Research Software Engineer Position (C++ and HPC) at University of Nottingham

[mirams]

Chaste – Cancer, Heart and Soft Tissue Environment is a C++ library for computational cell biology and physiology problems including cardiac simulations, lung airway simulations and individual-cell based modelling.

I’m pleased to say that a BBSRC grant led by Alex Fletcher in Sheffield, Dave Gavaghan in Oxford and me in Nottingham was awarded recently to support Chaste development as a resource for biological modelling. It funds a research software engineer (RSE) half-time in each institution – click to find out more about the RSE role if you aren’t familiar with it. Because it’s a cross-institution grant there will be a lot of teamwork involved.

In Nottingham, we have teamed up with the Digital Research Service, which houses a lot of Nottingham’s RSEs to offer a full time post for 30 months, by combining with a role to support researchers in getting their codes ready to take advantage of the UK Midlands (Tier 2) supercomputer called Sulis.

Chaste is a big and mature piece of software in scientific research terms, development began in 2005 and it has lasted so well because rigorous software engineering was applied from the start – including version control, unit testing, memory testing, etc. We describe that all in detail in a 2013 PLoS CB paper if you’d like more of a flavour of how Chaste has been developed, and what Chaste does.

The workplan for the Chaste grant includes:

• New features in the individual-cell based models (3D versions of vertex models, subcellular element and immersed boundary models – so Chaste will be able to do 3D versions of many different modelling approaches).
• Modernising the C++98 codebase to use C++17 and optimisations/improvements that allows.
• Taking advantage of GPGPUs via FLAME GPU.
• Create python bindings for the C++ simulator.
• SBML import for cell cycle/signalling pathway models (analagous to the CellML import we already have for cardiac models).
• Interfacing with inference software in R, Python, etc.
• Lowering barriers to entry with Docker containers, Jupyter notebooks and workshop material.
• Supporting researchers in using Chaste for scientific studies.

  At Nottingham we’ll focus on SBML import and interfacing with other software, but will get stuck in to all the other tasks as well.

Here’s a link to the full ADVERT AND LINKS TO APPLY, deadline is 14th Feb. I am happy to take informal questions/enquiries on the Chaste side of the role at gary.mirams@nottingham.ac.uk, and Maurice Hendrix (Maurice.Hendrix@nottingham.ac.uk) is another RSE who will be involved in Nottingham who can answer questions on both sides of the role and working in the Digital Research Service.

 

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