Cardiac electrophysiology web lab - Chaste

Cardiac electrophysiology web lab - Chaste

CARDIAC ELECTROPHYSIOLOGY WEB LAB Introduction and overview Gary Mirams and Jonathan Cooper Computational Biology Group, Department of Computer Science A vision of the future Knowledge about mechanisms is captured in quantitative models Best experiments to do are therefore

the ones that best [select and] parameterise the model Provide these to experimentalists Automate model development Deploy in the Virtual Physiological Human!

Motivation What does the Web Lab enable? Key features summary Consistent application of a protocol to any model Interface described at the level of biophysical concepts Units conversions are all handled automatically Specify model inputs and outputs Simulator works out which equations it needs for that simulation

Replace components For example encode your own stimulus protocol, or apply voltage clamps Includes all the post-processing and plotting instructions Ability to do complex parameter sweeps, analysis, etc. Whats in a protocol? Protocol Inputs Default values given

Library Variables & functions Imports from protocol libraries Nested simulation loop(s)

Model Model Interface definition Can be simulated / run Outputs are n-dimensional arrays

Post-processing Functional array-based language Outputs N-d arrays (with units) Has inputs and outputs (n-d arrays with units) Plots

Interfacing using ontologies Models use different names for variables e.g. V, Vm, voltage, membrane_V, Em An ontology gives unique labels to concepts Can also describe relationships between them Model variables can be annotated with these labels e.g. https://chaste.comlab.ox.ac.uk/cellml/ns/oxfordmetadata#membrane_voltage Protocols also refer to these labels

Models and protocols need to agree on the labels to use A single variable can have many labels Demo https://chaste.cs.ox.ac.uk/FunctionalCuration What will it enable in the future? Acknowledgments Gary Mirams

Jonathan Cooper Additional development work by: Martin Scharm Aidan Daly Erich Kerekes Ideas and inspiration: Dagmar Waltemath Jon Olav Vik Steven Niederer Alan Garny

David Gavaghan Denis & Penny Noble Over to you! Practical session tasks are at https://goo.gl/jl62gh Ask us if anything is unclear Please do record any feedback as you go

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