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Agenda


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Wednesday, October 6

Time Topic Speaker/Leader Files Recordings
09:00–09:30 Registration, coffee
09:30–10:00 Welcome, introduction to COMBINE 2010 Nicolas Le Novère Slides Video
Stuart Moodie Slides Video
10:00–11:30 Physiome languages (main room) chair: Peter Hunter
"Intro. PMR2" Peter Hunter Slides
"CellML 1.1 modularity" Poul Nielsen Slides
"Workflows/GUI interfaces (nephron model), linking CellML to fields thru FieldML" David Nickerson Slides
"OpenCell, status and plans" Alan Garny Slides
10:00–11:30 breakouts
11:30–12:00 Coffee break
12:00–13:30 SED-ML (main room) chair: Frank T. Bergmann
"Intro to the session, libsedml" Frank T. Bergmann Slides
"jlibsedml and its application in SBSI" Richard Adams Slides
"jlibsedml utility functions" Ion Moraru Slides
12:00–13:30 breakouts
13:30–14:30 Lunch
14:30–16:00 SBGN languages (main room) chair: Stuart Moodie
14:30 ""Report on the status of SBGN ER and proposed extensions." Nicolas Le Novère Slides
14:45 "SBGN PD: current status, future changes and unresolved issues." Stuart Moodie Slides
15:00 "Update on SBGN-AF" Huaiyu Mi Slides
15:15 "SBGN-ER for physiology mechanisms." Bernard de Bono Slides
14:30–16:00 breakouts
16:00–16:30 Coffee break
16:30–18:00 libSBGN and SBGN support (main room) chair: Alice Villeger
"LibSBGN: current status and future plans" Alice Villeger Slides
"SBGN-ED for Editing, Validating, and Translating of SBGN Maps and Application Examples" Falk Schreiber and Tobias Czauderna Slides
"SBGN support in BIOCHAM" Dragana Jovanovska Slides
16:30–18:00 breakouts

Thursday, October 7

Time Topic Speaker/Leader Files Recordings
08:30–09:00 Welcome, introduction to the day
09:00–10:30 Graphical layout and rendering (main room) chair: Ralph Gauges
"SBML layout and render news" Ralph Gauges slides
"BioPAX support in CellDesigner" Huaiyu Mi slides
"Encoding and exchanging graphical representation: architecture and formats" Andrei Zinovyev for Fedor Kolpakov slides
09:00–10:30 breakouts
10:30–11:00 Coffee break
11:00–12:30 Interactions and reactions (main room) chair: Henning Hermjakob
"The HUPO Proteomics Standards Initiative" Henning Hermjakob slides
"Exchanging experimental kinetic data via SabioML" Martin Golebiewski slides
Pathways Integration Emek Demir slides
"The Reactome Pathway Database; its functionality and data exchange formats" David Croft slides
11:00–12:30 breakouts
12:30–13:30 Lunch
13:30–15:00 Semantics and metadata resources (main room) chair: Camille Laibe
"Systems Biology Ontology: Update" Nick Juty slides
"MIRIAM Resources: next steps" Camille Laibe slides
"about BioPAX and RDF" Andrea Splendiani slides
13:30–15:00 breakouts
15:00–15:30 Coffee break
15:30–17:00 Encoding and using semantics (main room) chair: Neil Swainston
"Ranked retrieval of annotated models" Ron Henkel slides
"The SBML Level 3 Annotation package: an initial proposal" Neil Swainston slides
"Model search and parameter balancing in semanticSBML" Wolfram Liebermeister slides
15:30–17:00 breakouts
19:30 Dinner at "Wee Windaes" (partially self-funded)

Friday, October 8

Time Topic Speaker/Leader Files Recordings
08:30–09:00 Welcome, introduction to the day
09:00–10:30 Format conversion (main room) chair: Martijn Van Iersel
"Collaborative pathway editing & analysis with WikiPathways and PathVisio" Martijn van Iersel slides
"The General Converter Package" Jean-Baptiste Pettit slides
"Insights in SBML Interoperability and Interconversion" Alice Villéger slides
09:00–10:30 breakouts
10:30–11:00 Coffee break
11:00–12:30 Multi-standard software (main room) chair: Lucian Smith
"Tales from the Code Front: Translating Modularity" Lucian Smith slides
"BioModels Database: next generation model repository" Camille Laibe and Michael Hoehl slides
"The PSI Common Query Interface (PSICQUIC) - Standard API for 12 interaction databases" Henning Hermjakob slides
"Software for Molecular Interaction Maps (MIMs): Editor, API, and Validation" Augustin Luna slides
"BiNoM Cytoscape Plugin for constructing, quering and analyzing biological networks, using systems biology standards" Andrei Zinovyev slides
"BioUML integrated platform for building virtual cell and virtual physiological human" Andrei Zinovyev for Fedor Kolpakov slides
11:00–12:30 breakouts
12:30–13:30 Lunch
13:30–15:00 BioPAX status and future directions (main room) chair: Emek Demir
"Community update and structure", "Workgroups Priorities" Nadia Anwar, Gary Bader slides
"L 4 Proposals" Emek Demir slides
"BioPAX Core/AddOn Proposal" Emek Demir slides
"Layout Workgroup" Martijn van Iersel slides
13:30–15:00 breakouts
15:00–15:30 Coffee break
15:30–17:00 Gaps in coverage and concepts (main room) chair: Robert Cannon
"Towards a comprehensive set of descriptive standards for biology" Nicolas Le Novère slides
"Types, models and instances: a perspective from neuroscience" Robert Cannon slides
"Metabolic network representation in SBGN PD: EC and identity gate." Alexander Mazein slides
"A generic approach for representing complex structures in biological models" Robert Muetzelfeldt slides
"Exploring the challenges of pathway depiction and the development of modified Edinburgh Pathway Notation (mEPN) scheme" Tom Freeman slides
15:30–17:00 breakouts

Saturday, October 9

Time Topic Speaker/Leader Files Recordings
08:30–09:00 Welcome, introduction to the day
09:00–10:30 SBML Level 3 (main room) chair: Mike Hucka
"SBML Level 3 Update" Mike Hucka slides
"The SBML Level 3 Spatial Package" James Schaff slides
"The SBML Flux Balance Analysis Package" Brett Olivier slides
"The SBML Hierarchical Composition Package" Lucian Smith slides
09:00–10:30 breakouts
10:30–11:00 Coffee break
11:00–12:30 libSBML and SBML support (main room) chair: Sarah Keating
"Update on libSBML status" Sarah Keating slides
"Implementation of L3 Support within iBioSim" Chris Myers slides
"Update on JSBML status" Nicolas Rodriguez slides
"Context-based generation of kinetic equations with SBMLsqueezer 1.3 " Andreas Draeger slides
11:00–12:30 breakouts
12:30–13:30 Lunch

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