COMBINE 2013

Dates: September 16–20, 2013
Location: Paris, France
Hosted by: U900 Computational Systems Biology of Cancer Department, Institut Curie

The "Computational Modeling in Biology" Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology and related fields. The COMBINE forum is a workshop-style event with oral presentations, posters and breakout sessions.

The fourth annual COMBINE meeting took place at the Institut Curie in Paris, from Monday September 16 through Friday Sep. 20, 2013.


List of attendees

Abstracts

Accommodation

Travel Information

Documentation

Exit Survey

Thanks for a great meeting!

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Agenda

A separate page presents the detailed agenda, as well as links to slides and videos.

The first day of the meeting, Monday 16th September, was dedicated to presentations of modelling approaches in biology either not currently covered by our efforts, or using them in new or innovative ways. Oral presentations were selected from the submitted abstracts. The meeting took place in the amphitheatre Constant Burg, Institut Curie, 12 rue Lhomond - Paris 5.

Speaker Title
10:45 - 11:15 Welcome and coffee
11:15 - 13:00 Session 1 Chair: Andrei Zinovyev
11:15 - 11:45 Michael Hucka, Caltech Recent developments in the world of SBML (the Systems Biology Markup Language)
11:45-12:00 Frank Bergmann, Heidelberg University Applying the Scientific Method to Simulation Experiments: SED-ML
12:00-12:30 Vincent Danos, CNRS, University Paris-Diderot, University of Edinburgh Rule-based approaches to modelling
12:30-13:00 Denis Thieffry, École Normale Supérieure Logical modelling of cell fate specification
13:00-14:00 lunch
14:00 - 15:45 Session 2 Chair: Emmanuel Barillot
14:00-14:15 Marco Antoniotti, BIMIB Modelling Colonic Crypts with VCell and SBML/Spatial
14:15-14:45 Hiroaki Kitano, SBI, OIST Garuda Platform: An integrated inter-operability for biomedical software and data resources
14:45-15:15 Andrew Davison, CNRS Interoperability and model sharing in large-scale neuronal network modelling and neuromorphic computating
15:15-15:45 Marc Lavielle, INRIA, University Paris-Sud Monolix and other new tools for population pharmacometrics
15:45-16:15 Coffee
16:15 - 18:00 Session 3 Chair: Éric Bonnet
16:15-16:30 Herve Turlier, Institut Curie A model for furrow constriction in animal cell cytokinesis
16:30-17:00 Benjamin Ribba, INRIA Modeling of efficacy data in clinical oncology
17:00-17:30 Andrei Zinovyev, Institut Curie Mathematical modeling of cancer-related molecular mechanisms
17:30-18:00 Dirk Drasdo, INRIA, University of Leipzig Agent-based models of tissue organisation - concepts and components


The remaining four meeting days, from Tuesday 17th to Friday 20th September, included talks about the COMBINE standards and associated or related standardization efforts and discussion sessions.

Tue Sep 17 Wed Sep 18 Thu Sep 19 Fri Sep 20
08:30 - 09:00 welcome welcome welcome welcome
09:00 - 10:30 Amphi Marie Curie: Update on SBML, CellML, NeuroML and PharmML (chair: Nicolas Le Novère) Amphi Marie Curie: Data representation and use (chair: Frank Bergmann) Amphi Marie Curie: Model sharing (1): Metadata (chair: Nick Juty and Dagmar Waltemath) Amphi Marie Curie: SBGN: overview and update (chair: Falk Schreiber)
10:30 - 11:00 break break break (Hall BDD) break (Green café)
11:00 - 12:30 Amphi Marie Curie: SBML Level 3 Version 2 (chair: Mike Hucka) Amphi Marie Curie: SED-ML future: L2 / L1V3, parameter estimation (chair: David Nickerson) Amphi Marie Curie: Model sharing (2): Repositories (chair: Nick Juty and Dagmar Waltemath) Amphi Marie Curie: Visual Markup (SBGN-ML, SBML Layout etc.) (chair: Tobias Czauderna)
12:30-14:00 lunch lunch (poster session) lunch (Hall BDD) lunch (Green café)
14:00 - 15:30 Amphi Marie Curie: Using distributions in model descriptions (chair: Lucian Smith)
Cour Anglaise 1: SBML Flux Balance Constraints (chair:Brett Olivier)
Cour Anglaise 2:
Amphi Marie Curie: SBML Spatial (chair: Ion Moraru)
Cour Anglaise 1:
Cour Anglaise 2:
Amphi Marie Curie: COMBINE archive (chair: Nicolas Rodriguez)
Cour Anglaise 1:
Cour Anglaise 2: PALS meeting
Amphi Marie Curie: SBML Arrays & Hierarchical Model Composition Packages (chair:Lucian Smith)
Salle Joliot: SBGN: development of L2 (chair: Huaiyu Mi)
Cour Anglaise 2:PALS meeting
15:30-16:00 break break (poster session) break (Hall BDD) break (Green café)
16:00 - 17:30 Amphi Marie Curie: SBML Qualitative Modeling package (chair: Claudine Chaouiya)
Cour Anglaise 1: Modelling physiology (chair: Padraig Gleeson)
Cour Anglaise 2:
Amphi Marie Curie: Community building and links with other efforts (chair: Martin Golebiewski)
Cour Anglaise 1:
Cour Anglaise 2:
Amphi Marie Curie: SBML Multi package (chair: Fengkai Zhang)
Salle Joliot: BioPAX TC
Cour Anglaise 1 & 2: PALS meeting
Amphi Marie Curie: SBML Dynamics Package (chair:Chris Myers)
Salle Joliot: SBGN: development of L2 (chair: Falk Schreiber)
Cour Anglaise 2: PALS meeting
20:00-22:00 Conference Dinner

For the precise location of the rooms Amphi Marie Curie, Cour Anglaise 1 and Cour Anglaise 2, please see the "Venue" paragraph below.

Funding Acknowledgements

Support for COMBINE 2013 was provided by the following organizations:


Institut des Systemes Complexes

Fondation Pierre-Gilles de Gennes

Groupement de Recherche en Bioinformatique Moléculaire

Venue

COMBINE 2013 was hosted at:
Institut Curie
Amphithéatre Marie Curie
1, rue Pierre et Marie Curie
75005 Paris
France



The modelling day took place in the Amphithéatre Constant Burg, located 12, rue Lhomond.

The breakout rooms, coffee, lunch and poster rooms were nearby. Click here to download a map of the different locations for COMBINE 2013.


Agrandir le plan

Accommodation


Agrandir le plan

Organization

COMBINE 2013 was organized by:

  • Eric Bonnet, Institut Curie, France.
  • Emmanuel Barillot, Institut Curie, France.
  • Nicolas Le Novère, Babraham Institute, UK.
  • Gary Bader, University of Toronto, Canada.
  • Michael Hucka, California Institute of Technology, USA.
  • Falk Schreiber, IPK Gatersleben & MLU Halle-Wittenberg, Germany.

Contact for scientific organization was: Combine Coordination

Contact for local organization:
Eric Bonnet
Institut Curie
11, rue Pierre et Marie Curie
F- 75005 Paris
Phone: +33 (0)1 56 24 69 32
e-mail: eric.bonnet@curie.fr

Additional notes

Electrical supply

If you were traveling from abroad, you needed to bring an appropriate power plug converter for your laptop and all other electrical devices you brought. The domestic electric system in France uses 220 V at 50 Hz. The plug type is described here.

Internet access

The meeting room (Amphithéatre Marie Curie) had wireless internet access available.