Software and research: the Institute's Blog

Code is Science at GCCBOSC

Latest version published on 12 September, 2018.

By Yo Yehudi, University of Cambridge. GCCBOSC this year was a combination of two open source bioinformatics conferences: GCC, the Galaxy Community Conference, and BOSC, the Bioinformatics Open Source Conference. Galaxy is a highly-successful bioinformatics workflow management tool, and BOSC is run by the Open Bioinformatics Foundation (OBF), an organisation dedicated to open-source biology and bioinformatics related software.

EuroPython 2018

Latest version published on 28 August, 2018.

By Raniere Silva, Software Sustainability Institute. EuroPython is the biggest conference dedicated to Python in Europe, with around 1200+ participants every year, run entirely by volunteers. It is also sister event to many national events around the continent, such as PyCon UK. This year, EuroPython was hosted in Edinburgh and, like in previous years, some of the talks were related with research software written in Python. We attended to learn how people are carrying out better research with Python.

Unexpected changes to storage of local variables when compiling Fortran with OpenMP

Latest version published on 23 August, 2018.

By Ryan Pepper and James C. Womack. During the Bath Numerical Debugging Workshop, we participated in a bug hunting session where people brought along real-world bugs which we attempted to tackle.

Software engineering in practice

Latest version published on 10 September, 2018.

By Becky Arnold, University of Sheffield. Jos Martin, senior engineering manager at MathWorks, gave a talk on software engineering in practice on the 27th of June at the University of Sheffield.

Software Deposit Guidance for Researchers

Latest version published on 9 August, 2018.

By Mike Jackson, Software Architect. The Software Sustainability Institute has published a set of guides about depositing research software into digital repositories. These guides cover the main aspects of software deposit.

Lessons from a workshop on “Debugging Numerical Software”

Latest version published on 8 August, 2018.

By Eike Mueller, University of Bath. If you are anything like me, you write code which contains bugs (in my case: lots of bugs). You probably also use code or tools written by others, which might contain even more bugs (e.g. in compilers, scripts, external numerical libraries etc.).

PaperStream: a software that collects data from multiple-answer questions documents

Latest version published on 2 August, 2018.

By Julio Vega, University of Manchester. As part of my PhD where we are researching if we can use smartphone data to monitor the progression of Parkinson’s Disease, we found out that we had to go “Back to Analogue” as a paper diary was the best tool for patients to self-report their symptoms.

Software Deposit and Preservation Workshop

Latest version published on 24 July, 2018.

By Mike Jackson, Software Architect. On the 11th July, the Software Sustainability Institute and Jisc ran a Software Deposit and Preservation Workshop at St. Anne’s College, Oxford. This workshop brought together 12 research data managers, digital repository vendors, publishers, policymakers and researchers.

TICTeC 2018 – An Introduction to the World of Civic Technologies

Latest version published on 24 July, 2018.

By Reka Solymosi, University of Manchester. In April 2018, I was given the opportunity to explore the world of Civic Tech, through participating in TICTec2018, a conference for practitioners, commentators, academics, and funders of civic technologies.

JavaCard: The execution environment you didn’t know you were using

Latest version published on 13 July, 2018.

By Vasilios Mavroudis and Petr Svenda. This is the story of the most popular execution environment, its shortcomings, and how open source and hacking saved the day.According to recent revelations, the MINIX operating system is embedded in the Management Engine of all Intel CPUs released after 2015. A side-effect of this is that MINIX became known as the most widespread operating system in the world almost overnight. However, in the last decade another tiny OS has silently pushed itself into even more devices around the world while remaining unknown to most: JavaCard.