Detailed Programme

Day 1.  Sunday 5th April


9am: Ferry departs Auckland Downtown Ferry Building. Shuttle buses at the Waiheke Wharf will meet this ferry to take delegates to the conference centre.

10.30am Session 1  "CellML: where it's been and where it's going"
Chair: Peter Hunter (Auckland Bioengineering Institute)

  • 10.30am  Welcome & Introduction to CellML
    Poul Nielsen (Auckland Bioengineering Institute) (pdf) (audio)

  • 10.50am  Modularity in CellML
    David Nickerson (National University of Singapore) (pdf) (audio)

  • 11.10am  Modelling Tools: PCEnv, COR & OpenCell
    Justin Marsh (Auckland Bioengineering Institute) & Alan Garny (University of Oxford) (pdf) (audio)
  • 11.30am  Chaste: a general purpose simulation package aimed at multi-scale, computationally demanding models
    Jonathan Cooper (University of Oxford) (pdf) (audio)
  • 11.45am  insilicoML: an extensible markup language format for describing multi-level biophysical models
    Yoshiyuki Asai (Osaka University) (pdf) (audio)

12-1.15pm  Lunch

1.15pm Session 2  "Events, Time Delays and Typing"
Chair: Mike Hucka (Caltech)

  • 1.15pm  CellML: time delays and events
    Poul Nielsen (Auckland Bioengineering Institute) (pdf) (audio)

  • 1.30pm  CellML: type systems
    Andrew Miller (Auckland Bioengineering Institute) (pdf) (audio)
  • 1.45pm  Introduction to SBML & a summary of SBML's definition of events
    Mike Hucka (Caltech) (pdf) (audio)
  • 2.10pm  Technical issues in implementing event support
    Frank Bergman (University of Washington) (pdf) (audio)

2.30-3pm  Discussion (everyone): Towards defining the specification of CellML events, time delays and type systems.

3-3.30pm  Coffee

3.30pm Session 3 "Space & Hierarchy"
Chair: Poul Nielsen (Auckland Bioengineering Institute)

  • 3.30pm  FieldML: a standard for modelling and interchanging field descriptions
    Richard Christie (Auckland Bioengineering Institute) (pdf) (audio)

  • 3.45pm  OpenCMISS
    David Nickerson (National University of Singapore) (pdf) (audio)
  • 4pm  Space in VCell
    Ion Moraru (University of Connecticut Health Center) (pdf) (audio)
  • 4.15pm  CompuCell3D
     Benjamin Zaitlen (Indiana University) (pdf) (audio)
  • 4.30-5pm  Discussion (everyone)
Leading question: how far are we from having interoperable spatial & hierarchical models? (FieldML, OpenCMISS, modularity in CellML & SBML)


Day 2.  Monday 6th April


9am Session 4 "Model exchange and interoperability"
Chair: Nicolas Le Novère (EMBL-EBI)

  • 9am  The New Model Repository (PMR2): the underlying software and support of CellML 1.1 models
    Tommy Yu (Auckland Bioengineering Institute) (pdf) (audio)

  • 9.15am  euHeartDB: a web-enabled database for geometrical models of the heart
    Daniele Gianni (University of Oxford) (pdf) (audio)
  • 9.30am  BioModels Database
    Nicolas Le Novère (EMBL-EBI) (pdf) (audio)
  • 9.45am  VCell and its model database
    Ion Moraru (University of Connecticut Health Center) (pdf) (audio)
  • 10-10.30am  Discussion (everyone)
Leading question: what are the prospects for interoperabilty between model repositories?

10.30-11am Coffee

11am Session 5 "Minimum Information About a Simulation Experiment (MIASE)"
Chair: Peter Hunter (Auckland Bioengineering Institute)

  • 11am MIBBI and the MI guidelines (http://www.mibbi.org/) (pdf)

  • 11.05am MIASE (http://www.ebi.ac.uk/compneur-srv/miase/)

      Nicolas Le Novère (EMBL-EBI) (pdf) (audio)
  • 11.20-12.30am  Discussion (everyone)
The goal of the session is to involve everyone, so as to get to widest coverage of needs possible. We will hopefully start drafting rules for MIASE.

12.30-2pm Lunch

2pm Session 6 "Encoding simulation description"
Chair: Nicolas Le Novère (EMBL-EBI)
  • 2pm Presentation of relevant CellML metadata
     David Nickerson (National University of Singapore) (pdf) (audio)
  • 2.30pm Implementation in OpenCell
     Andrew Miller (Auckland Bioengineering Institute) (pdf) (audio)
  • 3pm Presentation of SED-ML [and libSED-ML]
     Dagmar Koehn (Rostock University) (pdf)
  • Jlibsedml - a Java library for manipulating SED-ML files. 
     Stuart Moodie on behalf of Richard Adams (CSBE, University of Edinburgh) (pdf)

3.30-4pm Coffee

4pm Session 7 "Encoding simulation description - continued"
Chair: Nicolas Le Novère (EMBL-EBI)
  • 4pm Implementation of SED-ML
     Frank Bergmann (University of Washington) (pdf) (audio)
  • 4.15pm Implementation of SED-ML continued
     Ion Moraru (University of Connecticut Health Center) (pdf) (audio)
  • 4.30-5.30pm  Discussion (everyone) (audio)
Technical discussion on SED-ML, and its use with CellML and SBML. Topics:
  • How to address the various "times" (simulation time, model time etc.)
  • Modifications of models: changeAttribute, changeXML, changeMat
  • Format extensions for different simulation types, parameter scans, steady state analyses and non-kinetic simulations


Day 3.  Tuesday 7th April


9am Session 8 "Ontological representation and visualization"
Chair: Dan Cook (University of Washington)
  •  9am  Introduction and explanation of goals
      Mike Hucka (Caltech) (pdf)
  •  9.10am  SBO: where it's been & where it's going
      Nick Juty (EMBL-EBI) (pdf)
  •  9.35am  OPB: Ontology of Physics for Biology
      Dan Cook (University of Washington) (pdf)
  •  10am  Multi-scale interoperability of Virtual Physiological Human data and models
      Bernard de Bono (EMBL-EBI) (pdf)

10.25-11am  Coffee

11am Session 9 "Ontological representation and visualization - continued"
Chair: Poul Nielsen (Auckland Bioengineering Institute)
  •  11am  BioPAX
      Emek Demir (MSKCC) (pdf) (audio)
  •  11.25am  Core CellML metadata
      James Lawson (Auckland Bioengineering Institute) (pdf) (audio)
  •  11.50am  Model visualisation
      Sarala Wimalaratne (Auckland Bioengineering Institute) (pdf) (audio)
  •  12.10pm  SBGN
      Nicolas Le Novère (EMBL-EBI) (pdf)

12.30-2pm Lunch

2pm Session 10 "Ontological representation and visualization - continued"
Chair: Mike Hucka (Caltech)
  •  2pm  SBGN Process Diagrams
      Stuart Moodie (University of Edinburgh) (pdf)
  •  2.20pm  SBGN Entity Relationship Diagrams
      Nicolas Le Novère (EMBL-EBI) (pdf)
  •  2.40pm  SBGN Activity Flow Diagrams
      Huaiyu Mi (SRI International) (pdf)
  •  3pm  CellDesigner and SBGN
      Yukiko Matsuoka (The Systems Biology Institute) (pdf)

3.30-4pm Coffee

4pm Session 11 "Ontological representation and visualization - continued"
Chair: Stuart Moodie (University of Edinburgh)
  •  4pm  Progress on SBGN PD in EPE
      Stuart Moodie on behalf of Anatoly Sorokin (University of Edinburgh) (pdf)
  •  4.15pm  Progress on SBGN in Arcadia
      Alice Villeger (University of Manchester) (pdf) (audio)
  •  4.30pm  Progress on SBGN
      Frank Bergman (University of Washington) (pdf) (audio)
  •  4.45pm  Progress on SBGN layout
      Sarah Boyd (Monash University) (pdf)
  •  5pm Open Flow Biological Network Initiative: Pathway map building, standards, simulation, and knowledge sharing
     Hiroaki Kitano (1,2) ((1) The Systems Biology Institute, (2) OIST) (pdf) (audio)

  • 5.30-6.15pm  Discussion (everyone): where do these various efforts overlap, and where are they different?  Make this concrete by writing a table on the board listing the different features and goals of each effort.


Day 4.  Wednesday 8th April


9am Session 12 "Interoperability and integration"
Chair: Emek Demir (MSKCC)
  •  9am  BioPAX, PAXtools & pathway integration
      Emek Demir (MSKCC) (pdf) (audio)
  •  9.20am  Conversion between BioPAX and SBML
      Camille Laibe (EMBL-EBI) (pdf) (audio)
  •  9.35am  BioPAX for semantic web based data integration
      Andrea Splendiani (Rothamsted Research) (pdf) (audio)
  •  10am  BISEN: Biochemical Simulation Environment
      Daniel Beard (Medical College of Wisconsin) (pdf) (audio)

10.25-11am  Coffee

11am Session 13 "Interoperability and integration - continued"
Chair: Nicolas Le Novère (EMBL-EBI)
  • 11-12.30pm  Discussion (everyone)
The technical hurdles in mapping between BioPAX, CellML, SBO, SBGN...  plus any other related topics that people may want to discuss.

12.30-2pm  Lunch

12pm Session 14 "Umbrella organisations"
Chair: Peter Hunter (Auckland Bioengineering Institute)
  • 2pm  Should we create an umbrella organisation?
     Emek Demir (MSKCC) (audio)
  • 2.15-3.30pm  Discussion (everyone)
Umbrella organisations, international collaboration, shared efforts, and related topics.

3.30-4pm Coffee

4pm Session 15 "Joint Efforts Group Discussion"

Conference dinner at Te Whau Vineyard.