Software and research: the Institute's Blog

Latest version published on 10 May, 2018.

413592672_0b437c7519_z.jpgBy Anna Krystalli, University of Sheffield, and Toby Hodges, EMBL Bio-IT

01: Background

So many of us have been fired up by the UK Research Software Engineer (RSE) initiative and it's spread throughout further European Countries. The spark for this particular meeting started at the Second RSE conference held in 2017.

For me, the initiatives described by Toby Hodges at European Molecular Biology Laboratory (EMBL) at Heidelberg and Tobias Schlauch at the German Aerospace Center (DLR) had been two of my favourite talks and motivated me to find out more. I kept in touch with Toby and we informally swapped notes over online meetings. In the meantime Toby and Tobias had already been synthesising some of their experiences, published in this post at the Software Sustainability Institute's website. I was also excited to see the results of the German RSE survey presented by …

Continue Reading

Latest version published on 2 May, 2018.

518462367_515a386c64_z.jpgBy Anton Shterenlikht, Bristol University

With over 1100 members, the Computational Physics Group (CPG) is one of the largest IOP groups. The interests of CPG members are extremely broad, from computer algebra and numerical methods to large scale calculations in hydrodynamics, astrophysics, plasma physics, meteorology and geophysics; from HPC tools and parallel visualisation to large scale quantum mechanical simulations in nuclear, atomic, molecular and condensed matter physics; from theoretical calculations to experimental data analysis, image processing, AI, machine learning and "big data". Advances in microelectronics, numerical analysis and computer science all impact on computational physics, and it is important that practitioners of the subject are aware of developments in these fields.

CPG membership is very diverse and represents industry, academia and government organisations. The only unifying topic is the use of numerical tools to further physics research. The Group arranges specialised meetings on topics such as condensed matter simulations, applications of parallel computing, algebraic computing, image processing and computers in physics teaching, often in collaborations with other groups or organisations external to IOP. CPG has representation in the European Physics Society allowing international co-ordination.

CPG produces a…

Continue Reading

Latest version published on 1 May, 2018.

mugitmerge_0.pngBy Matthew Upson, Freelance Data Scientist.

On 8th March I was lucky enough to go to the annual Git conference: 'Git Merge', held this year in Barcelona. With it being just 30 minutes from home, it was not something I could miss, especially after being kindly offered a ticket by Raniere from the Software Sustainability Institute, who could not make it.

First of all it is worth saying congratulations (and thank you) to all the organisers and sponsors of Git Merge from: GitHub, GitLab, Bitbucket, Microsoft, and Sticker Mule. It was a slick and well organised event that went without hitch, served excellent food, and took place in the impressive 16th Century Convent of the Angels at Barcelona's Museum of Contemporary Art in the centre of the city.

One of the interesting things about going to a conference about all things Git is that there is a huge range of people who attend. To many (perhaps most) software developers, version control is an essential part of their daily work, so the range of people who might attend is very wide. Aside from software developers who use and are interested in Git, there were two other distinct…

Continue Reading

Latest version published on 1 May, 2018.

reka1.pngBy Reka Solymosi, University of Manchester.

I have been co-organiser of the University of Manchester's R user group for about a year now. I started when I moved to Manchester, because I’ve always found that software user groups are a sure way to meet people with the same interests and motivations as myself, outside of my discipline. Having started work at the School of Law, I found that there were not many people as excited about open data, and data analysis as myself, and decided to reach out.

For the first year, we followed a steady format for the R user group meetings where we met monthly to listen to presentations given by volunteers about their work. This received generally positive feedback (and was in line with previous user group format) but often ended up with myself or my co-organiser Heather Robinson presenting as we struggled to motivate volunteers. After a year we took a poll, and while people seemed to like the format, there were some concerns raised about it being passive, and not engaging more novice users. An approach of organising a collaborative hackathon was suggested.


As we were considering possible topics for the hackathon that would engage people from a wide range of disciplines, we came across the…

Continue Reading

Latest version published on 13 April, 2018.

8572856136_f746c2dfa3_o.jpgBy Cyril Pernet, University of Edinburgh.

This blog post was first published at

Feedback from reproducible science workshops

Only a minority of scientists think there is no 'reproducibility crisis' (Nature 533, 452–454), yet many are not engaging in reproducible practices. Results from a recent survey among psychology researchers suggest that discussion and education about the utility and feasibility of practices like data sharing are needed if we want the community to adopt those standards. In short, people don't know those practices and don't want to journey there.

One of the things I did during my Software Sustainability Institute Fellowship, was to run a series of small group workshops for post-graduate students and principal investigators, on data sharing, code sharing, and good practices around code. This took place the last of September 2018 in Oxford the 25th, Birmingham the 27th and Glasgow the 29th, and in…

Continue Reading