Life sciences

The culmination of two years’ work by the Pistoia Alliance project team, the UXLS Toolkit provides material on UX education, methods and use cases compiled especially for life scientists. It is pitched at busy UX specialists, in silico analysts and bench scientists in an easily, accessible self-help style who all need better software. UX for Life Sciences Toolkit was created to enable businesses to adopt UX principles and methods as they develop scientific software.

UX is a powerful tool for supporting the creation of effective and usable interfaces. Whilst UX is relatively widespread, the full potential of UX is still to be realised in the life sciences. The goal of this project is to empower life science professionals to get the most from these UX resources. The unique selling point of the UXLS toolkit is its focus on issues faced in developing digital products specifically for R&D in the life science and healthcare environments. More generally, it is a useful resource about the often forgotten area of UX, and the toolkit’s core ideas should be transferable to any research area. This new toolkit might be of particular interest to the RSE community who develop software products for a range of research areas.

Additionally, the Pistoia Alliance UXLS Project Team will be holding its inaugural USA conference at Novartis Institute for Biomedical Research in Cambridge, MA, on Tuesday 15th May 2018.

life-sciences-fair.pngBy Justin Clark-Casey, Research Software Engineer, Department of Genetics, University of Cambridge.

InterMine is an open-source life sciences data integration platform created at the University of Cambridge in the UK. It takes biological data from many sources and combines it into a unified whole, adding visualisations and search facilities that aim to provide insights for scientists and engineers that can accelerate research and the growth of the bioeconomy. Over the next three years, through a grant from the UK Government’s BBSRC funding agency, the InterMine team is going to be making sure that the data it makes available is as findable, accessible, interoperable and reusable—”FAIR”, for short—as possible. Keep reading to find out why we believe that making the world of data a “FAIRer” place is so important.

The Oxford Dictionaries define data as the “facts and statistics collected together for reference or analysis.”. We’re gathering ever more of it every year, and it’s no wonder that The Economist, for one, calls it “a driver of growth and change”, creating “new infrastructure, new businesses, new monopolies, new politics…

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By Alexander Hay, the Institute’s Policy & Communications Consultant, talking with Andreas Hegar, CGAT.

This article is part of our series: Breaking Software Barriers, in which Alexander Hay investigates how our Research Software Group has helped projects improve their research software. If you would like help with your software, let us know.

Life Sciences often suffer from a lack of programming skills. This isn’t always a problem – you don’t need to know how to code in order to gauge the diurnal eating habits of squirrels, for example – but it does become an issue when you need to work with large datasets.

This is a growing problem. Next Generation sequencing techniques produce vastly more data than ever before, and more people are needed to properly handle this and analyse it. Many life scientists do not need these skills, or at least, have not needed them until recently. The most sensible solution to this, then, is to train biologists these skills.

Enter CGAT

One solution to this problem is Computational Genomics: Analysis and Training, or CGAT, based at the MRC Functional Genomics Unit at the University of Oxford. This is run by a core staff of five, which includes Technical Director Dr Andreas Hegar, and was founded as a…

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By Derek Groen, Research Associate at University College London.

This September, Joanna Lewis and I organised a Paper Hackathon event in Flore, Northamptonshire, with support from both the Software Sustainability Institute and 2020 Science.

Our highly ambitious goal was to write a scientific draft paper over the course of two and a half days within a highly informal setting. Did we manage to accomplish that? In many of the projects we did!

The projects

In the end we ended up accepting five proposed Hackathon projects (see the Appendix for their original descriptions) and rejecting two projects. Two weeks before the event, we already distributed the 21 participants among the five project teams, which were:

  • Project #1 - A software reproducibility investigation. Led by Joanna Lewis, proposed by Jonathan Cooper.
  • Project #2 - A comparison of code development approaches and techniques in academia. Led by James Osborne and Derek Groen, proposed by James Osborne.
  • Project #3 - A study of animal/cell dispersal. Led and proposed by Maria Bruna.
  • Project #4 - A protocol paper on Bayesian inference of animal receptor models. Led and proposed by Ben Calderhead and Zhuoyi Song.
  • Project #5 – A lattice-Boltzmann solver written in JULIA. Led by Mayeul D…
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The University of Oxford's Department of Computer Science has announced a new vacancy for a programmer to work on a major life sciences project.

The successful applicant will work on the Cancer, Heart and Soft Tissue Environment, or Chaste, a general purpose package aimed at solving complex problems in biology and physiology research.

Their duties will include finding the best way to help external users both install the software and provide feedback more easily.

Candidates should have experience in cross-platform C++ programming and build frameworks, as well as Git version control, continuous integration environments, and both Windows development environments and tools. They will also be expected to work effectively both on their own and with other colleagues as their duties require.

The post is fixed term and for nine months, though applicants who wish to work on a part-time and flexible basis are also welcome to apply. The salary for the position will be at Grade 7, or between £30,434 and £37,394 p.a., and with a discretionary range of up to £40,847 p.a.

For further details and to apply for the position, please visit the main University of Oxford recruitment page. Applicants are also advised that they will undergo pre-employment screening as standard and that the deadline for applications is at 12.…

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A new collection of visualisation tools for representing biological information is now available thanks to TGAC, EMBL-EBI and F1000Research.

TGAC’s BioJS collection, published today by the journal F1000Research, comprises 14 open-access articles detailing the functionality, design, implementation and potential applications for a suite of open-source, JavaScript software components contributed by developers all over the world. The collection marks a significant step towards improving the way scientists can visualise biological data.

Data visualisations help researchers generate hypotheses and translate them into knowledge. Now, for the first time, developers can freely access a central software library for sharing standardised, community-approved JavaScript tools for visualising biological information. BioJS, an open-source, community-based project, has a modular, structured design that is ideal for scientists working in data-intensive research. The BioJS community, initiated at EMBL-EBI and coordinated by TGAC, has enabled the creation of 39 different software components in a very short time. Its new collection, like the community itself, provides a valuable resource for disseminating knowledge swiftly.

Manuel Corpas, Guest Editor of the F1000Research BioJS collection, and Project Leader for Plant and Animal Genomes at TGAC, said: “…

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