Functional Curation with the Cardiac Electrophysiology Web Lab

Gary Mirams

Computational Biology, University of Oxford

CellML Workshop, 14th April 2015

Outline

• Motivation

• What does it enable now?

• Demo

• What will it enable in the future?

• Where are we going?

Cardiac Web Lab1.

Gary’s Vision of the Future!

• Biological knowledge is represented as a quantitative mathematical model

• Experimentalists perform the experiments necessary to select, fit and test the model

• (we aren’t a million miles off this in ion channel modelling)

• When something new is discovered they know what protocols to perform, whilst varying the ‘new thing’.

• It should be a science to make a new model, not an art. And it should be fast!

• We should pre-define how well it has to perform, and in what validation experiments, for acceptance (as per σ standards in Physics)

• See my story at:http://mirams.wordpress.com/2014/04/02/a-vision-of-the-future/

Cardiac Web Lab1.

Motivation

Cardiac Web Lab1.

What does it enable now?

Cardiac Web Lab1.

Functional Curation Protocol Language

Cardiac Web Lab1.

• Based on proposed extensions to SED-ML (will accept SED-ML protocols)

• Has a text-like simplified view (as per openCOR)

• You define the interface to the model (e.g. Voltage in, sodium current out) and the interface is built dynamically (as per SemGen?)

• You can inherit bits of protocol from other libraries (like CellML 1.1 does for models), for example an action potential duration calculation

• You can perform nested simulations – even call whole other protocols in loops

• Post-processing on N-dimensional arrays

• Plotting with some simple options

Some of the nice features

Cardiac Web Lab1.

Units conversions are all handled automatically

Specify inputs and outputs – simulator works out which equations it needs for that simulation

Replace components – for example encode your own stimulus protocol, or replace an entire current with a certain formulation

Includes all the postprocessing and plotting instructions

Nest protocols within other protocols for parameter sweeps etc.

Makes a COMBINE archive for each model/protocol combo.

Demo

Cardiac Web Lab1.

https://chaste.cs.ox.ac.uk/FunctionalCuration

https://chaste.cs.ox.ac.uk/q/2014/fc/s1s2

What will it enable in the future?

Cardiac Web Lab1.

Where are we going with it?

Cardiac Web Lab1.

Further improvements to ease of use:• Especially for writing new protocols• Nicer debugging/error handling in protocols• Better documentation• More flexibility in the language

Cloud based rather than on an Oxford server

More structure in ontology• to allow e.g. “clamp all cytoplasmic concentrations”, “plot the sum of

the membrane potassium currents”

Allow exploratory investigation of data? (plot against experimental data)

MICEE – Minimum Information about a Cardiac Electrophysiology Experiment – the description of the wet lab experiment should include enough detail to also provide the machine-readable web lab protocol.

Explicit link to experimental data — parameter fitting

Things for discussion here

Cardiac Web Lab1.

Adding our metadata tags to the Physiome Model Repository in some form

Want to remove our own copies of CellML files in Chaste and Web Lab, and get to one reference version.

Is there a nice easy web service or something to i. list all modelsii. get a model (+ metadata)

In other programs or websites?

Use some of this to enrich electrophysiology model curation in PMR?

Anything you’d like me to report back on using/accessing real data?

Acknowledgements

• Jonathan Cooper

• Martin Scharm

• Aidan Daly

• Erich Kerekes

Cardiac Web Lab1.

Advance notice of a Workshop – Oxford, 10-11 Sept 2015https://chaste.cs.ox.ac.uk/trac/wiki/FunctionalCuration/Workshop2015

Covers all aspects of using the Web Lab, especially uploading your own models & protocols, and using the underlying software directly. An opportunity to steer future developments and get involved. Some travel bursaries will be available.

• Dagmar Waltemath

• Jon Olav Vik

• Steven Niederer

• Alan Garny