Detailed agenda of COMBINE 2011


Day 1 (Saturday, September 3rd)

Time Topic Speaker Slides Recordings
09:15-09:25 Welcome address by the managing director of HITS Andreas Reuter Video
09:25-09:30 Technical remarks to the COMBINE 2011 meeting Martin Golebiewski Slides Video
09:30-09:45 COMBINE, what it is, what it could be Nicolas Le Novère Slides Video
Simulation and analysis
Chair: David Nickerson
09:45-10:05 SED-ML Intro / History Dagmar Waltemath Slides Video
10:05-10:25 Java software support for SED-ML Richard Adams Slides Video
10:25-10:45 SED-ML Web Tools Frank Bergmann Slides Video
10:45-11:05 Functional Curation: Potential Future Directions for SED-ML Jonathan Cooper Slides Video
11:05-11:15 Discussion All
11:15-11:45 Break
11:45-12:05 KiSAO: Kinetic Simulation Algorithm Ontology Anna Zhukova (remotely) Slides Video
12:05-12:25 SProS Andrew Miller (remotely) Slides Video
12:25-12:45 SBRML Interoperability Frank Bergmann Slides Video
12:45-13:15 Discussion All
13:15-14:15 Lunch
Chair: Nicolas Le Novère
14:30-14:50 Camille Laibe Slides Video
14:50-15:10 Update on MIRIAM Registry and SBO Nick Juty Slides Video
15:10-15:40 Integrating systems biology and biomedical ontologies Robert Hoehndorf Slides
15:40-16:10 Break
Chair: Camille Laibe
16:10-16:40 Semantic annotations and querying of SBML simulations Michel Dumontier Slides Video
16:40-17:10 OneStop: JWS Online's access point to SBML, SBGN and MIRIAM compliant annotation Franco Du Preez Slides Video
17:10-17:30 Systems Biology Format Converter Martina Kutmon Slides Video
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
Parallel focused discussion sessions—see the Google spreadsheet) for up-to-the-minute schedule and sign-up sheets

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 Slides Video
11:15-11:30 Status update on libSBML Sarah Keating Slides Video
11:30-11:45 JSBML update N Rodriguez/A Dräger Slides Video
11:45-12:00 Updates on SBML Team facilities and software Bergmann/Keating Slides Video
12:00-12:15 Interconversion between SBML Levels and packages Keating/Bergmann Slides Video
12:15-12:30 Coordination Topics for Discussion with Developers Keating/Bergmann Slides Video
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 Video
13:50-14:10 A Modelling Ecosystem for Libraries of Modular, Reusable Components Mike Cooling Slides Video
14:10-14:30 NetBuilder' - Modelling and simulating genetic regulatory networks Katja Wegner Slides Video
14:30-14:50 How to integrate COPASI with other software Sven Sahle Slides Video
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 Video
15:45-16:05 Current developments in qualitative modelling of biological networks Claudine Chaouiya Slides Video
16:05-16:25 Updates on the SBML Level 3 Hierarchical Model Composition (“comp”) package Lucian Smith Slides Video
16:25-16:45 Dynamic structures in SBML Chris Myers Slides Video (1)
16:45-17:00 Spatial models in SBML James Schaff Slides Video (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 Video

(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 Video
9:25-9:50 CellML: current status and future plans David Nickerson Slides Video
9:50-10:15 SBML & synthetic biology Chris Myers Slides Video
10:15-10:45 SBML Editors' Report Lucian Smith Slides Video
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 Video
11:45-12:30 Discussion All Video
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 Video
14:00-14:30 CellOrganizer: Image-derived Models of Subcellular Organization over Time and Space Robert F. Murphy Slides Video
14:30-15:00 Systems Biology on Bio-Linux Mesude Bicak Slides Video
15:00-15:20 Reflect: an augmented browsing tool for life scientist Janos Binder Slides Video
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 Video
16:10-16:40 SBPAX: Turning Biological Knowledge into Mathematical Models, Automated Oliver Ruebenacker Slides Video
16:40-17:00 Formal Representation of BioPAX as OWL ontologies Michel Dumontier Slides Video
17:15-18:30 Keynote
Chair: Nicolas Le Novère
Peer Bork Video
19:30-23:00 Conference Dinner at S'Kastanie

Day 4 (Tuesday, September 6th)

Time Topic Speaker Slides Recordings
Parallel focused discussion sessions—see the Google spreadsheet) for up-to-the-minute schedule and sign-up sheets

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 Video
11:45-12:15 Visual Representations - from Atoms to Organisms Agnieszka Bronowska Slides Video
12:15-12:45 SBGN-ED – working with the Systems Biology Graphical Notation Falk Schreiber Slides Video
12:45-13:15 Tools for Molecular Interaction Maps and a Graphical Notation Validation Framework for PathVisio Augustin Luna Slides Video
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 Video
15:00-15:20 Update on SBGN PD Stuart Moodie Slides Video
15:20-15:40 Update on SBGN-ER Nicolas Le Novère Slides Video
15:40-16:00 Update on SBGN AF Huaiyu Mi Slides Video
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 Video
16:40-16:50 SBGN-ER vs rule-based modelling Michael Blinov Slides Video
16:50-17:20 Generic-specific relationships representation in SBGN PD Alexander Mazein Slides Video
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 Video
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 Video
11:30-12:00 Updates of PANTHER pathway Huaiyu Mi Slides Video
12:00-12:20 Challenges in Modeling and Curation of a Influenza Viral Life Cycle and Host Response Map Yukiko Matsuoka Slides Video
12:20-12:40 FieldML Poul Nielson Slides Video
13:00-14:00 Lunch Break
12:40-13:00 Current state of JUMMP Martin Gräßlin Slides Video
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 Video
14:50-15:20 BioUML - open source integrated platform for collaborative and reproducible research in systems biology Alexander Kel Slides Video (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 Video
16:20-16:50 SABIO-RK: Access to Biochemical Reaction Kinetics Data Martin Golebiewski Slides Video
16:50-17:20 Bringing data into VCell Modeling Framework: Pathway Commons and SABIO-RK Michael Blinov Slides Video
17:20-17:30 Closing remarks Nicolas Le Novère Video
17:30-17:40 Mike Hucka's Lament Lucian Smith Slides Video
17:40-17:50 Conclusion Martin Golebiewski Slides Video

(3) Video is missing for a portion of this presentation, but audio continues.