Workshop programme

 

Auckland skyline at night

Wednesday 24th February

(Location: ABI, level 5 seminar room, 70 Symonds Street)
 
8.30 - 10.30     CellML overview and tutorial
10.30 - 11.00   Morning tea and coffee
11.30 - 12.30   Welcome and opening of the hackathon
12.30 - 13.30   Lunch
13.30 - 15.00   Second hackathon session
15.00 - 15.30   Afternoon tea and coffee
15.30 - 17.00   Third hackathon session    
   
Suggested topics for discussion include: using CellML models with SED-ML, using the CellML API in drug toxicity assessment, and CellML/SBML language converters.

Thursday 25th February

(Location: school of engineering, large lecture theatre (401-400L4/439), 20 Symonds Street)
 
9.00 - 9.15      Welcome (Poul Nielsen) (pdf)
9.15 - 10.30    Building a CellML 1.1 Model Library
  • Best practice guidelines - case study pathway models  (Mike Cooling) (pdf)
  • Best practice guidelines - case study heart cell models  (David Nickerson) (pdf)
  • Best practice guidelines - towards model visualisation  (Poul Nielsen on behalf of Sarala Wimalaratne) (pdf)
    • Group Discussion: What are the advantages and disadvantages of the proposed methods?
10.30 - 11.00   Morning tea and coffee
 
11.00 - 12.30   Building a CellML 1.1 Model Library
  • Model annotation: the requirements of a 1.1 model  (Poul Nielsen) (pdf)
  • PMR2: embedded workspaces and storage of 1.1 models  (Tommy Yu) (pdf)
  • Building a 1.1 model in OpenCell  (Randall Britten) (pdf)
    • Group Discussion: How can tools help us to create a 1.1. model library?
12.30 - 13.30   Lunch
 
13.30 - 15.00     Tools and User Interfaces
  • Cell modelling software  (Takao Shimayoshi) (pdf)
  • OpenCell development (COR-like View) (Alan Garny) (pdf)
  • The CellML API  (Andrew Miller) (pdf)
  • Metadata editor - what do we want/need?  (Catherine Lloyd) (pdf)
    • Group Discussion: Feature requests for future software releases.
15.00 - 15.30   Afternoon tea and coffee
 
15.30 - 17.00    Language, Language Interconversion, Interoperability and Collaboration
  • smbl2cellml  (Nicolas Rodriguez) (pdf)
  • cellml2sbml  (Andrew Miller) (pdf)
  • ModML  (Andrew Miller) (pdf)
  • CellML 1.2 and future interoperability between CellML and SBML  (Poul Nielsen) (pdf)
    • Group Discussion: What are the prospects for interoperability between CellML and SBML? 
Evening: Dinner at La Cigale, Parnell

Friday 26th February

(Location: school of engineering, large lecture theatre (401-400L4/439), 20 Symonds Street)

9.00 - 10.30    Metadata and Model Annotation
  • An ontology of cell physiology  (Takao Shimayoshi) (pdf)
  • Saint - A lightweight model annotation tool  (Morgan Taschuk and Allyson Lister - via Evo) (pdf)
  • SED-ML  (Dagmar Waltemath - via Evo) (pdf)
  • Model annotation methods  (Abhishek Tiwari) (pdf)
    • Group Discussion: How do we want to annotate CellML models and what tools do we need to make this a reality?
10.30 - 11.00   Morning tea and coffee
 
11.00 - 12.30   Databases and Model Repositories
  • BioModels database  (Lukas Endler) (pdf)
  • PMR2 - so far so good and what's next?  (Tommy Yu) (pdf)
  • Collaborating via the model repository  (David Nickerson) (pdf)
    • Group Discussion: How can modellers use PMR2 to facilitate collaboration?
12.30 - 13.30   Lunch
 
13.30 - 15.00   Model Curation
  • Model curation: the CellML approach  (Catherine Lloyd) (pdf)
  • Model curation: the BioModels approach  (Lukas Endler) (pdf)
  • From stars to flags  (Catherine Lloyd) (pdf)
    • Group Discussion: How can we pool limited curation resources?
15.00 - 15.30   Afternoon tea and coffee
 
15.30 - 17.00   Multi-scale Modelling
  • Modelling the patch electrode allows accurate characterization of small connective-tissue cells  (Jim Wilson) (pdf)
  • Multi-scale modelling of aneurysm formation - linking continuum mechanics and growth to signalling events  (Holger Schmid) (pdf)
  • Connecting circulation and nerve systems: some ideas  (Harvey Ho) (pdf)
  • Update on FieldML 0.2  (Randall Britten) (pdf)
    • Group Discussion: The challenges of linking CellML and FieldML models.
17.00   Overview of the VPH/Physiome Developments: the roles of CellML, FieldML and PMR2  (Peter Hunter) (pdf)
 
Evening: Lantern Festival, Albert Park.