Full agenda
Agenda
Day 1 (Monday, September 16)
| Time | Topic | Speaker | Slides | Recordings |
|---|---|---|---|---|
| 11:00 - 11:10 | Welcome to COMBINE 2013 | Éric Bonnet | <html><a href="/sites/combine/files/combine2013/combine-2013-eric-bonnet-intro-2013-09-16-sm.mov">Video</a></html> | |
| 11:10 - 11:25 | COMBINE 2013 | Nicolas Le Novère | <html><a href="/sites/combine/files/combine2013/2013-09-16-lenovere.mov">Video</a></html> | |
| 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 | <html><a href="/sites/combine/files/combine2013/2013-09-16-hucka.mov">Video</a></html> |
| 11:45-12:00 | Applying the Scientific Method to Simulation Experiments: SED-ML | Frank Bergmann | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-16-bergmann.mov">Video</a></html> |
| 12:00-12:30 | Rule-based approaches to modelling | Vincent Danos | <html><a href="/sites/combine/files/combine2013/2013-09-16-danos.mov">Video</a></html> | |
| 12:30-13:00 | Logical modelling of cell fate specification | Denis Thieffry | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-16-thieffrey.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2013/2013-09-16-antoniotti.mov">Video</a></html> |
| 14:15-14:45 | Garuda Platform: An integrated inter-operability for biomedical software and data resources | Hiroaki Kitano | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-16-kitano.mov">Video</a></html> |
| 14:45-15:15 | Interoperability and model sharing in large-scale neuronal network modelling and neuromorphic computating | Andrew Davison | <html><a href="/sites/combine/files/combine2013/2013-09-16-davison.mov">Video</a></html> | |
| 15:15-15:45 | Monolix and other new tools for population pharmacometrics | Marc Lavielle | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-16-lavielle.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2013/2013-09-16-turlier.mov">Video</a></html> |
| 16:30-17:00 | Modeling of efficacy data in clinical oncology | Benjamin Ribba | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-16-ribba.mov">Video</a></html> |
| 17:00-17:30 | Mathematical modeling of cancer-related molecular mechanisms | Andrei Zinovyev | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-16-zinovyev.mov">Video</a></html> |
| 17:30-18:00 | Agent-based models of tissue organisation - concepts and components | Dirk Drasdo | <html><a href="/sites/combine/files/combine2013/2013-09-16-drasdo.mov">Video</a></html> | |
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 | <html><a href="/sites/combine/files/combine2013/2013-09-17-nickerson.mov">Video</a></html> | |
| Update on NeuroML | Padraig Gleeson | <html><a href="/sites/combine/files/combine2013/2013-09-17-gleeson.mov">Video</a></html> | ||
| Update on PharmML | Maciej Swat | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-17-swat.mov">Video</a></html> | |
| 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 | <html><a href="/sites/combine/files/combine2013/2013-09-17-hucka.mov">Video</a></html> | |
| Introduction to L3v2 changes | Lucian Smith | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-17-smith.mov">Video</a></html> | |
| 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 | <html><a href="/sites/combine/files/combine2013/2013-09-17-swat-2.mov">Video</a></html> | |
| Distributions in COPASI | P. Mendes | <html><a href="/sites/combine/files/combine2013/2013-09-17-mendes.mov">Video</a></html> | ||
| The SBML 'Distributions' package updates | L. Smith | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-17-smith-2.mov">Video</a></html> | |
| 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 | <html><a href="/sites/combine/files/combine2013/2013-09-17-cohen.mov">Video</a></html> | |
| 16:20 - 16:40 | LogicalModel: a Java library for the manipulation and conversion of Qualitative Models | A. Naldi | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-17-naldi.mov">Video</a></html> |
| 16:40 - 17:30 | time for discussion | <html><a href="/sites/combine/files/combine2013/2013-09-17-chaouiya-discussion.mov">Video</a></html> | ||
| 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 | <html><a href="/sites/combine/files/combine2013/2013-09-18-bergmann.mov">Video</a></html> |
| 09:15 - 09:35 | Numerical Markup Language and LibNUML | J. Dada | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-18-dada.mov">Video</a></html> |
| 09:35 - 09:55 | Data in PharmML | M.Swat | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-18-swat.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2013/2013-09-18-nickerson.mov">Video</a></html> |
| 11:15 - 11:35 | Qualitative models simulations | C. Chaouiya | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-18-chaouiya.mov">Video</a></html> |
| 11:35 - 11:55 | SED-ML in the simulation core library | A. Draeger | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-18-draeger.mov">Video</a></html> |
| 11:55 - 12:30 | time for discussion, including discussion points from Chris Myers/iBioSim | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-18-discussion.mov">Video</a></html> | |
| 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 | <html><a href="/sites/combine/files/combine2013/2013-09-18-schaff.mov">Video</a></html> | |
| 14:15 - 14:30 | Modelling Colonic Crypts with VCell and SBML/Spatial | Marco Antoniotti | <html><a href="/sites/combine/files/combine2013/2013-09-18-antoniotti.mov">Video</a></html> | |
| 14:30 - 14:45 | Simmune and its support to SBML and SBML packages | Fengkai Zhang | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-18-zhang.mov">Video</a></html> |
| 14:45 - 15:00 | CellML, FieldML, and SBML spatial | David Nickerson | <html><a href="/sites/combine/files/combine2013/2013-09-18-nickerson-2.mov">Video</a></html> | |
| 15:00 - 15:30 | time for discussion | <html><a href="/sites/combine/files/combine2013/2013-09-18-discussion-spatial.mov">Video</a></html> | ||
| 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 | <html><a href="/sites/combine/files/combine2013/2013-09-18-golebiewski.mov">Video</a></html> |
| 16:05 - 16:25 | The Systems Biology Format Converter framework: a generic conversion framework between Systems Biology formats | Nicolas Rodriguez | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-18-rodriguez.mov">Video</a></html> |
| 16:25 - 16:40 | International standardization organizations (and what they have to offer) (via Skype) | J. Lonien (DIN) | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-18-lonien.mov">Video</a></html> |
| 16:40 - 17:00 | The Infrastructure for Systems Biology in Europe (ISBE) – A Partner for Advancing Standardisation (via Skype) | B. Regierer | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-18-regierer.mov">Video</a></html> |
| 17:00 - 17:15 | A unified publication platform for Systems Biology standards | F. Schreiber | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-18-schreiber.mov">Video</a></html> |
| 17:15 - 17:30 | time for discussion | <html><a href="/sites/combine/files/combine2013/2013-09-18-discussion-comm-building.mov">Video</a></html> | ||
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 | <html><a href="/sites/combine/files/combine2013/2013-09-19-juty.mov">Video</a></html> | |||
| 09:00 - 09:20 | Strategies for integrated management of computational biology models and associated simulations | R. Henkel | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-19-henkel.mov">Video</a></html> | |||
| 09:20 - 09:40 | BiVeS & BudHat: Difference Detection for Computational Models | M. Scharm | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-19-scharm.mov">Video</a></html> | |||
| 09:40 - 10:00 | Sharing, Versioning and Annotating SBML Models using the e!DAL Data Repository API | D. Arend | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-19-arend.mov">Video</a></html> | |||
| 10:00 - 10:30 | time for discussion, focus on a common annotation standard for COMBINE efforts | D. Waltemath | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-19-waltemath.mov">Video</a></html> | |||
| 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 | <html><a href="/sites/combine/files/combine2013/2013-09-19-kuperstein.mov">Video</a></html> | |||
| 11:20 - 11:40 | Physiome Model Repository | T. Yu | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-19-yu.mov">Video</a></html> | |||
| 11:40 - 12:00 | Reporting reproducible model studies; an example study using JWS Online and SEEK | J. Snoep | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-19-snoep.mov">Video</a></html> | |||
| 12:00 - 12:30 | time for discussion | <html><a href="/sites/combine/files/combine2013/2013-09-19-discussion-model-sharing.mov">Video</a></html> | |||||
| 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 | <html><a href="/sites/combine/files/combine2013/2013-09-19-bergmann.mov">Video</a></html> | ||||
| 14:20 - 14:50 | Linking between COMBINE standards | Tobias Czauderna | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-19-czauderna.mov">Video</a></html> | |||
| - 15:30 | Discussion | <html><a href="/sites/combine/files/combine2013/2013-09-19-discussion-archive.mov">Video</a></html> | |||||
| 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 | <html><a href="/sites/combine/files/combine2013/combine-2013-sbml-multi-session-2013-09-19.mov">Video</a></html> | |||
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 | <html><a href="/sites/combine/files/combine2013/2013-09-20-schreiber.mov">Video</a></html> |
| 09:30 - 09:45 | SBGN survey | S. Moodie (via Skype) | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-20-moodie.mov">Video</a></html> |
| 09:45 - 10:00 | The LEGO project from Gene Ontology - How SBGN can support it | H. Mi | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-20-mi1.mov">Video</a></html> |
| 10:00 - 10:15 | What is the optimal representation of a generalized metabolic model using SBML and SBGN? | A. Zhukova | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-20-zhukova.mov">Video</a></html> |
| 10:15 - 10:30 | Identity gates | A. Sorokin (via Skype) | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-20-sorokin.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2013/2013-09-20-czauderna1.mov">Video</a></html> |
| 11:15 - 11:25 | Update SBML Layout | F. Bergmann | Slides pp. 1-12 | <html><a href="/sites/combine/files/combine2013/2013-09-20-bergmann1.mov">Video</a></html> |
| 11:25 - 11:35 | Proposal for colours in SBGN-ML | F. Bergmann | Slides pp. 13-18 | <html><a href="/sites/combine/files/combine2013/2013-09-20-bergmann2.mov">Video</a></html> |
| 11:35 - 11:50 | Conversion of mEPN Pathway Diagrams to SBGN in BioLayout Express3D | D. Wright | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-20-wright.mov">Video</a></html> |
| SBGN: continued | ||||
| 11:50 - 12:00 | Pathway of the month | H. Mi | Slides | <html><a href="/sites/combine/files/combine2013/2013-09-20-mi2.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2013/combine-2013-Lucian-song.mov">Video</a></html> |
| 12:30-14:00 | lunch | |||
| 14:00 - 15:30 Amphi Marie Curie | SBML Hierarchical Model Composition | Chair: L. Smith | Slides | <html><a href="/sites/combine/files/combine2013/combine-2013-sbml-comp-session.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2013/combine-2013-sbml-arrays-session.mov">Video</a></html> |
| 16:00 - 17:30 Salle Joliot | SBGN: development of L2 | Chair: Falk Schreiber | ||