Software development

Exploring the integration of Subversion and Git with CVS

Author: Mike Jackson
Posted: 7 Apr 2014 | 07:33

A brain scan.Michael Chappell leads the Quantitative Biomedical Inference (QuBIc) research group within the Institute of Biomedical Engineering at the University of Oxford. Michael has developed a method of processing functional magnetic resonance image (MRI) data that can be used to recognise blood flow patterns in the brain. I have been helping Michael through one of The Software Sustainability Institute's consultancy projects, which he applied for through the Institute's open call. Part of our collaboration looked at issues around integrating Subversion or Git repositories with CVS.

Re-imagining the lab. Or, when science meets art

Author: Mike Jackson
Posted: 13 Mar 2014 | 15:07

LabBook being used with a tablet and stylusLabBook is a mobile app and online service that allows users to securely record and share their experiment notes. LabBook's developers - Mark Woodbridge, Geraint Barton and Derek Huntley of Imperial College London's Bioinformatics Support Service - asked The Software Sustainability Institute for consultancy as part of the Institute's open call.

I've been working with them to provide advice on the LabBook software, how it is developed, and how it can be moved towards an open source product.

When applications go exascale — the CRESTA project

Author: Guest blogger
Posted: 10 Feb 2014 | 09:22

Dr Jason Beech-Brandt, Manager Exascale Research, Europe at Cray writes about the CRESTA project, which is addressing the challenges of exascale computing.

Seymour Cray, the pioneer of supercomputing, famously asked if you would rather plough a field with two strong oxen or 1024 chickens.

Answering Questions

Author: Alistair Grant
Posted: 22 Jan 2014 | 09:23

On Monday 2 December, I took part in a panel on Software Engineering for the Professional Software Development course at the University of Glasgow's Computing Science department. Organised by Dr Tim Storer, a lecturer in Software Engineering, the panel was an opportunity for 3rd-year students of the computing science and software engineering programmes to quiz a varied group of software engineers.

R users can calculate Hamming distance faster

Author: Terry Sloan
Posted: 10 Jan 2014 | 14:09
 
EPCC and the Division of Pathway Medicine at the University of Edinburgh have released version 1.0.5 of the SPRINT R software package. This includes a new faster parallel implementation of the Hamming distance function.

Digging deeper into digital preservation

Author: Alistair Grant
Posted: 2 Sep 2013 | 19:20

A few months have gone by on the Pericles project (see my earlier post), more meetings have passed and more are coming up, but in between meetings, we do actually get some work done as well!

Preserving art, records and other items has been a challenge throughout history, not just how to store them but how to help future generations to understand them. Even in the short time digital art and records have been around, this problem has become increasingly apparent in modern technology. It is exacerbated by the rapid cycles that technology follows. Pericles is attempting to define and develop a framework or method to manage how digital data is stored in archives and how to keep the archives relevant and accessible. A small challenge it is not.

MPI: sending and receiving in multi-threaded MPI implementations

Author: Daniel Holmes
Posted: 5 Jul 2013 | 16:06

Have you ever wanted to send a message using MPI to a specific thread in a multi-threaded MPI process? With the current MPI Standard, there is no way to identify one thread from another. The whole MPI process has a single rank in each communicator.

CP2K-UK: Now recruiting!

Author: Iain Bethune
Posted: 20 Jun 2013 | 13:48

'CP2K-UK' is a new project starting shortly at EPCC, aiming to nurture the growth of a self-sustaining user and developer community around the CP2K materials science code here in the UK. I have been working on CP2K for nearly 5 years now thanks to a series of HECToR dCSE and PRACE projects, so it is great to get a chance to work on some of the more fundamental issues around usability and sustainability of the code, thanks to success in the EPSRC 'Software for the Future' call.

Making waves: TPLS code released as Open Source

Author: Iain Bethune
Posted: 10 Jun 2013 | 12:26

TPLS (Two-Phase Level Set) is a Computational Fluid Dynamics code developed by Dr Prash Valluri of the University of Edinburgh's School of Engineering and Dr Lennon Ó Náraigh of University College Dublin. It simulates the interface between two fluid phases, a phenomenon with a number of industrial applications including oil and gas hydrate transport, cleaning processes, distillation/absorption, and evaporative cooling of microelectronics.

Changing technology – thinking about digital preservation

Author: Alistair Grant
Posted: 7 May 2013 | 13:52

How do we deal with technology change? Ever thought about accessing the stuff you did twenty years ago? What’s that? You are having a hard time getting a floppy disk drive? Maybe the data format is unreadable or the media has been damaged? 8-inch, 5,25-inch, and 3,5-inch floppy disks: Public Domain 7 June 2009: George Chernilevsky

This is a problem that will continue to face us in many fields: how do you ensure that today’s data is still accessible in twenty or even fifty years' time? For a lot of areas, maybe we do not want to bother, it's the here and now that counts.

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