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cannin edited this page Jun 10, 2016 · 1 revision


  • Stuart Moodie (SM)
  • Nicolas Le Novère (NLN)
  • Alice Villeger (AV)
  • Emek Demir (ED)
  • Huaiyu Mi (HM)
  1. Actions review (SM)

1.1) NLN: finalise the survey on reversible arcs

NLN: we don't have a sufficient majority to change anything at that point. This really is a survey to assess people's opinion, not a vote leading to a final decision.

The second part of the survey contains useful information which can be used to feed future discussions.

The results don't appear on the editor list yet, but NLN will send it [ACTION]

1.2) SM: initiate debate on subunits

SM: not done yet [ACTION]

1.3) SM: develop page for PD survey results

SM: DONE, need to put up [ACTION]

  1. Report on LibSBGN (AV)

The release happened as planned at the end of January. A small meeting took place between Alice, Martijn, Tobias and Falk around February 7-11th:

  • Draft of ER implementation (to be discussed at Harmony) => they found a few bugs in the ER specifications
  • Tool proposed to handle validation: Schematron
  • Discussions on a potential paper

=> unresolved question: Bioinformatics Application Note, or Nature Methods? (NLN is in favour of the latter)

  1. Role of SBGN Editors (NLN)

NLN will write some guidelines [ACTION]

  1. SBGN list: code of conduct and/or moderation? [NLN]

NLN is in favour of it. HM and ED are rather against (don't want to deter people)

It was agreed that SBGN discuss list should not be moderated, although we will monitor the situation.

AV will write some "netiquette" guidelines (usage and code of conduct) [ACTION]

  1. HARMONY 2011 (NLN/ED)

SM: can we have an update on funding, etc? (esp. accommodation)

How much money is available? (SM has UK/US grant available to cover LibSBGN/SBGN hackathon events)

ED: 210 hotel rooms are booked, a bit short

NLN: has japan partnering grant that can be used too.

ED: currently 3000 USD short, but have 4000 USD buffer from Chris (?)

SM: can commit to more money. Maybe 10,000 to 20,000 USD?

ED: must know! Some decision must be made tomorrow so that accommodation can be finalised.

NLN: this is all very late. Ideally accommodation should be ready 5 months in advance.This could cut attendance massively. ED must announce accommodation is covered ASAP. There is a risk some people will have booked another hotel already, which would make reimbursement very difficult.

ED: delays because of multiple source of funding, different organisations, + misunderstanding about how much money SM had. It's suboptimal, but still manageable. Will send email right now to BioPAX, SBGN, and SBML discuss

SM: will get back to ED ASAP re: how much money is available from his grant

  1. COMBINE 2011 (NLN)

The next meeting will be held in Heidelberg, 3 - 7 September 2011. The precise location not defined yet. Re: funding, grant will be applied for to cover most expenses. Will get done, but details have not been finalised yet.

The COMBINE website is up and running. The visual identity is being finalised. we are now waiting for answers to grant applications. The first meeting with COMBINE as a "sponsor" will happen in March (encoding models and metadata for drug discovery).

  1. Funding for SBGN development

HM: has started contacting program officer at NSF ABC advance. Can fund bioinformatics related project, as small as a workshop, as big as a maintenance grant. HM has sent an email to get feeling of what they think is appropriate re LibSBGN. Will talk on phone to get feedback.

NLN: money for workshops runs out in 2012 (=> HARMONY 2012). 2011 is covered. Must get some meeting money for 2012 and beyond.

HM: will ask for money for meetings (+ guidance)... 3 options:

  1. for workshops only (small grant)
  2. workshops + some specs development (1 person) and writing (small/medium grant)
  3. software development (Panther, other? + BioPAX => COMBINE angle) (big grant?) => need feedback on that

Deadline: July => some time left, but must submit by end of June

SM: what size of grant?

HM: how much is the US/UK grant?

SM: 60,000

NLN: 50,000 is what you need for 1 joint meeting.

HM: can apply for 2, 3, etc years. Need to check budget with NSF. If we want to fund people in UK, that can be complicated (possible with NIH, but HM doesn't know about NSF). No answer to email so far.

NLN: some funding schemes are better for hackathons (tech/tools, HARMONY), other are more science oriented (BBSRC funding for COMBINE). Grant applications may better try to only fund HARMONY, or COMBINE, not all meetings. We should also try to get sponsors: easier with COMBINE than HARMONY. So HARMONY needs more help with grants (can't get sponsors)

SM: NLN is sceptical about getting money for specs development.

NLN: it's hard. But LibSBGN development is more likely to get funding, and could include specs writing.

SM: should we wait till we have a grant to submit a LibSBGN paper? (i.e. if a paper is already out, does it make it more difficult to get funding?)

NLN: was not problem with LibSBML (paper 2003), which does get funded for development.

HM: looked at website of potential grants: there's some very small grants, about development of ontologies. There's also bigger grants about database infrastructure (million dollars over 3 to 5 years). So, a large range. This is the "advanced biological informatics" call. It may be possible to get funding for spec development for SBGN, but need feedback (will ask question). This is not a pure software development call, it's got a pretty wide range (very experimental projects too).

SM: so what's the plan?

HM: sent email last week, would like to talk next week. Will follow up by end of week if no answer. Will just call them next week anyway. And when get answer, decision at next SBGN meeting [ACTION]

Other potential grants?


  • Next call of BBSRC strategic TRDF? For LibSBGN
  • COMBINE? If could become self-sustainable (like the W3C), people could be employed on it.
  • In the long term, ELIXIR (need to convince that standards is infrastructure)

NLN: also, need to convince collaborators to include SBGN/LibSBGN in large scale European projects. E.g. Manchester is involved in several projects which use standards but don't dedicate any part of their budget to standardisation. We need to influence grant writing to include support and development of standards in these projects. A partnership on one project would solve most problems.

  1. ER status

NLN: switch discussion on outcome/etc. to discussion rather than survey. He will update the specs based on the feedback from the LibSBGN team [ACTION]

AV: has some more feedback, will put it in the tracker [ACTION]

SM: re: current ER discussions on mailing list, are we all talking of different things when talking about ER? Or does the confusion arise simply from using different terminology?

  1. PD status (SM)

SM will start working on it again next month

  1. AF status (HM)

[skipped, no time]

  1. Next meeting

The next meeting is scheduled for 16:00 GMT 15/3/11

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