Minutes of Authors' Meeting 26 Aug 08

Location

ICSB 2098, Gothenburg

Attendees

Hiroaki Kitano (HK) Nicolas Le Novère (NL) Stuart Moodie (SM) Anatoly Sorokin (AS) Mike Hucka (MH) Falk Schreiber (FS) Yukiko Matsuoka (YM) Huaiyu Mi (HM) Katja Wegner (KW)

Apologies

Emek Demir

Agenda/Notes/Actions

1) Draft Paper

Agreed to aim for submission by SBGN 4 (16th Oct).

Aim to submit to Nature Biotech.

Deadlines:

- Initial contributions to be sent to NL by Fri 19 Sep.

   SM/AS/FS to work on rules box
   HW to work on application to the biologist

   All to contribute as they see fit.

- Final draft ready by 30 Sep.

2) SBGN 4 Rostock (16-17 Oct)

NL has booked the hotel and venue and paid for the venue.

Rough agenda is to spend approximately 1/2 day each for Tools, ER, AF, PD Level 2.

The aim should be to concentrate primarily on ER and AF as we need to make progress on these.

It was agreed that representatives of the following tools should be invited (in addition to Vanted, Netbuilder, EPE and CellDesigner):

- Cytoscape (AS to approach) - Terranode (? to approach) - Ingenuity (? to approach) - Athena (Frank Bergman) - Arcadia (Alice Vegner) (SM approached)

3) SBGN Hackathon

It was agreed that in order to get the ER and AF Level 1 standards ready by ICSB09 we should have a "Hackathon" similar to the Okinawa super-hackathon in early 09.

NL agreed to host and fund the meeting at the EBI for 4 days in the 2nd half of Jan 09. Participants should fund their own travel. (NL can you clarify if you planned to fund accommodation too?).

FS volunteered to host it too, but Jan is too soon to book the venue. It was suggested that he host a future Hackathon or meeting.

4) Dissemination

Not having presented a poster at the meeting the meeting felt that we should do more to present and promote SBGN to the wider community.

Actions proposed where:

KW to prepare a poster for us to use to promote SBGN at meetings.

The poster should be made available for download from the SBGN website.

NL will find out if we can present a poster at CMSB 08 in Rostock.

It was agreed that we should ask ED to promote SBGN to the BioPAX community.

5) Funding

We want mostly money to fund meetings and travel to meetings.

In addition it would be useful to get money to fund development on toolkits.

The best funding opportunities identified were:

NIH (next deadlines Oct 08, Feb(?) 09) 10 month delay before get money. Requires US PI.

BBSRC grants (no relevant calls currently known about).

BBSRC/US Partnering awards are coming up. This would help fund a meeting in US and/or UK and travel between both countries. NL and AS/SM could apply for this - not clear who was going to.

EU funding - would need to be part of a larger grant. May be possible.

6) SBGN Governance

NL proposed that we adopt a governance structure similar to that used by the SBML community. This would be 5 Editors elected by the community for 3 year terms, with a 3 year period thereafter during which they cannot be elected.

This structure was agreed, with the first elections to take place at the next Hackathon.

NL nominated FS t be the additional editor and this was agreed.

Therefore the current SBGN editors are:

NL, SM, AS, MH, FS

7) Champagne

During celebratory drinks there were a number of additional suggestions:

- We should have a competition for the most attractive and SBGN diagram (it would have to be an SBGNB diagram).

- We should aim to draw a large SBGN diagram (similar to the Kitano EGFR and TLR diagrams) that could be included as a download with the paper. The aim would be to help promote the paper and SBGN.

- We should have a comprehension test. People submit SBGN models with a supplementary description of what was actually drawn. Another would read the map "blind" and write their description of what the map meant. We could then compare. Useful test of SBGN's claim to be unambigous.

- HK suggested the following: (1) Create "SBGN Gallary" in sbgn.org (2) reposit beautifully layouted SBGN diagram for typical pathways and interactions that can be used for textbook, class room, presentations, so that anyone can download and use it. (3) all these images and underlying files should be under Creative Commons license. We can think about typical pathways such as: GPCR, MAPK, Glucose, related Central metabolic cycle, Simplified apoptosis pathways etc. go and look at typical molecular biology text and redraw it in SBGN!! Maybe we can try 100 images in a month.

HM volunteered to work on the above with the Panther database.

Comments from ED

ED sent this email in response to the above minutes.

As with Cytoscape, Chris is one of the PIs of Cytoscape project - in fact we have 2 FTEs working on Cytoscape. Gary Bader is also very aware of the SBGN. I keep both of them updated about SBGN. I can simply ask them to bring SBGN up in the next Cytoscape conf. call. I am also in touch with two BioPAX- Cytoscape visualization plugins and I keep urging them to check out SBGN. I am also happy to oblige with your suggestion of promoting SBGN in BioPAX - in fact I am already doing it to my best capability. I recently talked to Wikipathways, GenMapp and Visant groups and asked them to check SBGN and tell us what they need to adopt it. For most of these parties there are technical issues they need to solve (like node decorations or compound graphs) before they can adapt SBGN but all of them were very interested in at least reading the spec and giving feedback. I need to follow-up with them - this is an action item for me and I will keep you guys updated.

Patika group is back from sabbatical - yes Ugur and all of his grad students were in SF last year and now they are back and working on pathway visualization again. They started with reading the SBGN spec. By the way there is a serious EU grant potential if you would include the Patika group and BigCat bioinformatics in NL ( wikipathways) - If I am not counting wrong we already have 6 EU groups and it is quite easy to extend this list.

I don't like rules ( says the guy who wants everyone to represent pathways with standard rules ) but it probably is the right time to ask: I am invited to speak in a workshop this November and I intend to include a few SBGN slides. What is the policy for speaking on behalf of SBGN? Are we just going to let everyone else know in advance and assume an ok unless nobody objects or are we going to adopt a more formal process?Also, in the past meetings, we had some disagreements about the scope of SBGN- especially I would be very sensitive to its relation to SBML and BioPAX and how it is presented. I believe we have to have some sort of official SBGN description and roadmap in order to be able to talk about SBGN and its goals in a consistent manner. I know it sounds a bit too strict but I had quite interesting experiences in the past. This calls for my fav. Charlie Brown quote: Sometimes I lie awake at night, and I ask, "Where have I gone wrong?" Then a voice says to me, "This is going to take more than one night.

As with US PI I am not sure if currently there are candidates, but if you would like to have Chris as a PI or co-PI I am pretty sure he would like to join in. At the least I am pretty sure we can obtain substantial amount of LOSs - and I can dedicate some of my time to help with grant writing ( although I must confess I am not very good when it comes to selling ideas ).

It is a shame that nat. biotech does not do open-access-for-a-fee. I feel that it is particularly important for this paper.

That's all - and kudos to all editors and participants for contributing countless moles of brain ATP . Oh, and thanks for bearing with my long digressions during the workshops and in mails.

See you in Rostock!