2nd International CellML Workshop (2008)

The second CellML workshop was held at Old Government House at The University of Auckland on March 26th 2008. The meeting was generously funded by the Maurice Wilkins Centre for Molecular Biodiscovery and was organised by Catherine Lloyd.

18 speakers presented their research and over 50 delegates attended the meeting, including visitors from England, Spain, the Netherlands, America, Japan, and Australia. The presentations were divided into 4 themed sessions: 1.) the CellML language and specification, 2.) tools and user interfaces, 3.) CellML model creation and curation, and 4.) the integration of CellML with larger scale models. Following each set of talks there were structured group discussions led by a chairperson. These lively discussions provided the CellML project team with valuable community feedback, ideas, and collaboration opportunities.

At the request of those who were unable to attend the workshop the majority of the presentations will be available for download, as PDFs, from the website. The proceedings were filmed and once the tape has been processed and edited, it will also be available for download from the CellML website.

Thank you to everyone who contributed to and attended the workshop. Overall it was a great success and we look forward to repeating the event in 2009.

The initial workshop announcement is available along with the workshop programme. The final programme on the day is given below with links to people's presentations.


Session 1.  CellML 1.2 and the Future of CellML

  • Poul Nielsen (The University of Auckland) - Welcome & Introduction (pdf)
  • Jose Puglisi (University of Chicago) - Mathematical Modelling in Biology (pdf)
  • David Nickerson (National University of Singapore) - Describing Mathematical Models of Cellular Physiology (pdf)
  • Steven Niederer (University of Oxford) - A Database Approach to Model Analysis
  • Andrew Miller (The University of Auckland) - The Future of the CellML Specification (pdf)

Session 2.  Tools and User Interfaces

  • Sarala Dissanayake (The University of Auckland) - Visualisation of CellML Models (pdf)
  • Yoshiyuki Asai (Osaka University) - Developing a CellML-Compatible Integrated Development Environment (pdf)
  • Takao Shimayoshi (Kyoto University) - Methods for Semantic Cell Modelling and Convenient Simulation (pdf)
  • Justin Marsh (The University of Auckland) - PCEnv: Status Update (pdf)
  • Alan Garny (University of Oxford) - Moving from COR to PCEnv/COR (pdf)

Session 3.  Model Implementation and Curation

  • Jonna Terkildsen (The University of Auckland) - Combining Models Using CellML (published paper)
  • Mike Cooling (The University of Auckland) - Modular CellML Models with Examples (published paper)
  • Tommy Yu (The University of Auckland) - CellML Model Development with Version Control System (pdf)
  • Catherine Lloyd (The University of Auckland) - In Pursuit of a Working Model: the Curation process (pdf)

Session 4.  The Role of CellML in Tissue Modelling

  • Socrates Dokos (University of New South Wales) - Excitable Cell and Tissue Modelling using CellML/FML - (pdf)
  • Maarten Nieber (Universitat Pompeu Fabra, Barcelona) - GIMIAS - Graphical Interface for Medical Image Analysis and Simulation (pdf)
  • Richard Christie (The University of Auckland) - FieldML: Data Structures for Modelling (pdf)
  • Chris Bradley (University of Oxford) - openCMISS and FieldML/CellML (pdf)