Detailed agenda of COMBINE 2011
Agenda
Day 1 (Saturday, September 3rd)
| Time | Topic | Speaker | Slides | Recordings |
|---|---|---|---|---|
| 09:15-09:25 | Welcome address by the managing director of HITS | Andreas Reuter | <html><a href="/sites/combine/files/2011-09-03-combine-reuter.mov">Video</a></html> | |
| 09:25-09:30 | Technical remarks to the COMBINE 2011 meeting | Martin Golebiewski | Slides | <html><a href="/sites/combine/files/2011-09-03-combine-golebiewski.mov">Video</a></html> |
| 09:30-09:45 | COMBINE, what it is, what it could be | Nicolas Le Novère | Slides | <html><a href="/sites/combine/files/2011-09-03-combine-lenovere.mov">Video</a></html> |
| Simulation and analysis Chair: David Nickerson | ||||
| 09:45-10:05 | SED-ML Intro / History | Dagmar Waltemath | Slides | <html><a href="/sites/combine/files/2011-09-03-combine-waltemath.mov">Video</a></html> |
| 10:05-10:25 | Java software support for SED-ML | Richard Adams | Slides | <html><a href="/sites/combine/files/2011-09-03-combine-adams.mov">Video</a></html> |
| 10:25-10:45 | SED-ML Web Tools | Frank Bergmann | Slides | <html><a href="/sites/combine/files/2011-09-03-combine-bergmann.mov">Video</a></html> |
| 10:45-11:05 | Functional Curation: Potential Future Directions for SED-ML | Jonathan Cooper | Slides | <html><a href="/sites/combine/files/2011-09-03-combine-cooper.mov">Video</a></html> |
| 11:05-11:15 | Discussion | All | ||
| 11:15-11:45 | Break | |||
| 11:45-12:05 | KiSAO: Kinetic Simulation Algorithm Ontology | Anna Zhukova (remotely) | Slides | <html><a href="/sites/combine/files/2011-09-03-combine-zhukova.mov">Video</a></html> |
| 12:05-12:25 | SProS | Andrew Miller (remotely) | Slides | <html><a href="/sites/combine/files/2011-09-03-combine-miller.mov">Video</a></html> |
| 12:25-12:45 | SBRML Interoperability | Frank Bergmann | Slides | <html><a href="/sites/combine/files/2011-09-03-combine-bergmann2.mov">Video</a></html> |
| 12:45-13:15 | Discussion | All | ||
| 13:15-14:15 | Lunch | |||
| Interoperability Chair: Nicolas Le Novère | ||||
| 14:30-14:50 | Identifiers.org | Camille Laibe | Slides | <html><a href="/sites/combine/files/2011-09-03-combine-laibe.mov">Video</a></html> |
| 14:50-15:10 | Update on MIRIAM Registry and SBO | Nick Juty | Slides | <html><a href="/sites/combine/files/2011-09-03-combine-juty.mov">Video</a></html> |
| 15:10-15:40 | Integrating systems biology and biomedical ontologies | Robert Hoehndorf | Slides | |
| 15:40-16:10 | Break | |||
| Interoperability Chair: Camille Laibe | ||||
| 16:10-16:40 | Semantic annotations and querying of SBML simulations | Michel Dumontier | Slides | <html><a href="/sites/combine/files/2011-09-03-combine-dumontier.mov">Video</a></html> |
| 16:40-17:10 | OneStop: JWS Online's access point to SBML, SBGN and MIRIAM compliant annotation | Franco Du Preez | Slides | <html><a href="/sites/combine/files/2011-09-03-combine-dupreez.mov">Video</a></html> |
| 17:10-17:30 | Systems Biology Format Converter | Martina Kutmon | Slides | <html><a href="/sites/combine/files/2011-09-03-combine-kutmon.mov">Video</a></html> |
| 17:30-18:00 | Discussion on COMBINE mission, governance, SOP etc. | All | ||
| 19:00-22:30 | Welcome Reception in the O' Reilly's Irish Pub * | |||
* They not only serve a fine pint, but also food (included in the meeting fee). There will be fireworks in the old town and the castle will be illuminated that night. This is one of the major events in Heidelberg each year and definitely a nice experience.
Day 2 (Sunday, September 4th)
| Time | Topic | Speaker | Slides | Recordings | |||
|---|---|---|---|---|---|---|---|
| 9:00-10:30 | Parallel focused discussion sessions—see the Google spreadsheet) for up-to-the-minute schedule and sign-up sheets | All | |||||
| 10:30-11:00 | Break | ||||||
| Mathematical model semantics - Recent SBML and SBML Team developments Chair: Mike Hucka | |||||||
| 11:00-11:15 | General update on SBML happenings | Mike Hucka | <html><a href="/sites/combine/files/2011-09-04-combine-hucka-sbml-update.pdf">Slides</a></html> | <html><a href="/sites/combine/files/2011-09-04-combine-hucka.mov">Video</a></html> | |||
| 11:15-11:30 | Status update on libSBML | Sarah Keating | Slides | <html><a href="/sites/combine/files/2011-09-04-combine-keating.mov">Video</a></html> | |||
| 11:30-11:45 | JSBML update | N Rodriguez/A Dräger | Slides | <html><a href="/sites/combine/files/2011-09-04-combine-draeger.mov">Video</a></html> | |||
| 11:45-12:00 | Updates on SBML Team facilities and software | Bergmann/Keating | Slides | <html><a href="/sites/combine/files/2011-09-04-combine-bergmann-keating1.mov">Video</a></html> | |||
| 12:00-12:15 | Interconversion between SBML Levels and packages | Keating/Bergmann | Slides | <html><a href="/sites/combine/files/2011-09-04-combine-bergmann-keating2.mov">Video</a></html> | |||
| 12:15-12:30 | Coordination Topics for Discussion with Developers | Keating/Bergmann | Slides | <html><a href="/sites/combine/files/2011-09-04-combine-bergmann-keating3.mov">Video</a></html> | |||
| 12:30-13:30 | Lunch | ||||||
| Mathematical model semantics - Software updates Chair: Chris Myers | |||||||
| 13:30-13:50 | Implementation of a spatial model simulator and its SBML support, and equation based network builder | Akira Funahashi | Slides | <html><a href="/sites/combine/files/2011-09-04-combine-funahashi.mov">Video</a></html> | |||
| 13:50-14:10 | A Modelling Ecosystem for Libraries of Modular, Reusable Components | Mike Cooling | Slides | <html><a href="/sites/combine/files/2011-09-04-combine-cooling.mov">Video</a></html> | |||
| 14:10-14:30 | NetBuilder' - Modelling and simulating genetic regulatory networks | Katja Wegner | Slides | <html><a href="/sites/combine/files/2011-09-04-combine-wegner.mov">Video</a></html> | |||
| 14:30-14:50 | How to integrate COPASI with other software | Sven Sahle | Slides | <html><a href="/sites/combine/files/2011-09-04-combine-sahle.mov">Video</a></html> | |||
| 15:00-15:30 | Break | ||||||
| Mathematical model semantics - SBML Level 3 updates Chair: Frank Bergmann | |||||||
| 15:30-15:45 | Updates on the SBML Level 3 Flux Balance Constraints (FBC) package | Brett Olivier | Slides | <html><a href="/sites/combine/files/2011-09-04-combine-olivier.mov">Video</a></html> | |||
| 15:45-16:05 | Current developments in qualitative modelling of biological networks | Claudine Chaouiya | Slides | <html><a href="/sites/combine/files/2011-09-04-combine-chaouiya.mov">Video</a></html> | |||
| 16:05-16:25 | Updates on the SBML Level 3 Hierarchical Model Composition (“comp”) package | Lucian Smith | Slides | <html><a href="/sites/combine/files/2011-09-04-combine-smith.mov">Video</a></html> | |||
| 16:25-16:45 | Dynamic structures in SBML | Chris Myers | <html><a href="/sites/combine/files/2011-09-04-combine-myers-dynamic.pdf">Slides</a></html> | <html><a href="/sites/combine/files/2011-09-04-combine-myers.mov">Video</a></html> (1) | |||
| 16:45-17:00 | Spatial models in SBML | James Schaff | Slides | <html><a href="/sites/combine/files/2011-09-04-combine-schaff-w-slides-960x720.mov">Video</a></html> (2) | |||
| 17:00-17:15 | Break | ||||||
| 17:15-18:30 | Keynote Chair: Martin Golebiewski Dynamics and Function of the NF-kB system: how mathematical modelling can assist experimental biology | Michael White | Slides | <html><a href="/sites/combine/files/2011-09-04-combine-white.mov">Video</a></html> | |||
(1) Video is missing for the end of this presentation, but audio continues.
(2) Video was not available for this presentation, but the slides are presented in synchronization with the audio.
Day 3 (Monday, September 5th)
| Time | Topic | Speaker | Slides | Recordings |
|---|---|---|---|---|
| Mathematical model semantics - General updates about model representation formats Chair: Lucian Smith | ||||
| 9:00-9:25 | An introduction to NineML | Ivan Raikov | Slides | <html><a href="/sites/combine/files/2011-09-05-combine-raikov.mov">Video</a></html> |
| 9:25-9:50 | CellML: current status and future plans | David Nickerson | Slides | <html><a href="/sites/combine/files/2011-09-05-combine-nickerson.mov">Video</a></html> |
| 9:50-10:15 | SBML & synthetic biology | Chris Myers | Slides | <html><a href="/sites/combine/files/2011-09-05-combine-myers.mov">Video</a></html> |
| 10:15-10:45 | SBML Editors' Report | Lucian Smith | Slides | <html><a href="/sites/combine/files/2011-09-05-combine-smith.mov">Video</a></html> |
| 10:45-11:15 | Break | |||
| Mathematical model semantics - Discussion Chair: Mike Hucka | ||||
| 11:15-11:45 | Some thoughts on the future of SBML | Nicolas Le Novère | Slides | <html><a href="/sites/combine/files/2011-09-05-combine-lenovere.mov">Video</a></html> |
| 11:45-12:30 | Discussion | All | <html><a href="/sites/combine/files/2011-09-05-combine-discussion.mov">Video</a></html> | |
| 12:30-13:30 | Lunch | |||
| Biological pathway semantics I - Tools Chair: Oliver Ruebenacker | ||||
| 13:30-14:00 | From KEGG to dynamic pathway models: a collection of tools to facilitate the modeling of biochemical networks | Andreas Dräger | Slides | <html><a href="/sites/combine/files/2011-09-05-combine-draeger.mov">Video</a></html> |
| 14:00-14:30 | CellOrganizer: Image-derived Models of Subcellular Organization over Time and Space | Robert F. Murphy | <html><a href="/sites/combine/files/2011-09-05-combine-murphy-cellorganizer.pdf">Slides</a></html> | <html><a href="/sites/combine/files/2011-09-05-combine-murphy.mov">Video</a></html> |
| 14:30-15:00 | Systems Biology on Bio-Linux | Mesude Bicak | Slides | <html><a href="/sites/combine/files/2011-09-05-combine-bicak.mov">Video</a></html> |
| 15:00-15:20 | Reflect: an augmented browsing tool for life scientist | Janos Binder | Slides | <html><a href="/sites/combine/files/2011-09-05-combine-binder.mov">Video</a></html> |
| 15:20-15:50 | Break | |||
| Biological pathway semantics II: Data Formats Chair: Oliver Ruebenacker | ||||
| 15:50-16:10 | Self-Organizing Ontology of Biochemically Relevant Small Molecules | Michel Dumontier | Slides | <html><a href="/sites/combine/files/2011-09-05-combine-dumontier.mov">Video</a></html> |
| 16:10-16:40 | SBPAX: Turning Biological Knowledge into Mathematical Models, Automated | Oliver Ruebenacker | Slides | <html><a href="/sites/combine/files/2011-09-05-combine-ruebenacker.mov">Video</a></html> |
| 16:40-17:00 | Formal Representation of BioPAX as OWL ontologies | Michel Dumontier | Slides | <html><a href="/sites/combine/files/2011-09-05-combine-dumontier2.mov">Video</a></html> |
| 17:15-18:30 | Keynote Chair: Nicolas Le Novère | Peer Bork | <html><a href="/sites/combine/files/2011-09-05-combine-bork.mov">Video</a></html> | |
| 19:30-23:00 | Conference Dinner at S'Kastanie | |||
Day 4 (Tuesday, September 6th)
| Time | Topic | Speaker | Slides | Recordings |
|---|---|---|---|---|
| 9:00-11:00 | Parallel focused discussion sessions—see the Google spreadsheet) for up-to-the-minute schedule and sign-up sheets | All | ||
| 11:00-11:30 | Break | |||
| 11:30-13:15 | Visual representation Chair: Tobias Czauderna | |||
| 11:30-11:45 | Introduction to SBGN | Nicolas Le Novère | Slides | <html><a href="/sites/combine/files/2011-09-06-combine-lenovere.mov">Video</a></html> |
| 11:45-12:15 | Visual Representations - from Atoms to Organisms | Agnieszka Bronowska | <html><a href="/sites/combine/files/2011-09-06-combine-bronowska-visual-rep.pdf">Slides</a></html> | <html><a href="/sites/combine/files/2011-09-06-combine-bronowska.mov">Video</a></html> |
| 12:15-12:45 | SBGN-ED – working with the Systems Biology Graphical Notation | Falk Schreiber | Slides | <html><a href="/sites/combine/files/2011-09-06-combine-schreiber.mov">Video</a></html> |
| 12:45-13:15 | Tools for Molecular Interaction Maps and a Graphical Notation Validation Framework for PathVisio | Augustin Luna | Slides | <html><a href="/sites/combine/files/2011-09-06-combine-luna.mov">Video</a></html> |
| 13:15-14:30 | Lunch | |||
| 14:30-16:00 | Visual representation Chair: Anatoly Sorokin | |||
| 14:30-15:00 | LibSBGN progress update | Martijn van Iersel & Tobias Czauderna | Slides | <html><a href="/sites/combine/files/2011-09-06-combine-vaniersel-czauderna.mov">Video</a></html> |
| 15:00-15:20 | Update on SBGN PD | Stuart Moodie | Slides | <html><a href="/sites/combine/files/2011-09-06-combine-moodie.mov">Video</a></html> |
| 15:20-15:40 | Update on SBGN-ER | Nicolas Le Novère | Slides | <html><a href="/sites/combine/files/2011-09-06-combine-lenovere2.mov">Video</a></html> |
| 15:40-16:00 | Update on SBGN AF | Huaiyu Mi | Slides | <html><a href="/sites/combine/files/2011-09-06-combine-mi.mov">Video</a></html> |
| 16:00-16:30 | Break | |||
| 16:30-18:00 | Visual representation Chair: Falk Schreiber | |||
| 16:30-16:40 | Converters and graphical representation for BioModels database. | Gaël Jalowicki | Slides | <html><a href="/sites/combine/files/2011-09-06-combine-jalowicki.mov">Video</a></html> |
| 16:40-16:50 | SBGN-ER vs rule-based modelling | Michael Blinov | Slides | <html><a href="/sites/combine/files/2011-09-06-combine-blinov.mov">Video</a></html> |
| 16:50-17:20 | Generic-specific relationships representation in SBGN PD | Alexander Mazein | Slides | <html><a href="/sites/combine/files/2011-09-06-combine-mazein.mov">Video</a></html> |
| 17:10-18:00 | Discussion | All | ||
Day 5 (Wednesday September 7th)
| Time | Topic | Speaker | Slides | Recordings |
|---|---|---|---|---|
| 9:00-10:30 | Visual representation Chair: Katja Wegner | |||
| 09:00-09:45 | Discussion libSBGN | All | Slides | <html><a href="/sites/combine/files/2011-09-07-combine-discussion.mov">Video</a></html> |
| Revisit the libSBGN milestone plan | ||||
| 9:45-10:30 | Discussion SBGN | All | ||
| Issues arising from ER V2 Spec | ||||
| Issues arising from PD V2 Spec | ||||
| 10:30-11:00 | Break | |||
| 11:00-13:00 | Applying Standards I: Tools and Databases Chair: Martin Golebiewski | |||
| 11:00-11:30 | Lecture: Standards – a modeller’s point of view | Ursula Kummer | Slides | <html><a href="/sites/combine/files/2011-09-07-combine-kummer.mov">Video</a></html> |
| 11:30-12:00 | Updates of PANTHER pathway | Huaiyu Mi | <html><a href="/sites/combine/files/2011-09-07-combine-mi-panther.pdf">Slides</a></html> | <html><a href="/sites/combine/files/2011-09-07-combine-mi.mov">Video</a></html> |
| 12:00-12:20 | Challenges in Modeling and Curation of a Influenza Viral Life Cycle and Host Response Map | Yukiko Matsuoka | <html><a href="/sites/combine/files/2011-09-07-combine-matsuoka-modeling-influenza.pdf">Slides</a></html> | <html><a href="/sites/combine/files/2011-09-07-combine-matsuoka.mov">Video</a></html> |
| 12:20-12:40 | FieldML | Poul Nielson | <html><a href="/sites/combine/files/2011-09-07-combine-nielson-fieldml.pdf">Slides</a></html> | <html><a href="/sites/combine/files/2011-09-07-combine-nielson.mov">Video</a></html> |
| 13:00-14:00 | Lunch Break | |||
| 12:40-13:00 | Current state of JUMMP | Martin Gräßlin | Slides | <html><a href="/sites/combine/files/2011-09-07-combine-graesslin.mov">Video</a></html> |
| 14:00-15:30 | Applying Standards II: Tools and Databases Chair: Martin Golebiewski | |||
| 14:00-14:30 | BioPAX and SBML output from Reactome: where we are, where we are heading | David Croft | Slides | <html><a href="/sites/combine/files/2011-09-07-combine-croft.mov">Video</a></html> |
| 14:50-15:20 | BioUML - open source integrated platform for collaborative and reproducible research in systems biology | Alexander Kel | <html><a href="/sites/combine/files/2011-09-07-combine-kel- biouml.pdf">Slides</a></html> | <html><a href="/sites/combine/files/2011-09-07-combine-kel.mov">Video</a></html> (3) |
| 15:20-15:50 | Break | |||
| 15:50-17:20 | Applying Standards III: Tools and Databases Chair: Sven Sahle | |||
| 15:50-16:20 | Lecture: BioSharing: policies, standards and communication in bioscience | Dawn Field | Slides | <html><a href="/sites/combine/files/2011-09-07-combine-field.mov">Video</a></html> |
| 16:20-16:50 | SABIO-RK: Access to Biochemical Reaction Kinetics Data | Martin Golebiewski | Slides | <html><a href="/sites/combine/files/2011-09-07-combine-golebiewski.mov">Video</a></html> |
| 16:50-17:20 | Bringing data into VCell Modeling Framework: Pathway Commons and SABIO-RK | Michael Blinov | Slides | <html><a href="/sites/combine/files/2011-09-07-combine-blinov.mov">Video</a></html> |
| 17:20-17:30 | Closing remarks | Nicolas Le Novère | <html><a href="/sites/combine/files/2011-09-07-combine-lenovere.mov">Video</a></html> | |
| 17:30-17:40 | Mike Hucka's Lament | Lucian Smith | Slides | <html><a href="/sites/combine/files/2011-09-07-combine-smith.mov">Video</a></html> |
| 17:40-17:50 | Conclusion | Martin Golebiewski | Slides | <html><a href="/sites/combine/files/2011-09-07-combine-golebiewski2.mov">Video</a></html> |
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