biosafety (Human Practices) in synthetic biology based on a standardized data model | ||
| + | |||
| + | |||
| + | ==Attributions== | ||
| + | '''ChoaChoa's Delivery Service is composed of 4 undergraduate wetlab students, 2 undergraduate computational students, 2 graduate student advisors, 2 faculty advisors, and administrative support.''' | ||
| + | |||
| + | Our wetlab group of Christoph Neyer, Amy Kristofferson, Daniela Mehech, Conor McClune, and Tahoura Samad built the Choano payload delivery devices, transposase devices, developed and performed all assays associated with this project. | ||
| + | Ben Bubenheim and Bing Xia built the infrastructure for Clotho's API, wrote the Datum layer, worked out the Netbeans and Hibernate platforms, the Biosafety framework, the Algorithm/Actor framework, and several Apps including SeqAnalyzer Algorithm, BBAligner, StringAppend Algorithm, and Groovy Scripter. | ||
| + | Tim Hsiau was the ringleader of the iGEM team providing training, advice, technical and moral support. | ||
| + | Jin Huh provided parts derived from his mammalian payload delivery project which yielded many of the basic parts used in the project in addition to parts used from Berkeley iGEM 2008. | ||
| + | Chris Anderson and Terry Johnson provided lab space, reagents, consumables, moral support, graphics, guidance, and training to the team. | ||
| + | Chris Anderson wrote many of the Apps not mentioned here included within the distributed version of Clotho. The specific data model of the Clotho API was determined through many conversations over the past two years between Ben, Bing, Josh Kittleson, Douglas Densmore, Tim Ham, Michal Galdzicki, and Chris Anderson in collaboratin with the broader SBOL standards community. The new clothocad.org website was provided with support by Autodesk with guidance from Carlos Olguin and produced by Noble Studios. | ||
| + | The UC Berkeley iGEM is selected by the Berkeley iGEM Advising Group composed of Adam Arkin, Jay Keasling, Chris Anderson, Terry Johnson, and Susan Marqusee. We are blessed to receive administrative support from Kate Spohr. | ||
Latest revision as of 03:53, 28 October 2010
- Home
- Project
- Parts
- Self-Lysis
- Vesicle-Buster
- Payload
- [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2010&group=Berkeley Parts Submitted]
- Results
- Judging
- Clotho
- Human Practices
- Team Resources
- Who We Are
- Notebooks:
- [http://www.openwetware.org/wiki/Berk2010-Daniela Daniela's Notebook]
- [http://www.openwetware.org/wiki/Berk2010-Christoph Christoph's Notebook]
- [http://www.openwetware.org/wiki/Berk2010-Amy Amy's Notebook]
- [http://www.openwetware.org/wiki/Berk2010-Tahoura Tahoura's Notebook]
- [http://www.openwetware.org/wiki/Berk2010-Conor Conor's Notebook]
In brief, this year's Berkeley 2010 iGEM team accomplished the following:
- A foundational advance in protein and DNA payload delivery to lower metazoans, opening the door to genetic modification of potentially very useful and previously intractable organisms using synthetic biology.
- An automated, user-friendly, forward-thinking approach to biosafety implemented in the software program Clotho, improving human practice in synthetic biology.
- Developed and deployed the new core of Clotho 2.0 as an App platform for synthetic biology tools
Requirements
Bronze Medal
- Register the team, have a great summer, and have fun attending the Jamboree.
- Create and share a Description of the team's project via the iGEM wiki.
- Present a Poster and Talk at the iGEM Jamboree.
- Enter information detailing at least one new standard BioBrick [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2010&group=Berkeley Part or Device] in the Registry of Parts
Silver Medal
- Demonstrate that at least one Part or Device of your own design and construction works as expected. (See Self-Lysis and Vesicle-Buster)
- Characterize the operation of at least one new BioBrick [http://partsregistry.org/wiki/index.php?title=Part:BBa_K426020 Part or Device] and enter this information on the Parts or Device page via the Registry of Parts.
Gold Medal
- Characterize or [http://partsregistry.org/wiki/index.php?title=Part:BBa_K426020 improve] an [http://partsregistry.org/wiki/index.php?title=Part:BBa_K112808 existing] BioBrick Part or Device and enter this information back on the Registry.
- Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.
Bronze Mousepad
- Registered the team, had a great summer, and had fun attending the Jamboree.
- Created and share a Description of the team's project via the iGEM wiki.
- Present a Poster and Talk at the iGEM Jamboree.
- Develop and make available via the Registry an open source software tool that supports synthetic biology based on BioBrick standard biological parts. Source code available from sourceforge (http://sourceforge.net/projects/clothocad/). Though we highly recommend downloading one of the more user-friendly distributables from the clothocad.org website or the source using subversion from sourceforge, a zip file containing the source code can also be downloaded here.
Silver Mousepad
- Provided a detailed, draft specification for the next version of your software tool, or a second, distinct software tools project
Gold Mousepad
- Outlined and detailed a new technical standard for managing biosafety (Human Practices) in synthetic biology based on a standardized data model
Attributions
ChoaChoa's Delivery Service is composed of 4 undergraduate wetlab students, 2 undergraduate computational students, 2 graduate student advisors, 2 faculty advisors, and administrative support.
Our wetlab group of Christoph Neyer, Amy Kristofferson, Daniela Mehech, Conor McClune, and Tahoura Samad built the Choano payload delivery devices, transposase devices, developed and performed all assays associated with this project. Ben Bubenheim and Bing Xia built the infrastructure for Clotho's API, wrote the Datum layer, worked out the Netbeans and Hibernate platforms, the Biosafety framework, the Algorithm/Actor framework, and several Apps including SeqAnalyzer Algorithm, BBAligner, StringAppend Algorithm, and Groovy Scripter. Tim Hsiau was the ringleader of the iGEM team providing training, advice, technical and moral support. Jin Huh provided parts derived from his mammalian payload delivery project which yielded many of the basic parts used in the project in addition to parts used from Berkeley iGEM 2008. Chris Anderson and Terry Johnson provided lab space, reagents, consumables, moral support, graphics, guidance, and training to the team. Chris Anderson wrote many of the Apps not mentioned here included within the distributed version of Clotho. The specific data model of the Clotho API was determined through many conversations over the past two years between Ben, Bing, Josh Kittleson, Douglas Densmore, Tim Ham, Michal Galdzicki, and Chris Anderson in collaboratin with the broader SBOL standards community. The new clothocad.org website was provided with support by Autodesk with guidance from Carlos Olguin and produced by Noble Studios. The UC Berkeley iGEM is selected by the Berkeley iGEM Advising Group composed of Adam Arkin, Jay Keasling, Chris Anderson, Terry Johnson, and Susan Marqusee. We are blessed to receive administrative support from Kate Spohr.
