"
Team:Berkeley Software/Misc
From 2009.igem.org
Contents |
Draft Specification
This section details a draft specification for the next version of Eugene, Spectacles, and the Clotho environment.
Eugene:
Support for
Collaboration
For all of our projects, we worked with a number of different groups both to make our tools more visible, as well as get valuable feedback. This section discusses some of these collaborations.
UC Berkeley iGEM team - we worked very closely with our wet team counter parts to tie our Kepler based assembly workflows with the Beckman Coulter BioMek 3000 liquid handling robot that they used. In addition we beta tested our software with them, incorporated their feedback, and ran tutorial sessions on Clotho use and how to write Clotho plug-ins.
Stanford iGEM team - we provided early versions of Spectacles to the Stanford iGEM team so that they could test it out. In addition we worked with them to incorporate new iconography as they added it to the SBOL Visual effort.
University of Minnesota - Emma Weeding worked with us
Joint BioEnergy Institute (JBEI) -
Valencia - In addition to many other iGEM teams, we filled out their survey and received a gold medal (100% team participation).
Support for New Technical Standard
This entire project is very tied to the [http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical/Exchange Synthetic Biology Open Language] (SBOL) effort. This is a set of three activities related to the standardization of a number of required synthetic biology concepts with the goal of facilitating software development. We contributed in the following ways.
SBOL Visual- We worked with Suzie Bartram and Cesar Rodriquez at Stanford to make sure that Spectacles was 100% compliant with the the SBOL Visual standard. This included support to assign functional concepts to the icons as well as providing a very smooth upgrade path in the event the images evolve.
SBOL Semantic - By revamping the Clotho data model we have enabled the internal structure of Clotho to adapt to new ideas regarding the representation of biological data. Bing Xia and Douglas Densmore participated in the SB Data Exchange working group meeting at Stanford on 26/07/2009. Clotho as a project is committed to the support of this standard.
SBOL Script - SBOL scriupt is an effort to develop a human readable specific. Eugene has been created to be a super-set of the eventual SBOL script. A key piece that we added support for in Eugene is the exporting of Eugene as an XML description. This will lead to the manipulation of Eugene by other tools as well as translating Eugene into a more restricted form which will be SBOL script.
Human Practices
Related Links
iGEM 2009 Berkeley Wet Lab Team
[http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical/Exchange SBOL Effort]
[http://groups.google.com/group/synbiodex Synthetic Biology Data Exchange Group]
