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 | <html><a href="/sites/combine/files/combine2012/2012-08-15-combine-bader.mov">Video</a></html> | |
| 09:15 - 09:30 | COMBINE 2012 | Nicolas Le Novère | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-15-combine-lenovere.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2012/2012-08-15-combine-hucka.mov">Video</a></html> |
| 09:50 - 10:10 | SBML Specifications for Revised Multi, Simple Spatial and Multi-Spatial | Fengkai Zhang | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-15-combine-zhang.mov">Video</a></html> |
| 10:10 - 10:30 | The Open Source Brain Initiative | Padraig Gleeson | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-15-combine-gleeson.mov">Video</a></html> |
| 10:30-11:00 | Break | |||
| 11:00 - 11:20 | Experience with SBML Packages within iBioSim | Chris Myers | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-15-combine-myers.mov">Video</a></html> |
| 11:20 - 11:40 | Multiscale multicellular simulations using Cell Based Chaste | James Osborne | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-15-combine-osborne.mov">Video</a></html> |
| 11:40 - 12:00 | Towards CellML 1.2 | Jonathan Cooper | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-15-combine-cooper.mov">Video</a></html> |
| 12:00 - 12:20 | The new JWS Online simulation interface: SBGN schema generation, MIRIAM annotation and SBML model specification | Franco B du Preez | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-15-combine-dupreez.mov">Video</a></html> |
| 12:20 - 1:40 | Lunch | |||
| 1:40 - 2:10 | Tutorial: BioModels Database | Camille Laibe | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-15-combine-laibe.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2012/2012-08-15-combine-waltemath.mov">Video</a></html> |
| 3:10 - 3:30 | Nested Tasks Proposal for SED-ML | Frank Bergmann | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-15-combine-bergmann.mov">Video</a></html> |
| 3:30 - 4:00 | Possibilities for SED-ML | Jonathan Cooper | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-15-combine-cooper-sedml-possibilities.mov">Video</a></html> |
| 4:00 - 5:00 | Keynote: How to Be an Educated Ontology Consumer | Michael Grüninger | <html><a href="/sites/combine/files/combine2012/2012-08-15-combine-grueninger.mov">Video</a></html> | |
| 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 | <html><a href="/sites/combine/files/combine2012/2012-08-16-combine-deuchars.mov">Video</a></html> | |
| Session 2 (continued) | Simulation Algorithm, Experiments andResults Chair: DagmarWaltemath | |||
| 09:30 - 09:50 | DDMoRe - Developing new representationstandards in PK/PD | Maciej Swat | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-16-combine-swat.mov">Video</a></html> |
| 09:50 - 10:10 | Bridging Experiments and Modelling: The SABIO-RK Reaction Kinetics Database | Martin Golebiewski | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-16-combine-golebiewski.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2012/2012-08-16-combine-bonnet.mov">Video</a></html> |
| 2:00 - 2:20 | Budhat - a tool for SBML model version control | Dagmar Waltemath | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-16-combine-waltemath.mov">Video</a></html> |
| 2:20 - 2:50 | Break | |||
| 2:50 - 3:10 | JUMMP just a model management platform | Juergen Eils | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-16-combine-eils.mov">Video</a></html> |
| 3:10 - 3:30 | PhosphoSitePlus Updates | Jon Kornhauser | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-16-combine-kornhauser.mov">Video</a></html> |
| 3:30 - 4:00 | Recent developments in libSBML and JSBML | Frank Bergmann | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-16-combine-bergmann.mov">Video</a></html> |
| 4:00 - 5:00 | Keynote: Comprehensive measure and modeling of C. elegans behavior | Will Ryu | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-16-combine-ryu.mov">Video</a></html> |
| 5:00 - 5:15 | Reports on breakout sessions | <html><a href="/sites/combine/files/combine2012/2012-08-16-combine-breakoutsessionreports.mov">Video</a></html> | ||
| 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 | <html><a href="/sites/combine/files/combine2012/2012-08-17-combine-jurisica.mov">Video</a></html> | |
| 10:30-11:00 | Break | |||
| 11:00 - 11:15 | SBGN Update | Nicolas Le Novère | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-17-combine-lenovere.mov">Video</a></html> |
| 11:15 - 11:25 | libSBGN update | Tobias Czauderna | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-17-combine-czauderna-sbgn-update.mov">Video</a></html> |
| 11:25 - 12:00 | Tutorial: SBGN-ED - a tool for the Systems Biology Graphical Notation | Tobias Czauderna | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-17-combine-czauderna-sbgn-ed.mov">Video</a></html> |
| 12:00 - 12:20 | Cytoscape.js - network and pathway visualization on the web | Gary Bader for Max Franz | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-17-combine-bader-cytoscape-js.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2012/2012-08-17-combine-bader-pathway.mov">Video</a></html> |
| 2:10 - 2:20 | Paxtools | Emek Demir | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-17-combine-demir.mov">Video</a></html> |
| 2:20 - 2:50 | Break | |||
| 2:50 - 3:10 | Multifunctional Proteins in Multilevel Networks | Raúl A. Ortiz-Merino | <html><a href="/sites/combine/files/combine2012/2012-08-17-combine-ortiz.mov">Video</a></html> | |
| 3:10 - 3:30 | Cytoscape 3.0 | Gary Bader for Michael Smoot | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-17-combine-bader-cytoscape-3.mov">Video</a></html> |
| 3:30 - 4:00 | Integration of external references for BioPAX Pathways and Models | Michel Dumontier | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-17-combine-dumontier.mov">Video</a></html> |
| 4:00 - 5:00 | Keynote: Model-based Engineering of Metabolism | Radhakrishnan Mahadevan | <html><a href="/sites/combine/files/combine2012/2012-08-17-combine-mahadevan.mov">Video</a></html> | |
| 5:00 - 6:00 | Outreach discussion | <html><a href="/sites/combine/files/combine2012/2012-08-17-discussion.mov">Video</a></html> | ||
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 | <html><a href="/sites/combine/files/combine2012/2012-08-18-combine-haw.mov">Video</a></html> |
| 9:50 - 10:30 | Tutorial: Access Reactome Database via Application Programming Interfaces | Guanming Wu | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-18-combine-wu.mov">Video</a></html> |
| 10:10 - 10:30 | SEEK and JERM: standards-compliant integration of systems biology data | Olga Krebs | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-18-combine-krebs.mov">Video</a></html> |
| 10:30-11:00 | Break | |||
| Session 8 | Parallel Breakouts | |||
| 11:00 - 12:20 | Parallel breakouts: Biological Models and Simulations | Red Room | <html><a href="/sites/combine/files/combine2012/2012-08-18-combine-breakout.mov">Video</a></html> | |
| 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 | <html><a href="/sites/combine/files/combine2012/2012-08-18-combine-wimalaratne.mov">Video</a></html> |
| 2:00 - 2:20 | Towards ML-agnostic modelling | Mike Cooling | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-18-combine-cooling.mov">Video</a></html> |
| 2:20 - 2:50 | MIRIAM Registry and Identifiers.org | Nick Juty | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-18-combine-juty.mov">Video</a></html> |
| 2:50 - 3:10 | Break | |||
| 3:10 - 3:30 | Reusing SB Standards to Exchange PK/PD Models | Stuart Moodie | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-18-combine-moodie.mov">Video</a></html> |
| 3:30 - 3:50 | The COMBINE archive | Nicolas Le Novère | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-18-combine-lenovere.mov">Video</a></html> |
| 3:50 - 4:05 | Bio2RDF's namespace SPARQL endpoint | François Belleau | Slides | <html><a href="/sites/combine/files/combine2012/2012-08-18-combine-belleau.mov">Video</a></html> |
| 4:00 - 4:45 | Reports on breakout sessions. | <html><a href="/sites/combine/files/combine2012/2012-08-18-combine-breakoutreports.mov">Video</a></html> | ||
| 4:50 - 5:00 | Traditional Closing Song | Lucian Smith | <html><a href="/sites/combine/files/combine2012/2012-08-18-combine-closing-song.mov">Video</a></html> | |
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 | <html><a href="/sites/combine/files/combine2012/2012-08-19-combine-tutorial-sabiork.mov">Video</a></html> | |
| 10:20 - 11:20 | Creating mathematical models in CellDesigner | Akira Funahashi | <html><a href="/sites/combine/files/combine2012/2012-08-19-combine-tutorial-celldesigner.mov">Video</a></html> | |
| 11:20 - 11:40 | Break | |||
| 11:40 - 12:40 | Setting up and simulating quantitative models in Virtual Cell (VCell) | Ion Moraru | <html><a href="/sites/combine/files/combine2012/2012-08-19-combine-tutorial-vcell.mov">Video</a></html> | |
| 12:40 - 1:00 | Lunch | |||
| 1:00 - 1:45 | Simulating models in COPASI | Sven Sahle | <html><a href="/sites/combine/files/combine2012/2012-08-19-combine-tutorial-copasi.mov">Video</a></html> | |
| 1:45 - 2:15 | Simulating models with JWS Online and setting up models with OneStop | Franco du Preez | <html><a href="/sites/combine/files/combine2012/2012-08-19-combine-tutorial-jws.mov">Video</a></html> | |
| 2:15 - 2:20 | Integrated handling of data, models and processes via SEEK and setting up models online using SYCAMORE | Martin Golebiewski | <html><a href="/sites/combine/files/combine2012/2012-08-19-combine-tutorial-seek-sycamore.mov">Video</a></html> | |