Skip to content
This repository has been archived by the owner on Jan 20, 2023. It is now read-only.


cannin edited this page Jun 10, 2016 · 1 revision
Clone this wiki locally


  • Tobias Czauderna (TC)
  • Stuart Moodie (SM)
  • Anatoly Sorokin (AS)
  • Falk Schreiber (FS)


TC: one afternoon for libSBGN (all issues which showed TC in Edinburgh)

TC: proposal were prepared, will be on COMBINE discuss list

TC: will send the minutes about HARMONY discussions to libSBGN discussion list

TC: submaps support discussed, colour and style have been discussed, compartment shapes (Martijn will send proposal to libSBGN-discuss),

SM: Who will implement is?

FS: Frank (Bergmann) and Tobias could meet for a week (invite Frank here or send Tobias to Heidelberg) and they could spent time on it, has to be discussed with Frank

TC: Idea of SM and TC - just brute force (...?)

discussion about file formats

proposals for connections to other file formats (level and version explicitly or in url, both in the file), mine type

MS reports about his discussion with H. Sauro (SBGN for Synth. Biology), was interested in SBGN, but thinks it is too complicated (looks for cut-down SBGN)

SM: Meeting in London (2. week in July) Synth. Biology open language (, who could attend? SM thinks that there would be a possibility to bring both standards closer together and include Synt. Biology in SBGN

SM: chat with Michael Blinov: open world PD (as discussed in Edinburgh)

SLM trip to see Mirit & Kurt

SM: useful, spoke to Mirit,still involved in SBGN, also met with Kurt (Kohn) and Augustin, great conversation

SM: seems that there is still involvement in SBGN, we have lots in common (SBGN and MIM), could try to bring it more together


How to get it done?

Status: draft of design, the problem is that it is not clear

TC and FS will rethink the design

deadline end of this week, otherwise we have an Amazon gift voucher


MC: 3 more results, will close the survey, will write a report for web site (send it to discussion list)

Actions from SBGN-9

editor actions:

  • Alice, SM contacted Alice, FS will send email to SBGN-discuss (explaining what happened, ask if there are objections)
  • Anatoly takes ownership of the L2 issues and make sure that the actions for the meeting get dealt with.

Status of specs


  • PD: L1 V2 need to do examples.
  • ER: proposal, L1 V2 mid June request for comments
  • AF: update of spec until COMBINE - aiming for L1 V1.2(?)

Outreach ideas

ICSB workshop in Copenhagen?

(Tutorial: Modelling and Simulation of Quantitative Biological Models - Martin Golebiewski, Frank Bergmann, Akira Funahashi, Noriko Hiroi, Mike Hucka, Nicolas Le Novère, Pedro Mendes, Ion Moraru, Sven Sahle, Jacky Snoep, Dawie van Niekerk, Andreas Weidemann, Katy Wolstencroft)

  • Would Tobias be able to go?
  • SM spoke to Martin, there would be the possibility for an SBGN representative to present the standard/tools

Collaboration with WikiPathways?

  • speak to WikiPathways people
  • TC will speak to Martijn and we’ll follow up at next meeting.

How will be promote discussion of SBGN L2?

put discussion on the mailing list

get more ideas, more issues to get people involved

discussion on Wiki, using google docs

SBGN Town Hall meeting: fixed time (ones every month / two months) for discussion, agenda beforehand on the discussion list - agreement

FS: shall we have a one day editor workshop via skype?

Future meetings - COMBINE 2013

FS reports briefly about current the COMBINE planning

FS will discuss with other COMBINE coordinators, especially what is about SBGN (so that it would be put on discuss list)

Next SBGN meeting?

SM: Huaiyu tries to fund COMBINE 2014, two days SBGN

SM: other possibilities for meetings

mixed real/virtual workshop to avoid problem that people may not get funding

Robin was interested in hosting an Edinburgh-like meeting in 2014


FS: not much happening, some members difficult to read; no objection to Nicolas

Next TC