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Second CoLoMoTo meeting (Hinxton, March 2012)

The second CoLoMoTo meeting took place on March 27-28 2012, at the Wellcome trust conference centre, Hinxton UK. It was organized by the Systems Biomedicine group, EMBL-EBI.

Also see the minutes of the discussions.


Thurday, 18

Presentations by Colomoto members, focusing on getting to know each other, and progress update.

Time Who Topic
13:00   Arrival, lunch
14:00 J Saez-Rodriguez CellNOpt, modelling prior knowledge networks trained to data
14:20 C Chaouiya GINsim, current status and future developments
14:40 D Thieffry Compression of state transitions graph for the analysis of cell fate decisions
15:00 A Dräger Modeling the influence of nuclear receptors and statins on hepatocyte metabolism
15:20 T Helikar The Cell Collective: Towards a more open, collaborative, and integrated systems biology
15:35   Coffee break
16:00 S Klamt Qualitative modeling approaches for signaling and regulatory networks [CANCELED]
16:30   Brainstorm on governance, funding
18:00   End of meeting
19:30   Conference dinner in Cambridge

Friday, 19

Developers presentations.

Time Who Topic
09:00 A Naldi Colomoto toolbox
09:30 M van Iersel SBML-qual validation workshop
10:00 S Keating SBML packaging workshop
10:30   Coffee break
11:00 N Rodriguez JSBML workshop
11:30   Brainstorm on development process, validation and interoperability
12:30   Lunch
13:30   Brainstorm on future development


  • Julio Saez-Rodriguez, EMBL-EBI, Cambridge, UK
  • Sarah Keating, EMBL-EBI, Cambridge, UK
  • Nicolas Rodriguez, EMBL-EBI, Cambridge, UK
  • Nicolas Le Novère, EBML-EBI, Cambridge, UK
  • Martijn van Iersel, EMBL-EBI, Cambridge, UK
  • Emanuel Gonçalves, EMBL-EBI, Cambridge, UK
  • Thomas Cokelaer, EMBL-EBI, Cambridge, UK
  • Claudine Chaouiya, Instituto Gulbenkian de Ciência, Portugal
  • Aurelien Naldi, CIG-UNIL, Lausanne, Switzerland
  • Tomas Helikar, University of Nebraska USA
  • Andreas Dräger, University of Tübingen, Germany
  • Denis Thieffry, IBENS, Paris, France

Funding and Acknowledgements