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COMBINE 2010

Informatics Forum, University of Edinburgh
Edinburgh, Scotland
Oct. 6–9, 2010

In 2010, we inaugurated a new, broader series of meetings to replace, among other events, the SBML and SBGN forums. The new meetings are a recognition of the fact that there are multiple allied standardization efforts that should work together towards smooth interoperability. Moreover, we believe a joint meeting makes good economic sense: compared to multiple separate workshops, they reduce the overall number of meetings, travel, and money spent over the year. To reflect its broad scope, we have called the new workshop series the annual meeting of COMBINE:

the COmputational Modeling in BIology NEtwork


COMBINE 2010 took place on October 6–9, 2010, immediately before ICSB 2010, in Edinburgh, Scotland. The final session of COMBINE (October 9, 2010) was followed by a special event to mark the 10th anniversary of SBML.


List of
attendees


Supplementary
materials


Nature Precedings
COMBINE 2010 collection


Travel
information


Photo album


Results of
exit survey


Results of
survey about
future meetings


Agenda

The activities at COMBINE meetings are similar to typical workshops, with oral and poster presentations, break-out discussions, and more. The following table summarizes the organization of the 2010 event across the four days. A detailed agenda appears below.

Wednesday 6th Thursday 7th Friday 8th Saturday 9th
Session 1 Physiome languages Graphical layout and rendering Format conversion SBML Level 3
break
Session 2 SED-ML Interactions and Reactions Multi-standard software libSBML and SBML support
lunch
Session 3 SBGN languages Semantics and metadata resources BioPAX status and future directions
break SBML 10th Anniversary
Session 4 libSBGN and SBGN support Encoding and using semantics Gaps in coverage and concepts


In addition to being available for downloading from below, many of the presentations and the posters are now part of the Nature Precedings COMBINE 2010 collection.

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 Video
"CellML 1.1 modularity" Poul Nielsen Slides Video
"Workflows/GUI interfaces (nephron model), linking CellML to fields thru FieldML" David Nickerson Slides Video
"OpenCell, status and plans" Alan Garny Slides Video
Discussion Video
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 Video
"jlibsedml and its application in SBSI" Richard Adams Slides Video
"jlibsedml utility functions" Ion Moraru Slides Video
Discussion Video
12:00–13:30 breakouts
13:30–14:30 Lunch
14:30–16:00 SBGN languages (main room) chair: Stuart Moodie Video
14:30 ""Report on the status of SBGN ER and proposed extensions." Nicolas Le Novère Slides Video
14:45 "SBGN PD: current status, future changes and unresolved issues." Stuart Moodie Slides Video
15:00 "Update on SBGN-AF" Huaiyu Mi Slides Video
15:15 "SBGN-ER for physiology mechanisms." Bernard de Bono Slides Video
Discussion Video
SBGN Awards Video
14:30–16:00 breakouts
16:00–16:30 Coffee break
16:30–18:00 libSBGN and SBGN support (main room) chair: Alice Villeger Video
"LibSBGN: current status and future plans" Alice Villeger Slides Video
"SBGN-ED for Editing, Validating, and Translating of SBGN Maps and Application Examples" Tobias Czauderna Slides Video
"SBGN support in BIOCHAM" Dragana Jovanovska Slides Video
Discussion Video
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 Video
"BioPAX support in CellDesigner" Huaiyu Mi Slides Video
"Encoding and exchanging graphical representation: architecture and formats" Andrei Zinovyev for Fedor Kolpakov Slides Video
Discussion Video
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 Video
"Exchanging experimental kinetic data via SabioML" Martin Golebiewski Slides Video
Pathways Integration Emek Demir Slides Video
"The Reactome Pathway Database; its functionality and data exchange formats" David Croft Slides Video
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 Video
"MIRIAM Resources: next steps" Camille Laibe Slides Video
"about BioPAX and RDF" Andrea Splendiani Slides Video
Discussion Video
13:30–15:00 breakouts
15:00–15:30 Coffee break
15:30–17:00 Encoding and using semantics (main room) chair: Neil Swainston Video
"Ranked retrieval of annotated models" Ron Henkel Slides Video
"The SBML Level 3 Annotation package: an initial proposal" Neil Swainston Slides Video
"Model search and parameter balancing in semanticSBML" Wolfram Liebermeister slides Video
Discussion Video
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 Video
"The General Converter Package" Jean-Baptiste Pettit Slides Video
"Insights in SBML Interoperability and Interconversion" Alice Villéger Slides Video
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 Video
"BioModels Database: next generation model repository" Camille Laibe and Michael Hoehl Slides Video
"The PSI Common Query Interface (PSICQUIC) - Standard API for 12 interaction databases" Henning Hermjakob Slides Video
"Software for Molecular Interaction Maps (MIMs): Editor, API, and Validation" Augustin Luna Slides Video
"BiNoM Cytoscape Plugin for constructing, quering and analyzing biological networks, using systems biology standards" Andrei Zinovyev Slides Video
"BioUML integrated platform for building virtual cell and virtual physiological human" Andrei Zinovyev for Fedor Kolpakov Slides Video
11:00–12:30 breakouts
12:30–13:30 Lunch
13:30–15:00 BioPAX status and future directions (main room) chair: Emek Demir Audio
"Overview of BioPAX", discussion Nadia Anwar Audio
"BioPAX L2 and L3" Emek Demir Slides Video (1)
"Community update and structure", "Workgroups Priorities" Nadia Anwar Slides Video
"The Future of BioPAX" Gary Bader Slides n/a
"Layout Workgroup" Martijn van Iersel Slides n/a
"BioPAX L4 Proposals" Emek Demir Slides Video (2)
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 Video
"Types, models and instances: a perspective from neuroscience" Robert Cannon Slides Video
"Metabolic network representation in SBGN PD: EC and identity gate." Alexander Mazein Slides Video
"A generic approach for representing complex structures in biological models" Robert Muetzelfeldt Slides Video
"Exploring the challenges of pathway depiction and the development of modified Edinburgh Pathway Notation (mEPN) scheme" Tom Freeman Slides Video
15:30–17:00 breakouts
(1) This presentation begins with audio only. Video begins partway through.
(2) Audio and video begin partway through the presentation.

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 Video
"The SBML Level 3 Spatial Package" James Schaff Slides Video
"The SBML Flux Balance Analysis Package" Brett Olivier Slides Video
"The SBML Hierarchical Composition Package" Lucian Smith Slides Video (3)
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 Video
"Implementation of L3 Support within iBioSim" Chris Myers Slides Video
"Update on JSBML status" Nicolas Rodriguez Slides Video
"Context-based generation of kinetic equations with SBMLsqueezer 1.3 " Andreas Draeger Slides Video
11:00–12:30 breakouts
12:30–13:30 Lunch
(3) The video ends before the end of the talk. However, the audio continues throughout.

Posters

COMBINE 2010 offered the opportunity for attendees to display posters. This served as a means for people to inform each other about their software and other projects in a setting that allowed interaction and in-depth discussion.

The maximum poster size was A0, which is 841mm (width) x 1189mm (height), or approximately 33in x 46in, in a portrait orientation. This was essentially the same size as the ICSB 2010 posters.

Poster sessions were held semi-concurrently with lunch breaks. The basic approach was to make the breaks extra long, so that people could get some food & beverages, then come back and discuss their work in the poster room.

Location

The meeting was held in the Informatics Forum building at the University of Edinburgh. This is a new center for innovation and interaction—ideally suited to the goals of COMBINE. This venue is located in the centre of the University's main campus.

Informatics Forum
Room G07
University of Edinburgh
10 Crichton Street
Edinburgh, EH8 9AB
Scotland, United Kingdom

Funding Acknowledgments

Support for COMBINE 2010 was provided by the following organizations:

Icon-bbsrc-logo-30x123.jpg
Biotechnology and Biological Sciences Research Council
Icon-nigms-logo-30x30.jpg

NIH/NIGMS

ENFIN_logo.png

ENFIN

Organization

COMBINE 2010 was organized by the following people (listed in alphabetical order):

For general information about the meeting, and travel arrangements for the speakers of October 9th, contacts were:

Linda Taddeo Michael Hucka Nicolas Le Novère
ltaddeo at caltech.edu mhucka at caltech.edu lenov at ebi.ac.uk
Tel: +1 626 395 3375       Tel: +1 626 395 6911 Tel: +44 1223 494 521
Beckman Institute 139-74
California Institute of Technology
Pasadena, California 91125
USA
EMBL-EBI
Wellcome-Trust Genome Campus
Hinxton, CB10 1SD
UK

For practical information on the setting and local organisation, contacts were:

Stuart Moodie Anatoly Sorokin Fiona Clark
stuart.moodie at ed.ac.uk asorokin at inf.ed.ac.uk fclark1 at inf.ed.ac.uk
Tel: +44 1316 513 291
School of Informatics, Informatics Forum

University of Edinburgh
10 Crichton Street
Edinburgh
UK

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