Software development

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.

Broadcasting your shell output

Author: Mario Antonioletti
Posted: 18 Oct 2018 | 12:47

During a Software Carpentry course you, as an instructor, stand in front of a class typing your lesson content, eg bash or git, and the students type what you type into their own shell.

Depending on the layout of the room, you need to make the font on your terminal large enough for all students to see it, which can be somewhat disorientating as an instructor. Moreover if the layout of the room is not ideal, eg some students are facing away from the screen, they will have to constantly turn to see the screen, which can be a pain for them. But I recently found a Python app that changes all that.

Analysing humanities data using Cray Urika-GX

Author: Rosa Filgueira
Posted: 11 Oct 2018 | 14:52

During the last six months, in our role as members of the Research Engineering Group of the Alan Turing Institute, we have been working with Melissa Terras, University of Edinburgh's College of Arts, Humanities and Social Sciences (CAHSS), and Raquel Alegre, Research IT Services, University College London (UCL), to explore text analysis of humanities data. This work was funded by Scottish Enterprise as part of the Alan Turing Institute-Scottish Enterprise Data Engineering Programme.

Inaugural Edinburgh Research Software Engineering (RSE) Meeting

Author: Mario Antonioletti
Posted: 30 Sep 2018 | 20:28

Edinburgh just held its inaugural Research Software Engineer (RSE) meeting at the Bayes Centre (also home to EPCC). It was attended by about 50 people from the Edinburgh area. If you don't know what a Research Software Engineer is, I urge you to look at Andy's slides for context and background.

PickCells and exploratory image analysis in cell biology

Author: Mike Jackson
Posted: 11 Sep 2018 | 16:09

Cells being analysed within PickCells

PickCells is an image analysis platform developed by the Centre for Regenerative Medicine (CRM) at The University of Edinburgh. It combines generic image analysis algorithms, visualisation modules and data mining functionality within a stand-alone Java application.

RSE18 conference, Birmingham

Author: Fiona Reid
Posted: 6 Sep 2018 | 14:47

I recently attended the Third Research Software Engineers (RSE) conference in Birmingham, UK. RSE conferences bring together people who work in an RSE-type roll from across the UK and world.

For anyone who doesn’t know, an RSE is typically someone who has expertise in both coding and research but is not necessarily a pure computer programmer or pure researcher. Often RSEs can be the only such person in their department and thus the conference gives them a chance meet other people doing similar roles to share their experiences and help them feel part of a much larger community.

Collaborative environment for sales prospect generation

Author: Alistair Grant
Posted: 23 Aug 2018 | 07:41

 

deepminer logoSo, you read the title and thought, ‘What?'

Well maybe it is something you could be interested in using. Perhaps the technology or concepts will interest you. Or maybe you will see how EPCC can help bring your ideas into the world.

Let’s start from the beginning – there is this company called DeepMiner which was set up in August 2017 and they had this idea of using all this new-fangled data science, modelling and machine learning to gather huge amounts of disparate data on company news, business deals, research grants and many other things to help businesses to try and identify new business prospects – hence the 'sales prospect' in the title.

Software deposit guidance for researchers

Author: Mike Jackson
Posted: 8 Aug 2018 | 10:55

Safe deposit boxes

The Software Sustainability Institute has published a set of guides to depositing research software into digital repositories. The guides, development of which was funded by Jisc, are intended for researchers, principal investigators and research leaders, and research data and digital repository managers.

Research software is an integral part of the modern research ecosystem. Taken together, research software – alongside data, facilities, equipment, and an overarching research question – can be viewed as a research activity or experiment, worthy to be published. Conversely, a publication can be considered as a narrative that describes how the research objects are used together to reply to the research question.

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