Team:Paris Liliane Bettencourt/Project/Synbioworld

From 2010.igem.org

Revision as of 14:03, 27 October 2010

Synbioworld is a collaborative web platform created to give the synthetic biology community a place to talk, share data and resources, and stay abreast of new developments in the field.  The site is based on a CMS system that allows for all the normal features of a blog, but also allows for seamless user management in the various apps we have on the site.  SynBioWorld inludes the following features:

• News: SynBioWorld will aggregate several Twitter and RSS feeds related to synthetic biology. Original content will also be created by the team and members of the community.

• Librarian: Libriarian is an algorithm and UI frame that automatically aggregates, displays and allows to search through papers, scientists, and institutions relevant to synthetic biology.

• Forum: This feature will finally answer the repeated request of members of the community, in particular iGEM participants. It will be moderated by volunteers from the community (over 50 people have already expressed interest in helping out.)
• Events: All events relevant to the synthetic biology community will be announced on the site. Furthermore, we are working on a partnership with the new talk aggregation site SittingO, which has been described as the “imdb of the conference circuit” to provide a huge annotated database of synthetic biology talks.

- and - as contribution of this year's from our team...:

• openProtocol: openProtocol is a standardized but highly flexible tool for generating and sharing protocols.  Creation of a protocol is as simple as filling out a form, and uploading any relevant media (video, pictures, or even an animation.)  All protocols share the same layout, but the specifics of each protocol can be tweaked such that any protocol can easily be adapted into our system.  Further, in keeping with several studies on the usefulness of annotated protocols (show that EUREKA study, as well as the other oss study here) openProtocol makes use of a wonderful set of open-source commenting tools provided by the Public Library of Science (PLoS) to provide in-text notes on any protocol.  There are two rather different useage cases for this tool, which we outline below.

First, those new to synthetic biology often require a single, simple, well-agreed upon protocol for a procedure.  The protocol has to be easily available, and must bear the marks of a mature protocol, that is: it must be commented upon, must be well designed, must take into account all the possible pitfalls and difficulties an experimenter may encounter when carrying out the experiment.  

Second, the experienced researcher often would like to have a protocol that is personalised to their lab situation, but that can nonetheless be shared with colleagues and used as a record for a lab journal.  openProtocols are perfect for this usage, as they are saved centrally, and use a versioning system that allows for unlimited modification and reversion on a single protocol. Finally, we hope that by providing a pleasant and useful interface for making protocols public, more authors will begin to include links to an openProtocol in their “methods” sections, greatly increasing the immediate reproducibility of published experiments.
read more about our design and specs of the openProtocol here