Software development

Understanding protein synthesis via analysis of ribosome profiling data

Author: Mike Jackson
Posted: 8 Aug 2019 | 10:51

The molecular structure of a yeast ribosome, composed of 79 proteins

A multi-disciplinary team of biologists, bioinformaticians and research software engineers based at EPCC and The Wallace Lab at University of Edinburgh, The Shah Lab at Rutgers University, and The Lareau Lab at University of California, Berkeley, will enhance and extend a software suite called RiboViz to extract biological insight from "ribosome profiling" data and drive forward understanding of protein synthesis.

Taking the sting out of gout

Author: Amy Krause
Posted: 1 Jul 2019 | 10:48

 

 

 

 

Gout is estimated to affect 2.5% of the UK population, and is increasing globally in association with cardiovascular disease and obesity. EPCC has been working with Dr Philip Riches of the MRC Institute of Genetics and Molecular Medicine to develop a new app that could lead to improved treatment and better quality of life for patients.

Gout is a type of arthritis caused by excess uric acid in the blood. It is characterised by sudden attacks of intense pain that result in reduced quality of life, work absence and disability. The standard treatment for the condition involves close monitoring of blood urate levels and medication, but the high level of health professional support required to ensure a long term cure of gout is rarely delivered: fewer than half of eligible patients receive preventive treatment and fewer than half of those on treatment receive an adequate dose of medication.

Too much choice?

Author: Nick Brown
Posted: 17 Jun 2019 | 14:24

When is enough, enough? With so many parallel programming technologies, should we focus on consolidating them?

At the ISC conference in June I will moderate a panel discussion on whether it is time to focus on the consolidation and interoperability of existing parallel programming technologies, rather than the development of new ones.

Building research collaborations across Europe

Author: Catherine Inglis
Posted: 12 May 2019 | 14:31

The HPC-Europa3 project funds short collaborative “Transnational Access” research visits using HPC.

In just 17 months EPCC has supported 50 HPC-Europa visits from research groups in a total of 15 countries. We are already seeing great results from our visitors, including at least seven publications.

Applications for repeat or reciprocal visits – either between the same researchers, or different members of the same groups – are testimony to the strength of the ongoing collaborative links fostered by the programme. Two of our first HPC-Europa3 visitors have even returned to their former host research groups for longer visits.

Software Sustainability Institute's Collaborations Workshop 2019 (CW19)

Author: Mario Antonioletti
Posted: 19 Mar 2019 | 10:16

The Software Sustainability Institute's (SSI) Collaborations Workshop 2019 (CW19) will be held at the West Park Teaching Hub, Loughborough University, Loughborough from 1-3 April 2019. This year the workshop will be themed around topics based on interoperability, documentation, training, and sustainability. Keynote speakers will include Catherine Stihler, CEO of Open Knowledge International, and Franziska Heine (link points to a German article), Head of Software & Development at Wikimedia Deutschland. They will open the event on 1st April.

Proof-driven queries to preserve patient privacy

Author: Mike Jackson
Posted: 4 Mar 2019 | 09:42

StethoscopeIn our role as members of the Research Engineering Group of the Alan Turing Institute, Anna Roubickova and I worked with Efi Tsamoura and Benjamin Spencer (Department of Computer Science at the University of Oxford) on PDQ, a proof-driven query planner that has great potential within the realm of data science for medical research. 

The Julia programming language

Author: Magnus Morton
Posted: 22 Feb 2019 | 16:09

Julia logo

Peeved with Python? Revolted by R? SAS make you sad? The Julia Language may be for you. Recently reaching version 1.0, Julia claims to be more than just another data science language.

In this post I’ll give a tour of some of the more interesting features of Julia, and its implementation.

Rocket surgery for PickCells

Author: Mike Jackson
Posted: 14 Dec 2018 | 17:33

PickCells usability evaluation PickCells is image analysis software developed by the Centre for Regenerative Medicine (CRM) at The University of Edinburgh. PickCells allows biologists to explore multidimensional biological images of stem cell niches, organoids, and embryos. In late October, with the assistance of six researchers, we evaluated the usability of PickCells to help guide its future development.

To run our usability evaluation, we followed Steve Krug's highly-recommended and very readable book "Rocket Surgery Made Easy: The Do-It-Yourself Guide to Finding and Fixing Usability Problems". This book describes a practical way to carry out usability evaluations with minimal overhead.

Applications to Software Sustainability Institute Fellowship Programme 2019 are now open

Author: Guest blogger
Posted: 10 Dec 2018 | 10:59

By Raniere Silva, Community Officer at the Software Sustainability Institute.

Apply to the Software Sustainability Institute Fellowship Programme 2019.

The Software Sustainability Institute is pleased to announce applications to our Fellowship Programme 2019 are now open. Below we detail the application process and what to expect from us during the recruitment and post-recruitment stages.

Edinburgh Research Software Engineering (RSE) meeting at Edinburgh College of Art

Author: Giacomo Peru
Posted: 26 Nov 2018 | 18:07

The community of Edinburgh research software engineers (CERSE) held their second gathering on Wednesday 21st November in the Edinburgh College of Art (ECA) main building. 

The meeting was attended by around 50 participants, an interesting mix of researchers, software developers, systems admins and research support/management staff, from the University of Edinburgh and Heriot-Watt University. It is intended to keep these gatherings open to all Higher Education and research institutions of the Edinburgh area.

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