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Tommy Yu
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- From: Jonathan Cooper <jonathan.cooper AT cs.ox.ac.uk>
- To: cellml-discussion AT lists.cellml.org
- Subject: [cellml-discussion] Cardiac Electrophysiology Web Lab Workshop
- Date: Sun, 17 May 2015 21:01:52 +0100
- Organization: University of Oxford
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<!--filtered-->Dear
all,<br />
<br />
<!--filtered-->
<!--filtered--><!--filtered-->We
would like to invite you to attend our first workshop on the
“Cardiac Electrophysiology Web Lab” on 10-11th September 2015.
This new <!--filtered--><!--filtered--><!--filtered-->online
system<!--filtered--><!--filtered--><!--filtered-->
developed in the Computational Biology Group at Oxford supports
easy definition of experimental protocols, and allows any CellML
model to be tested under these protocols. This enables
comparison of the behaviours of cellular models under different
experimental protocols: both to characterise a model’s
behaviour, and comparing hypotheses by seeing how different
models react under the same protocol.<!--filtered--><!--filtered-->
<br />
<!--filtered--><!--filtered-->This
workshop will train attendees in how to make the most of the
facilities provided by the Web Lab (and the underlying Chaste
software) in order to practice open, reproducible science in
cardiac electrophysiology modelling. We aim to equip people with
the tools that are necessary to make not only their models, but
also their training and validation simulations well defined,
reproducible, and applicable to any model of the same system.
Sessions will include:<!--filtered--><!--filtered-->
<ul style="">
<!--filtered-->
<!--filtered--><!--filtered--></ul>How
to use the<!--filtered--><!--filtered--><!--filtered-->
<!--filtered--><!--filtered-->Web
Lab<!--filtered--><!--filtered--><!--filtered-->
for comparing simulated experiments<!--filtered--><!--filtered-->
<!--filtered-->
<!--filtered-->
<!--filtered--><!--filtered-->Uploading
your own models for analysis<!--filtered--><!--filtered-->
<!--filtered-->
<!--filtered-->
<!--filtered--><!--filtered-->Developing
your own protocol descriptions<!--filtered--><!--filtered-->
<!--filtered-->
<!--filtered-->
<!--filtered--><!--filtered-->How
to build on the underlying software directly<!--filtered--><!--filtered-->
<!--filtered-->
<!--filtered-->
<!--filtered--><!--filtered-->Provide
feedback to influence future development of these tools.<!--filtered--><!--filtered-->
<!--filtered-->
<!--filtered-->
<br />
<!--filtered--><!--filtered-->Logistics:<!--filtered--><!--filtered-->
<ul style="">
<!--filtered-->
<!--filtered--><!--filtered--></ul>Dates
& times: 10th & 11th September 2015, 9.30-5pm each
day<!--filtered--><!--filtered-->
<!--filtered-->
<!--filtered-->
<!--filtered--><!--filtered-->Location:
<!--filtered--><!--filtered--><!--filtered-->Department
of Computer Science<!--filtered--><!--filtered--><!--filtered-->,
University of Oxford, UK<!--filtered--><!--filtered-->
<!--filtered-->
<!--filtered-->
<!--filtered--><!--filtered-->Cost:
Thanks to the generous support of the <!--filtered--><!--filtered--><!--filtered-->2020
Science<!--filtered--><!--filtered--><!--filtered-->
project, registration for this workshop is <!--filtered--><!--filtered-->free<!--filtered--><!--filtered-->.
Lunches on both days and a conference dinner will be
provided. Partial support for travel and accommodation costs
is also possible.<!--filtered--><!--filtered-->
<!--filtered-->
<!--filtered-->
<!--filtered--><!--filtered-->Registration<!--filtered--><!--filtered-->:
please fill in the form at <!--filtered--><!--filtered--><!--filtered-->http://goo.gl/forms/hUU79BD8pd<!--filtered--><!--filtered--><!--filtered-->
<!--filtered-->
<!--filtered-->
<br />
<!--filtered--><!--filtered-->For
more information as it becomes available, see the workshop
website at <!--filtered--><!--filtered--><!--filtered-->https://chaste.cs.ox.ac.uk/trac/wiki/FunctionalCuration/Workshop2015<!--filtered--><!--filtered--><!--filtered-->.
We would also encourage you to forward this email to any of your
contacts who you think would be interested in attending.<!--filtered--><!--filtered-->
<br />
<!--filtered--><!--filtered-->Best
wishes,<!--filtered--><!--filtered-->
<!--filtered--><!--filtered-->Jonathan
Cooper and Gary Mirams<!--filtered--><!--filtered-->
<br />
<br />
<!--filtered--><!--filtered-->The
Web Lab Vision<!--filtered--><!--filtered-->
<!--filtered--><!--filtered-->Modellers
have adopted XML-based markup languages to describe mathematical
models over the past decade. This is great, as it means that
models can be defined unambiguously, and shared easily, in a
machine-readable format. We have been trying to do the same
thing with 'protocols' - to define what you have to do to
replicate/simulate an experiment, and analyse the results. We
can then curate models according to their functional behaviour
under a range of experimental scenarios. For the first time, we
can thus easily compare how different models react to the same
protocol, or compare how a model behaves under different
protocols. The Web Lab brings together models encoded using
CellML and virtual experiment protocols encoded in our own
language, using standardised tags to generate interfaces between
them, doing all the necessary units conversions, and running the
experiments: any protocol applied to any compatible model. The
stored results can then be viewed and compared.<!--filtered--><!--filtered-->
<br />
<!--filtered--><!--filtered-->The
key idea underpinning our work is that when mathematical and
computational models are being developed, a primary goal should
be the continuous comparison of those models against
experimental data. When computational models are being re-used
in new studies, it is similarly important to check that they
behave appropriately in the new situation to which you're
applying them. To achieve this goal, it's a prerequisite to be
able to replicate <!--filtered--><!--filtered-->in-silico<!--filtered--><!--filtered-->
precisely the same protocols used in an experiment of interest,
and this is what our protocol descriptions aim to do. As the Web
Lab evolves, we want to link directly to databases of
corresponding wet-lab experimental data, to allow comparison of
simulated and real experiments. This will allow us to provide
support for validating models, and begin to incorporate
parameter fitting and model identifiability.<!--filtered--><!--filtered-->
<br />
<!--filtered--><!--filtered--><!--filtered--><br />
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- [cellml-discussion] Cardiac Electrophysiology Web Lab Workshop, Jonathan Cooper, 05/18/2015
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