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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: – Project Overview: David Gavaghan – Past, present and future: Joe Pitt-Francis – Science enabled: Blanca Rodriguez • 11:45-12:30 Session 2 - Basic Installation: – Joe Pitt-Francis: how to download a binary from the website • 14:00-17:30 Session 3a and 3b - Use it – 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 Chaste – – – – – 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) – 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) – 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 installation – led by Joe Pitt-Francis and Jonathan Cooper • Session D2 - Tutorials – led by Pras Pathmanathan and Rafel Bordas • Session D3 - Adding functionality – led by Miguel Bernabeu, Matt Gibb and Martin Bishop