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Title:
Inter-compatibility of models and software systems
Organizers
Fred Howell
Robert Cannon
Institute of Adaptive and Neural Computation, Edinburgh
University
Format
Formal Discussion
Description
Much research in computational neuroscience is heavily
dependent on software development effort, and much
modeling work could usefully build on earlier work
undertaken with other software systems. There are
therefore two desirable levels of compatibility to be
achieved in neuroscience software:
- the ability to run the same model with different
software.
This would:
- reduce the need for re-implementing models in different
environments
- help in validating software by comparing results directly
with those from other implementations
- provide an implementation independent way of publishing
models (such that they can be run right away, compared
to simply reading a, frequently incomplete, description)
- prevent users being locked in to particular packages
and restricted to the facilities they provide
- the ability to use components of one software
system from within another system.
This would:
- reduce duplicate development effort
- improve software quality by letting developers work
within their expertise (numerics, graphical user
interfaces, databasing etc)
- allow the construction of more flexible models without
requiring one software package to cover all the desired
features.
Developments such as XML and the Grid
(www.gridforum.org)
provide technological frameworks for achieving these
goals, but there are no magic answers. The NeuroML project
provides a toolkit for using XML within independent
software packages, but does not claim to be a definitive
model description language. Indeed, it may be that the
easiest way to achieve point (1) above is not to
standardize model descriptions but to agree on a much
smaller set of standards for model implementations - ie,
to get (1) by first doing (2).
This workshop is aimed at model builders and software
builders who wish to discuss solutions to these
problems. Brief (20 minute) informal presentations are
invited on topics including, but not limited to:
- taxonomies and ontologies for model description
- moving models between simulation systems
- experience integrating modeling software
- technologies for data (model) sharing, eg XML, NeuroML
- integration efforts in related disciplines (see eg sbml.org)
- modeling software currently under development
The organizers will also present a brief introductory
overview of various technologies including java and XML to
explain some of the jargon and the hype that currently
surround them.
Participants wishing to make a presentation should contact Fred
Howell in advance, fwh@anc.ed.ac.uk
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