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Editors_Telecon_13_Jul_2012

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Systems Biology Graphical Notation

###Home

###Events

###Editor Meeting Notes

###LibSBGN

###Specification Development

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Present:

  • Alice Villéger (AV)
  • Emek Demir (ED)
  • Nicolas Le Novère (NLN)
  • Falk Schreiber (FS)

News from the SBGN world

  • NLN - Paper from Edinburgh group with best SBGN map, have been ask to submit for next competition
  • FS - SBGN bricks, standard representation of typical biological processes, will be part of SBGN-ED / VANTED
  • ED - supports Ugurs group, support for CytoscapeWeb under development

Funding

  • NLN - OpenMod project is unlikely to be funded
  • ED - grant proposal initial not successful, outreach should be improved, there will be new application in September

Specifications

  • Specification drafts are all publicy available - shall we make them only accessible to the editors?

NLN - also the user manual is affected. Specification and public draft on web site, other parts restricted to editors.

FS - does not see major negative aspects of resticting to editors

conclusion: restriction to the developers (NLN will do it)

  • Status of PD, ER, AF specifications - level 1 version 2 should be ready before COMBINE to be discussed there

NLN - will release user manual soon

NLN - all should read the specification by Stuart

FS - should be done for all specs

NLN - PD is the most important one (tool support, talks to two populations of users)

FS - shall each study all specifications or each one specific one

NLN - concentrate on PD

NLN - refactoring, validation rules, all participate and put it in the tracker

FS - what is problem with the structure

NLN - should be discussed if there is the need to restructure, maybe parts can be in the user manual

NLN - for each validation rule tracker

ED - will go through ER

NLN - we could seek assistence from others (e.g. Tobias, Astrid)

ED - where to put semantics discussions

NLN - put it in document and publish it

ED - would be something for SBML, BioPAX and SBGN

conclusion: focus on PD specification and user manual, carefully check structure, content, validation etc. to have both (spec and user manual) ready for COMBINE, AS and NLN will make changes of the documents

COMBINE

FS - it would be good if schedule is out soon

NLN - is involved in the program development

NLN - HARMONY in Connecticut propably May, ICSB in Copenhagen preliminary date 29/08 - 04/09/13, ISMB 2013 in Berlin

conclusion: NLN will contact COMBINE organizers

Web site

AV - checked all pages, some dead / inaccessible pages, broken links

AV - will fix it, will send info to mailing list

AV - experimented with CSS and will send screenshots, fixing style on the website is not straight forward (e.g. icons do look differently with non-black background)

NLN - finding icon set would be good (free icon sets available)

conclusion: AV will send information to mailing list, should be discussed on COMBINE