Full agenda

Agenda

Day 1 (Monday, September 16)

Time Topic Speaker Slides Recordings
11:00 - 11:10 Welcome to COMBINE 2013 Éric Bonnet Video
11:10 - 11:25 COMBINE 2013 Nicolas Le Novère Video
11:15 - 13:00 Session 1 Chair: Andrei Zinovyev
11:15 - 11:45 Recent developments in the world of SBML (the Systems Biology Markup Language) Mike Hucka Slides Video
11:45-12:00 Applying the Scientific Method to Simulation Experiments: SED-ML Frank Bergmann Slides Video
12:00-12:30 Rule-based approaches to modelling Vincent Danos Video
12:30-13:00 Logical modelling of cell fate specification Denis Thieffry Slides Video
13:00-14:00 Lunch
14:00 - 15:45 Session 2 Chair: Emmanuel Barillot
14:00-14:15 Modelling Colonic Crypts with VCell and SBML/Spatial Marco Antoniotti Slides Video
14:15-14:45 Garuda Platform: An integrated inter-operability for biomedical software and data resources Hiroaki Kitano Slides Video
14:45-15:15 Interoperability and model sharing in large-scale neuronal network modelling and neuromorphic computating Andrew Davison Video
15:15-15:45 Monolix and other new tools for population pharmacometrics Marc Lavielle Slides Video
15:45-16:15 Coffee
16:15 - 18:00 Session 3 Chair: Éric Bonnet
16:15-16:30 A model for furrow constriction in animal cell cytokinesis Herve Turlier Slides Video
16:30-17:00 Modeling of efficacy data in clinical oncology Benjamin Ribba Slides Video
17:00-17:30 Mathematical modeling of cancer-related molecular mechanisms Andrei Zinovyev Slides Video
17:30-18:00 Agent-based models of tissue organisation - concepts and components Dirk Drasdo Video

Day 2 (Tuesday, September 17)

Time Topic Speaker Slides Recordings
09:00 - 10:30
Amphi Marie Curie
Update on SBML, CellML, NeuroML and PharmML Chair: Nicolas Le Novère
Update on CellML David Nickerson Slides Video
Update on NeuroML Padraig Gleeson Video
Update on PharmML Maciej Swat Slides Video
10:30-11:00 Coffee break
11:00 - 12:30
Amphi Marie Curie
SBML Level 3 Version 2 Chair: Mike Hucka
Update on SBML Mike Hucka Slides Video
Introduction to L3v2 changes Lucian Smith Slides Video
time for discussion
12:30-14:00 lunch
14:00 - 15:30
Amphi Marie Curie
Using distributions in model descriptions Chair: Lucian Smith
Distributions in PharmML M. Swat Slides Video
Distributions in COPASI P. Mendes Video
The SBML 'Distributions' package updates L. Smith Slides Video
14:00 - 15:30
Cour Anglaise 1
SBML Flux Balance Constraints Chair: Brett Olivier
14:00 - 14:10 Modelling at genome scale: introducing the SBML3 FBC package B. Olivier Slides
14:10 - 14:20 Tools for the Flux Balance Constraints Package F. Bergmann Slides
14:20 - 14:40 CyFluxViz & CySBML - Visualization of Constrained-based and Kinetic Model Simulations in Cytoscape M. König Slides
14:40 - 15:30 time for discussion
15:30-16:00 Coffee break
16:00 - 17:30
Amphi Curie
SBML Qualitative Modeling package Chair: Claudine Chaouiya
16:00 - 16:20 Mathematical model of synthetic dosage gene interactions leading to EMT-like phenotype in vivo D. Cohen Video
16:20 - 16:40 LogicalModel: a Java library for the manipulation and conversion of Qualitative Models A. Naldi Slides Video
16:40 - 17:30 time for discussion Video
16:00 - 17:30
Cours anglaise 1
Modelling physiology Chair: Padraig Gleeson
16:00 - 16:20 Standardization in distributed research networks: The Virtual Liver Experience M. Golebiewski Slides
16:20 - 16:40 FieldML (remote) R. Britten Slides
16:40 - 17:00 Building virtual cell using BioUML platform F. Kolpakov Slides
17:00 - 17:30 time for discussion
20:00 Conference dinner at Le vin qui danse Location

Day 3 (Wednesday, September 18)

Time Topic Speaker Slides Recordings
09:00 - 10:30
Amphi Marie Curie
Data representation and use Chair: Frank Bergmann
09:00 - 09:15 Introduction to the session F. Bergmann Slides Video
09:15 - 09:35 Numerical Markup Language and LibNUML J. Dada Slides Video
09:35 - 09:55 Data in PharmML M.Swat Slides Video
09:55 - 10:30 time for discussion
10:30-11:00 Coffee break
11:00 - 12:30
Amphi Marie Curie
SED-ML future: L2 / L1V3, parameter estimation Chair: David Nickerson
11:00 - 11:15 Intro/SED-ML L1V2 changes D. Nickerson Slides Video
11:15 - 11:35 Qualitative models simulations C. Chaouiya Slides Video
11:35 - 11:55 SED-ML in the simulation core library A. Draeger Slides Video
11:55 - 12:30 time for discussion, including discussion points from Chris Myers/iBioSim Slides Video
12:30-14:00 lunch
14:00 - 15:30
Amphi Marie Curie
SBML spatial Chair: Ion Moraru
14:00 - 14:15 SBML Level 3 Spatial Processes Extension - Status and Applications Jim Schaff Video
14:15 - 14:30 Modelling Colonic Crypts with VCell and SBML/Spatial Marco Antoniotti Video
14:30 - 14:45 Simmune and its support to SBML and SBML packages Fengkai Zhang Slides Video
14:45 - 15:00 CellML, FieldML, and SBML spatial David Nickerson Video
15:00 - 15:30 time for discussion Video
15:30-16:00 Coffee break
16:00 - 17:30
Amphi Marie Curie
Community building and links with other efforts Chair: Martin Golebiewski
16:00 - 16:05 Introduction M. Golebiewski Slides Video
16:05 - 16:25 The Systems Biology Format Converter framework: a generic conversion framework between Systems Biology formats Nicolas Rodriguez Slides Video
16:25 - 16:40 International standardization organizations (and what they have to offer) (via Skype) J. Lonien (DIN) Slides Video
16:40 - 17:00 The Infrastructure for Systems Biology in Europe (ISBE) – A Partner for Advancing Standardisation (via Skype) B. Regierer Slides Video
17:00 - 17:15 A unified publication platform for Systems Biology standards F. Schreiber Slides Video
17:15 - 17:30 time for discussion Video

Day 4 (Thursday, September 19)

Time Topic Speaker Slides Recordings
09:00 - 10:30
Amphi Marie Curie
Model Sharing (1): metadata Chair: Nick Juty Slides Video
09:00 - 09:20 Strategies for integrated management of computational biology models and associated simulations R. Henkel Slides Video
09:20 - 09:40 BiVeS & BudHat: Difference Detection for Computational Models M. Scharm Slides Video
09:40 - 10:00 Sharing, Versioning and Annotating SBML Models using the e!DAL Data Repository API D. Arend Slides Video
10:00 - 10:30 time for discussion, focus on a common annotation standard for COMBINE efforts D. Waltemath Slides Video
10:30-11:00 Coffee break
11:00 - 12:30
Amphi Marie Curie
Model sharing (2): Repositories and exchange Chair: Dagmar Waltemath
11:00 - 11:20 Atlas of Cancer Signaling Networks I. Kuperstein Slides Video
11:20 - 11:40 Physiome Model Repository T. Yu Slides Video
11:40 - 12:00 Reporting reproducible model studies; an example study using JWS Online and SEEK J. Snoep Slides Video
12:00 - 12:30 time for discussion Video
12:30-14:00 lunch
14:00 - 15:30
Amphi Marie Curie
COMBINE archive Chair: Nicolas Rodriguez
14:00 - 14:20 An implementation of the COMBINE archive Frank Bergmann Video
14:20 - 14:50 Linking between COMBINE standards Tobias Czauderna Slides Video
- 15:30 Discussion Video
15:30-16:00 Coffee break
16:00 - 17:30
Amphi Marie Curie
SBML Multi package Chair: Fengkai Zhang
16:00 - 17:30 SBML-Multi draft Specification, V1.01, general introduction and update; all: discussion; remote access: google hangouts F. Zhang Slides Video

Day 5 (Friday, September 20)

Time Topic Speaker Slides Recordings
09:00 - 10:30
Amphi Marie Curie
SBGN: overview and update Chair: Falk Schreiber
09:00 - 09:10 Introduction F. Schreiber
09:10 - 09:30 Update PD, ER, AF F. Schreiber Slides Video
09:30 - 09:45 SBGN survey S. Moodie (via Skype) Slides Video
09:45 - 10:00 The LEGO project from Gene Ontology - How SBGN can support it H. Mi Slides Video
10:00 - 10:15 What is the optimal representation of a generalized metabolic model using SBML and SBGN? A. Zhukova Slides Video
10:15 - 10:30 Identity gates A. Sorokin (via Skype) Slides Video
10:30-11:00 Coffee break
11:00 - 12:30
Amphi Marie Curie
Visual Markup (SBGN-ML, SBML Layout) Chair: Tobias Czauderna
11:00 - 11:15 Update SBGN-ML and LibSBGN T. Czauderna Slides Video
11:15 - 11:25 Update SBML Layout F. Bergmann Slides pp. 1-12 Video
11:25 - 11:35 Proposal for colours in SBGN-ML F. Bergmann Slides pp. 13-18 Video
11:35 - 11:50 Conversion of mEPN Pathway Diagrams to SBGN in BioLayout Express3D D. Wright Slides Video
SBGN: continued
11:50 - 12:00 Pathway of the month H. Mi Slides Video
12:00 - 12:10 Symbol of the month T. Czauderna Slides
12:10 - 12:20 SBGN usage - paper review T. Czauderna Slides
Closing Ceremony
12:20 - 12:30 The Package Man L. Smith Slides Video
12:30-14:00 lunch
14:00 - 15:30
Amphi Marie Curie
SBML Hierarchical Model Composition Chair: L. Smith Slides Video
14:00 - 15:30
Salle Joliot
SBGN: development of L2 Chair: H. Mi
15:30-16:00 Coffee break
16:00 - 17:30
Amphi Marie Curie
SBML Arrays and Dynamics Packages Chair:Chris Myers Arrays, Dynamic Video
16:00 - 17:30
Salle Joliot
SBGN: development of L2 Chair: Falk Schreiber