Software and research: the Institute's Blog

Enabling analysis of sensitive data

By Paul Graham, EPCC and Software Sustainability Institute.

We've been working with Professor Paul Burton and Dr Becca Wilson of the School of Social and Community Medicine, University of Bristol and their software DataSHIELD (Data Aggregation Through Anonymous Summary-statistics from Harmonized Individual levEL Databases). This is a suite of software that enables remote and non-disclosive analysis of sensitive research data. Data providers can use it to make their datasets available for use in analysis without disclosing individual level data itself, and researchers can thus gain access to the data without risk of disclosing participants. DataSHIELD is used principally in the biomedical field, but the technology used has universal application wherever sensitive individual level data needs to be protected, but also usefully analysed.

Drishti Workshop at The University of Texas High-Resolution X-ray Computed Tomography Facility (UTCT)

By Farah Ahmed, Institute Fellow and CT Manager at the Natural History Museum, London

University of Texas is a huge institute, with approximately 50,000 students.  The Computed Tomography laboratories (CT lab) are one of the oldest and most established facilities in the world. They are well known for leading in sharing 3D data for visualisation, freely and openly. They also lead in various fields of geosciences related research. One aspect they recognised was the need to house free and open source software, to enable the researchers to carry out data analysis in their own environments. I led a workshop on the 28th and 29th September 2015, training staff and postgraduate students in the visualisation tool Drishti.

Software Carpentry for NHS Clinical Bioinformatics course

By Niall Beard, myGrid, University of Manchester

Early impact from the open call - testing Provenance Tool Suite

Boxes with TEST printed on them

By Mike Jackson, Software Architect.

In August I completed an open call project with Trung Dong Huynh, Luc Moreau and Danius Michaelides of Electronics and Computer Science at the University of Southampton. As part of their research into provenance, they have developed the Southampton Provenance Tool Suite, a suite of software, libraries and services to capture, store and visualise provenance compliant with the World Wide Web Consortium (W3C) PROV standards. I developed a test framework in Python, which tests Provenance Tool Suite toolkits and services operating collectively. Dong, Luc and Danius contacted me with their experiences on using the test framework to date...

The Fellows 2016 selection day - #SSIBattleRoyale

By Shoaib Sufi, Community Lead, Software Sustainability Institute

There is nothing quite like a competition to bring out the best or worse in people, but when you combine competition with transparency and collaboration you get a high energy event that people feel they have learnt from. They also better understand why decisions around selection are made and if they don’t make it they can decide whether they want to try again; ultimately it allows the cream to rise to the top.

Such was the Fellows 2016 face 2 face selection event that took place in Manchester at the School of Computer Science, University of Manchester on Wednesday 4 November 2015. This brought together 29 candidates which had been whittled down from the 113 that had applied for the Fellowship 2016; they were competing for just 15 places. There were 29 presentations, 12 discussion groups, 12 reports backs, 9 reviewers (comprising 5 Institute staff and 4 existing Institute Fellows) and a resulting 240+ reviews. A busy and packed day which only lasted from 10am to 4.30pm for candidates with a grueling and soul searching provisional candidate ranking and rating exercise for the reviewers from 5pm to 6pm.

Research Software Group update: Open Call round 6, integration testing Grid accounting software, and reviewing sustainability

By Steve Crouch, Research Software Group lead

With Autumn just around the corner, September has seen some exciting activities within the Institute’s Research Software Group. We’re helping improve the testing of Grid accounting software used by the Large Hadron Collider, we’re assessing the sustainability of a web service that supports greater fitness, and we’ve had a record number of applications into the recently closed Open Call!

Policy update: a new team member and European interest in software sustainability

By Simon Hettrick, Deputy Director.

This month, we welcome a new team member, attend a meeting of European organisations with an interest in software sustainability and support a bid to further bolster the RSE community.

We are happy to welcome Olivier Philippe to the Southampton team. He will be based in Southampton team as our new Policy Officer. Olivier brings with him experience in research design, surveying and is skills in both R and Python. One of Olivier’s first tasks will be to work on improving the transparency of last year’s software survey by repeating the analysis in R using Knitr to track every operation. He will also begin work on a survey of Research Software Engineers which will provide a valuable insight that we need to support the community.

Training update: taster sessions, notebooks and lots of workshops

By Aleksandra Pawlik, Training Lead.

Workshop on the Computational Science & Engineering Sustainability and Productivity Challenges

By Aleksandra Pawlik, Institute's Training group lead.

Developing an industry-led mentoring scheme for software engineering undergraduates

By Robert Haines, Caroline Jay and Suzanne Embury, School of Computer Science, University of Manchester