| 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
|
|
|
|
|
|
|
|
|
|
| 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)
|
|
|
| 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
|
|
|
|
|
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|
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|
