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Hi Don,

On 31/05/2004, at 3:14 PM, Donald Doherty, Ph.D. wrote:

> Hello,
>
> I've been trying to understand the goals of the CellML team for some
> time. Are they restricted to defining a set of XML vocabularies for the
> life sciences?

You are right, it is hard to figure out the goals of CellML from the
documentation available. Some of the publications in
<<http://www.cellml.org/public/about/publications.html>> should help
you out in that respect.

I'll split your question into two:
- we use XML where it makes sense to. Although CellML standards for
Cell Markup Language, we are restricted to defining simply XML
standards. Software tools, databases, and active integration with the
wider biological community are key aspects of work we are doing.
- while it appears we focus on life sciences, which makes sense in our
context, the modelling language and tools are really applicable to a
broad range of mathematical modelling problems. It is straight forward
to keep a clear separation of biological information from the
mathematical, but still process them as an integrated unit.

> Is there a large set of open source software planned? Or
> is the team working for largely proprietary reasons (even if for an
> academic institution)?


We are committed to open source software development. We are starting
a more formal attempt at making an open source development environment
for CellML. Initial documentation can be found here
<<http://n2.bioeng5.bioeng.auckland.ac.nz/development>>. This
documentation is pretty raw and embarrassingly incomplete. We are
working on it, so it is changing quite rapidly at the moment. Some
items such as timelines of material we are about to release, or nearly
ready to release, are also incomplete. I'd encourage you to join the
mailing list associated with that. We have a sourceforge area,
http://cellml.soureforge.net/ which will form the hub for releases of
software. In the next week or so I'll be emailing a list of people
that have wanted to collaborate on tool development. Hopefully we will
get them joining the list and some willing to be part of the core
working group. If you have questions about anything you read there,
please send them to the cellml-tools list and we can continue the
thread there.


>
> Specifically, it looks like a huge part of the Auckland team's effort
> is
> focused on CMISS. Is CMISS an open source effort?

The CellML project is important to the CMISS project, but not governed
by it. CMISS is not open source. There is debate about that
internally. If you have questions about this you would be best to
email the CMISS team.

Hope to hear more from you.

cheers
Matt



>
> Thank you!
> Don
>
> Donald Doherty, Ph.D.
> Brainstage Research, Inc.
> www.brainstage.com
> donald.doherty AT brainstage.com
> 412-478-4552
>
> -----Original Message-----
> From:
> cellml-discussion-bounces AT cellml.org
> [mailto:cellml-discussion-bounces AT cellml.org]
> On Behalf Of Autumn
> Cuellar
> Sent: Tuesday, May 18, 2004 8:02 PM
> To: announce; discussion
> Subject: [cellml-discussion] Electrophysiological CellML model
> simulationenvironment - CESE 1.3
>
> Hello,
>
> A new version (1.3) of Cell Electrophysiology Simulation Environment
> (CESE) has been released that offers CellML support. CESE is available
> from SourceForge:
>
> http://cese.sourceforge.net/
>
> And the site has pretty good documentation of the status of the
> project.
>
> Best wishes,
> Autumn
> --
> Autumn A. Cuellar
> Bioengineering Institute
> The University of Auckland
> New Zealand
>
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion AT cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion
>
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion AT cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion

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• [cellml-discussion] Electrophysiological CellML model simulation environment - CESE 1.3, Autumn Cuellar, 05/19/2004
  • [cellml-discussion] Should developers outside the Auckland team contribute?, Donald Doherty, Ph.D., 05/31/2004
    • [cellml-discussion] Should developers outside the Auckland team contribute?, Matt Halstead, 05/31/2004
      • [cellml-discussion] Should developers outside the Auckland teamcontribute?, Donald Doherty, Ph.D., 05/31/2004

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