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Stefanos Petsios wrote:
> Hi Andrew,
>
> I am a computer science phd student from greece,
> when I started my phd we focused in some application in Cellular
> modeling which could lead to a phd thesis in Computer science.
>
> after a lot of work between me, my professor and a biologist I am a little
> bit stuck :(
>
> all my research is around what can be done in order to solce some
> multi-dimensional cellml problems. I did made a programm that was able
> to solve ODEs and multidimensional biological models.
>
> I checked your background and I saw you work on similar issues!
>
> Please if you got some time tell me if you are interested to involve
> me in some of your tools throgh distance.
>
Hi Stefanos,

I am indeed involved in the development of CellML modelling tools. At
present our tools are focused on ODE models (which are most commonly
with respect to time), although other people at the Auckland
Bioengineering Institute are working on tools associated with FieldML,
to describe fields (e.g. over space).

The CellML tool projects which we started in Auckland are Free / Open
Source projects, and now have people (such as Alan Garny from Oxford)
from outside of Auckland involved in the development. We welcome
contributions from anyone.

The main projects you may be interested in are:
* The CellML API implementation, which provides programmatic access to
CellML models, and has extension models for a number of common tasks for
working with CellML models, such as translating to procedural code,
running simulations, efficiently working with units and components,
perform validations and so on.
* The Physiome CellML Environment (PCEnv), which is a graphical user
interface for editing CellML models, running simulations, plotting
results, and a range of other similar tasks. It uses the Mozilla framework.

You will find the following resources useful for working on these projects:
The source code repository (using the Subversion revision control
system).
The base of the repository is at
https://svn.physiomeproject.org/svn/physiome/
To check out the latest PCEnv source code:
svn co https://svn.physiomeproject.org/svn/physiome/pce/trunk
pcenv
To check out the latest CellML API implementation code:
svn co
https://svn.physiomeproject.org/svn/physiome/CellML_DOM_API/trunk
CellML_DOM_API
You can view source code changes on the web through the Trac interface:
http://trac.bioeng.auckland.ac.nz/projects/physiome
The tracker (for bugs, feature proposals, questions, and so on):
https://tracker.physiomeproject.org/ . Many technical
discussions on particular features take place here.
The mailing lists.
http://www.cellml.org/mailman/listinfo
All mailing lists have public archives and anyone who wants
to join can do so.
automated-notifications: Automated Subversion commit
messages and regression / unit test failures get
sent there.
cellml-discussion: The main list for discussing CellML.
cellml-tools-developers: The list for technical or general
discussions about CellML tools. This is a good place to ask questions
about tools and their development.
team: A list about managing and developing the CellML
community and resources for supporting the community. Anyone can join or
view the archives, although the list is moderated for new members.

Best regards,
Andrew

> Best Regards
>
> stefanos petsios
>
>

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• [cellml-dev] Cellml distributed computations etc, Andrew Miller, 08/25/2008

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