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.

What’s in a protocol? Protocol Inputs Default values given Plots Imports from protocol libraries Post-processing Functional array-based language Outputs N-d arrays (with units) Model Has inputs and outputs (n-d arrays with units) Can be simulated / run Nested simulation loop(s) Outputs are n-dimensional arrays Model Interface definition Library Variables & functions

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. metadata#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

What will it enable in the future?

Acknowledgments Gary MiramsJonathan 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 Ask us if anything is unclear Please do record any feedback as you go