SciCom2010

The first meeting of the SBGN scientific committee was held in the Edinburgh International Conference Center. Thanks to Igor Goryanin for arranging a room.

Attendees: Igor Goryanin Michael Hucka Hiroaki Kitano Nicolas Le Novere Augustin Luna on the behalf of Kurt Kohn

Report

Two new specifications have been released, just before COMBINE 2010. Both Process Descriptions Level 1 Version 1.2 and Entity Relationships Level 1 Version 1.1 are corrections and clarifications. No new glyph is introduced and the semantics is not changed. Although much material has been gathered for the versions 2 of both ER and PD, we did not have time to incorporate it yet.

Wittenberg hackathon: Its attendance was seriously reduced by the eruption of the Icelandic Volcano. There were a lot of discussions, mostly to clarify some semantics point and to reach consensus among editors rather than coming up with new developments. One of the main outcomes of the meeting is the concrete launch of the LibSBGN effort. It corresponds to a major involvement of Martijn van Iersel, which is good news considering his involvment in Wikipathways.

SBGN was part of the COMBINE 2010 meeting: The meeting in general was a resounding success. SBGN and graphical representations were center stage in many sessions. Even the speakers not working directly on SBGN development had slides containing some sort of SBGN. There was a breakout session about libSBGN and two SBGN breakout sessions in the evening (plus an editor dinner). We progressed on many issues: http://sbgn.org/Events/SBGN-6/SBGN_languages_breakout_topics

Plans for next meetings

The Scientific committee is happy for the SBGN hackathon to take place during the combined event HARMONY. HARMONY will take place in Memorial Sloan Kettering Cancer Center in New york, hosted by Chris Sander/Emek Demir.

In general, the scientific committee is happy that SBGN is affiliated to the umbrella organisation COMBINE. Letters of support will be provided by Igor Goryanin, Michael Hucka and Igor Goryanin to support a grant application to get things going.

Funding

1) The committee discussed possible solutions to fund the development of the specifications and the maintenance of the website. Envisioned solutions were for instance:

Participate to BBSRC responsive mode or EU projects with a particular biological focus, but involving pathways generation and analysis.

Enter in contact with NCBI Biosystems: http://www.ncbi.nlm.nih.gov/biosystems/ NLN: ask Henning what is it about. Relation with Reactome, UniPathways. Contact David Lipman?

Enter in contact with NCI pathway database: http://pid.nci.nih.gov/

Igor Goryanin and Hiroaki Kitano discussed possible funding in Okinawa, such as flagship project at OIST.

2) The committee discussed the pre-occuping situation of libSBGN development. Several key individuals are about to end their contracts or wish to move on with their career path.

Composition of the committee

Gary Bader is proposed as a new member. This would reflect the importance of BioPAX for SBGN.

Endorsement

We need more exposure of Activity Flows to show that SBGN can be simple.

The examples on the wiki should be grouped thematically. For instance, Signalling pathways, metabolic networks, synthetic biology etc.

We should expose the roadmap of future evolutions of SBGN, with our efforts to link to other communities. Maybe divide into branches: Unstable? Development? Experimental?

Engage critical people and gather their requirements, putting them in position of contributors rather than critics.

We need more papers on SBGN. An example could be a paper on using SBGN for education.

NLN: Ask Thomas Lemberger if MSB could advise SBGN as a structured format.