Chaste Workshop Welcome and Introduction David Gavaghan

Chaste History Commenced as a 4-week taught course in Software Engineering in May 2005 May 2005-September 2007 part-time activity, 1 day/week involving a group of around 6-10 PhD students and post-docs September 2007-date EPSRC-funding for two full time post-docs to join the team Focus remains primarily on cardiac electrophysiology, soft tissue modelling (including cardiac electro-mechanics) and cancer modelling

Development approach Focus from the start on software engineering issues –Object-oriented –C++ –Built on PETSc Agile approach –Test-driven (test first) –Pair programming –Short iterations –Frequent refactoring –Team ownership Code base now contains 119,974 lines of code and 69,737 lines of test

Current capability Cardiac –Monodomain and bidomain for a wide range of practical problems –Efficient parallel implementation –Open source release available under GNU LGPL license Soft Tissue Mechanaics –Non-linear (finite deformation) elasticity –Discrete cell-based models Cancer –Focus on colorectal cancer and tumour spheroids –Off-lattice cell-based simulations (cell-centre and (soon) cell-vertex –Variety of cell models and field equations

Performance of cardiac code Test Case: sequential simulation of 100ms of bidomain using the UCSD heart mesh (propagation) –September 2007 (start of EPSRC grant) 1383 minutes –Thursday of last week 117 minutes –Factor of ~12 Parallel performance –Example in next graph is parallel monodomain simulation of the UCSD heart mesh (propagation)

Parallel scalability

Workshop overview : Day 1 10:30-11:30 Session 1 - Introduction to Chaste Functionality:Session 1 –Project Overview: David Gavaghan –Past, present and future: Joe Pitt-Francis –Science enabled: Blanca Rodriguez 11:45-12:30 Session 2 - Basic Installation: Session 2 –Joe Pitt-Francis: how to download a binary from the website 14:00-17:30 Session 3a and 3b - Use itSession 3a and 3b –Miguel Bernabeu and Alberto Corrias –This first practical will cover examples of tissue simulations with Chaste: 1D cable simulation with LR cells. 2D tissue sheet. S1-S2 stimulation protocol for re-entry generation. 3D slab. Whole heart simulation

Workshop overview : Day 2 09:00-11:00 Session 4 – Examples of Cardiac Research undertaken using ChasteSession 4 –Rafel Bordas: Purkinje system. –Pras Pathmanathan: Electro-mechanics. –Jonathan Cooper: Automatic integration of CellML models in Chaste. –Miguel Bernabeu: HPC simulations with highly detailed cardiac models. –James Southern (Fujitsu Laboratories of Europe): HPC and Chaste - Towards real-time simulation Chair: Blanca Rodriguez Some of these examples will form the basis of the practicals in Sessions 5 and 6.

Workshop overview : Day 2 11:30-13:00 Session 5 - Case study 1 (led by Alberto Corrias and Gary Mirams)Session 5 –Practical demonstrating a Purkinje fibre stimulating a 3D tissue slab. Functionality covered: Simulating the activity of different cell types coupled within a 3D geometry. Implementation of spatially heterogeneous tissue conductivities. Stimulation of a Purkinje fibre to excite the ventricular tissue coupled to the fibre. 14:30-17:00 Session 6 - Case study 2 Using CellML (led by Jonathan Cooper and Alberto Corrias)Session 6 –Practical focusing on the integration of CellML and Chaste, covering the use of a tool for automatic conversion of CellML models into Chaste-compatible C++ code: How to generate a C++ implementation of a given CellML model. How to write a C++ main function that uses it and change (at least) one of the parameters in the cell model. Running two Chaste 2D tissue simulations that incorporating this parameter change into the cell model.

Workshop overview : Day 3 3 Sessions will run at different times (depending on individual requirements): – 9:00-12:30. Session D1 and D2. –14:00-17:00. Session D2 and D3. Session D1 - Developer installationSession D1 –led by Joe Pitt-Francis and Jonathan Cooper Session D2 - TutorialsSession D2 –led by Pras Pathmanathan and Rafel Bordas Session D3 - Adding functionalitySession D3 –led by Miguel Bernabeu, Matt Gibb and Martin Bishop