Workshop Programme

Programme for the 8th International CellML Workshop.

The list of posters to be presented during the workshop is available below.

Monday 14 AprilTuesday 15 April
8:15 Ferry from Auckland
9:00 Welcome & housekeeping (Andre) Welcome & editorial nominee introductions (Andre)
9:30
  1. The CellML model's walk through the repository: a retrospective study (Martin Scharm)
  2. Virtual Systems in CellML (Mike Cooling)
  3. Introduction to the Physiome Model Repository (Poul Nielsen)
 Related Standards
  1. SBML (Lucian Smith)
  2. SED-ML & NuML (Andre)
  3. BioSignalML (Dave Brooks)
  4. FieldML (Richard Christie)
10:30 Morning tea and posters
11:00
  1. OpenCOR (Alan Garny)
  2. Software introductions and demonstrations
  1. Functional Curation (Alan Garny on behalf of Jonathan Cooper and Gary Mirams)
  2. Agent based models (Tim Johan)
  3. Taming the BISEN? Towards metabolically-aware models in CellML (Mike Cooling)
  4. Software introductions and demonstrations
    • OpenCMISS + CellML (Andre)
    • Kepler Workflows for Data and Model Integration in Multi-Scale Systems Biology (Andrew McCulloch)
    • MAP client and plugins for the model repository & OpenCMISS (Hugh Sorby)
12:30 Lunch & posters & software demos
13:30
  1. Design principles for large scale model composition (Mike Cooling)
  2. PMR2 update (Tommy Yu)
  3. CellML in practice: modularity and reuse; versioning and provenance; embedded workspaces (Andre)
  1. Meaningful Modelling (Mike Cooling)
  2. Lessons from annotating the notch pathway (Nazanin Ebrahimi)
  3. Composite annotations (Dan Cook)
  4. Annotation discussion
15:00 Afternoon tea & posters
15:30 e-publishing and reproducibility
  1. Introduction (Herb Sauro)
  2. Discussion
 Discussion session: supporting tool developers wanting to make use of CellML.
17:00 Systems Biology in Melbourne (Vijay Rajagopal) Concluding remarks (Peter Hunter) followed by wine tasting
18:15 Ferry to Auckland
19:30 (self pay) Workshop Dinner @ Vivace

 

Posters

All posters will be on display for the duration of the workshop.

PresenterTitle
Mike Cooling NOSIES: A Case Study in Constraining Model Behaviour
Harvey Ho The software framework for the Silver Fern Farm lamb carcass modelling project
Randall Britten ABI Software Lab projects overview and recent developments and a high level roadmap
Richard Christie, Alan Wu OpenCMISS-Zinc: Visualising Research
Armand Patoir Virtual retail cut from lamb carcasses
Herbert Sauro
Yuriy Pichugin Modeling of the multilevel selection in Pseudomonas fluorescens
Tatyana Pichugina Models of the S.pombe genome in the G1 phase and G2 phases of the cell cycle
Andrew McCulloch Kepler Workflows for Data and Model Integration in Multi-Scale Systems Biology
Teun de Boer eSolv, a CellML-based simulation front-end for online teaching
David Brooks BioSignalML in OpenCOR