Detailed Agenda Combine 2012

Agenda

Day 1 (Wednesday, August 15)

Time Topic Speaker Slides Recordings
09:00 - 09:15 Welcome to COMBINE 2012 Gary Bader Video
09:15 - 09:30 COMBINE 2012 Nicolas Le Novère Slides Video
Session 1 Biological Models and Simulation
Chair: Mike Hucka
09:30 - 09:50 Update on SBML level 3 and the SBML Test Suite Mike Hucka Slides Video
09:50 - 10:10 SBML Specifications for Revised Multi, Simple Spatial and Multi-Spatial Fengkai Zhang Slides Video
10:10 - 10:30 The Open Source Brain Initiative Padraig Gleeson Slides Video
10:30-11:00 Break
11:00 - 11:20 Experience with SBML Packages within iBioSim Chris Myers Slides Video
11:20 - 11:40 Multiscale multicellular simulations using Cell Based Chaste James Osborne Slides Video
11:40 - 12:00 Towards CellML 1.2 Jonathan Cooper Slides Video
12:00 - 12:20 The new JWS Online simulation interface: SBGN schema generation, MIRIAM annotation and SBML model specification Franco B du Preez Slides Video
12:20 - 1:40 Lunch
1:40 - 2:10 Tutorial: BioModels Database Camille Laibe Slides Video
2:10 - 2:20 Discussion
2:20 - 2:50 Break
Session 2 Simulation Algorithm, Experiments and Results
Chair: Dagmar Waltemath
2:50 - 3:10 Introduction to SED-ML Dagmar Waltemath Slides Video
3:10 - 3:30 Nested Tasks Proposal for SED-ML Frank Bergmann Slides Video
3:30 - 4:00 Possibilities for SED-ML Jonathan Cooper Slides Video
4:00 - 5:00 Keynote: How to Be an Educated Ontology Consumer Michael Grüninger Video
5:00 - 6:00 Break
6:00 - 7:30 Welcome reception and Poster session


Day 2 (Thursday, August 16)

Time Topic Speaker Slides Recordings
09:00 - 09:15 Welcome to COMBINE 2012 - Day 2 Gary Bader
09:15 - 09:30 OGI Bioinformatics Initiative Kathy Deuchars Video
Session 2
(continued)
Simulation Algorithm, Experiments andResults
Chair: DagmarWaltemath
09:30 - 09:50 DDMoRe - Developing new representationstandards in PK/PD Maciej Swat Slides Video
09:50 - 10:10 Bridging Experiments and Modelling: The SABIO-RK Reaction Kinetics Database Martin Golebiewski Slides Video
Session 3
Parallel Breakouts
10:10 - 10:30 Biological Models and Simulations: 1st topic: SBML spatial and multi Red Room
10:10 - 10:30 Simulation Algorithm, Experiments and Results White Room
10:10 - 10:30 Model and Pathway Visualization Black Room
10:10 - 10:30 Biological Pathways and Networks 6th floor conference Room
10:30-11:00 Break
11:00 - 12:20 Biological Models and Simulations: 1st topic: SBML spatial and multi Red Room
11:00 - 12:20 Simulation Algorithm, Experiments and Results White Room
11:00 - 12:20 Model and Pathway Visualization Black Room
11:00 - 12:20 Biological Pathways and Networks 6th floor conference Room
12:20 - 1:40 Lunch
Session 4 Software Tools and Databases
Chair: Martina Kutmon
1:40 - 2:00 BiNoM, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats Eric Bonnet Slides Video
2:00 - 2:20 Budhat - a tool for SBML model version control Dagmar Waltemath Slides Video
2:20 - 2:50 Break
2:50 - 3:10 JUMMP just a model management platform Juergen Eils Slides Video
3:10 - 3:30 PhosphoSitePlus Updates Jon Kornhauser Slides Video
3:30 - 4:00 Recent developments in libSBML and JSBML Frank Bergmann Slides Video
4:00 - 5:00 Keynote: Comprehensive measure and modeling of C. elegans behavior Will Ryu Slides Video
5:00 - 5:15 Reports on breakout sessions Video
5:15 - 7:00 Break
7:30 Conference Dinner Messis Restaurant (http://www.messisrestaurant.ca/)


Day 3 (Friday, August 17)

Time Topic Speaker Slides Recordings
09:00 - 10:00 Keynote Not your mama’s network biology – dynamic cell-cell interaction networks in development and disease. Peter Zandstra
Session 5 Model and Pathway Visualization
Chair: Huaiyu Mi
10:00 - 10:30 NAViGaTOR Igor Jurisica Video
10:30-11:00 Break
11:00 - 11:15 SBGN Update Nicolas Le Novère Slides Video
11:15 - 11:25 libSBGN update Tobias Czauderna Slides Video
11:25 - 12:00 Tutorial: SBGN-ED - a tool for the Systems Biology Graphical Notation Tobias Czauderna Slides Video
12:00 - 12:20 Cytoscape.js - network and pathway visualization on the web Gary Bader for Max Franz Slides Video
12:20 - 1:40 Lunch
Session 6 Biological Pathways and Networks
Chair: Gary Bader
1:40 - 2:10 Pathway Commons and BioPAX, Validator Update + Factoid/Crowd source curation, Human Computation and Games Gary Bader Slides Video
2:10 - 2:20 Paxtools Emek Demir Slides Video
2:20 - 2:50 Break
2:50 - 3:10 Multifunctional Proteins in Multilevel Networks Raúl A. Ortiz-Merino Video
3:10 - 3:30 Cytoscape 3.0 Gary Bader for Michael Smoot Slides Video
3:30 - 4:00 Integration of external references for BioPAX Pathways and Models Michel Dumontier Slides Video
4:00 - 5:00 Keynote: Model-based Engineering of Metabolism Radhakrishnan Mahadevan Video
5:00 - 6:00 Outreach discussion Video


Day 4 (Saturday, August 18)

Time Topic Speaker Slides Recordings
Session 7 Software Tools and Databases
Chair: Martin Golebiewski
9:30 - 9:50 Reforming Reactome Robin Haw Slides Video
9:50 - 10:30 Tutorial: Access Reactome Database via Application Programming Interfaces Guanming Wu Slides Video
10:10 - 10:30 SEEK and JERM: standards-compliant integration of systems biology data Olga Krebs Slides Video
10:30-11:00 Break
Session 8
Parallel Breakouts
11:00 - 12:20 Parallel breakouts: Biological Models and Simulations Red Room Video
11:00 - 12:20 Parallel breakouts: Simulation Algorithm,Experiments and Results Black Room
11:00 - 12:20 Parallel breakouts: Model and Pathway Visualization Red Room (dual use)
11:00 - 12:20 Parallel breakouts: Biological Pathways and Networks 6th floor conference Room
12:20 - 1:40 Lunch
Session 9 Interoperability Between Standards
Chair: Nicolas Le Novère
1:40 - 2:00 Semantic interoperability framework Sarala Wimalaratne Slides Video
2:00 - 2:20 Towards ML-agnostic modelling Mike Cooling Slides Video
2:20 - 2:50 MIRIAM Registry and Identifiers.org Nick Juty Slides Video
2:50 - 3:10 Break
3:10 - 3:30 Reusing SB Standards to Exchange PK/PD Models Stuart Moodie Slides Video
3:30 - 3:50 The COMBINE archive Nicolas Le Novère Slides Video
3:50 - 4:05 Bio2RDF's namespace SPARQL endpoint François Belleau Slides Video
4:00 - 4:45 Reports on breakout sessions. Video
4:50 - 5:00 Traditional Closing Song Lucian Smith Video


Tutorials (Sunday, August 19)

Time Topic Speaker Slides Recordings
9:20 - 10:20 Accessing biochemical reaction kinetics data via the SABIO-RK database Martin Golebiewski Video
10:20 - 11:20 Creating mathematical models in CellDesigner Akira Funahashi Video
11:20 - 11:40 Break
11:40 - 12:40 Setting up and simulating quantitative models in Virtual Cell (VCell) Ion Moraru Video
12:40 - 1:00 Lunch
1:00 - 1:45 Simulating models in COPASI Sven Sahle Video
1:45 - 2:15 Simulating models with JWS Online and setting up models with OneStop Franco du Preez Video
2:15 - 2:20 Integrated handling of data, models and processes via SEEK and setting up models online using SYCAMORE Martin Golebiewski Video