Software and research: the Institute's Blog

Latest version published on 30 January, 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…

Continue Reading

Latest version published on 29 January, 2018.

andysouth.pngBy Andy South, Software Sustainability Institute fellow

Back in July, 2017 I attended the annual R users conference (useR! 2017) in Brussels and gave a lightning talk about my thoughts on the sustainability of releasing a small R package.

I love the diversity of domains at useR and the mix of interesting use cases and useful code ideas. This was the second time that I attended useR!. The first time was in 2013 when the conference was hosted in Spain. This year, there were 1100 attendees from 54 countries. For me, the diversity of domains makes it a very accessible event. It's OK to express ignorance of what your neighbour in the coffee queue is doing. I talked to an engineer analysing measurements collected every second for hundreds of power stations across Europe, a physiotherapy student automating sending injury questionnaires to sports teams, a statistics lecturer creating a new teaching platform and running a controlled test on two groups of students. Seeing this large number of people in a conference venue is a reminder of the size and diversity of the R community, that I mostly just experience online.

The Software Sustainability Institute funded my attendance out of my fellowship fund. I've been freelance for a few years and the cost on top of the time makes it difficult to justify attending conferences. I learnt a lot, met some nice people and hope to attend again when useR! is…

Continue Reading

Latest version published on 26 January, 2018.

CW18pic.pngBy Raniere Silva, Community Officer.

The mini-workshops & demos are key activities in all our Collaborations Workshops. Each session lasts 30 minutes, in which attendees share a particular software product, approach, standard, etc.

Some mini-workshops & demos are very hands-on and at the end of Collaborations Workshop learners are confident to use the software, approach or standard on their daily work. Others  present something earlier in the day, and the audience engages in a constructive discussion with the presenters which sometimes leads to some ideas for the hackday on the third day of the Collaborations Workshop.

Highlights from the Collaborations Workshop 2016 mini-workshops & demos were Robin Wilson's hands-on introduction to recipy, Oliver Laslett's hands-on validation of Jupyter notebooks with nbval and Clemence Tanzi's, from qLegal, discussion about public domain licensing and liability.

The highlights of 2017 edition were Neil Chue Hong's demonstration of the Software Assessment Framework, Edward Smith's hands-on session covering…

Continue Reading

Latest version published on 14 February, 2018.

9190581261_7cefddac29_z.jpgBy Gillian Law.

New Research Software Engineer (RSE) fellow Leila Mureşan will be using her microscopy image analysis skills to develop software for biologists, physicists and mathematicians as part of her RSE fellowship.

As a scientific software engineer at the University of Cambridge’s Cambridge Advanced Imaging Centre (CAIC) Mureşan designs and implements software to analyse imaging data. Computational microscopy uses software and computation to get around the limitations of optical systems, she says. Mureşan trained as a computer scientist in Romania, and went on to study the analysis of single molecule microscopy images with application to ultra-sensitive microarrays for her PhD at the Johannes Kepler University in Linz, Austria.  After doing post-doctoral research at the École Normale Supérieure in Paris and the Centre de Génétique Moléculaire at CNRS in Gif-sur-Yvette France she joined CAIC as it launched in 2014.

Mureşan has developed a particular interest in lightsheet microscopy imaging, which allows developmental biology scientists to follow the development of an embryo in a “fast and gentle” way over several days, she says. This process naturally produces an enormous amount of data, which requires software that can handle the analysis. Mureşan also works on super resolution microscopy, which increases resolution by an order of magnitude.

“I like this area a lot. The…

Continue Reading

Latest version published on 24 January, 2018.

5148710483_a9c0c77da4_z.jpgBy Gillian Law.

Joanna Leng is a computational scientist and visualisation expert who will focus her Research Software Engineer (RSE) fellowship on bringing research computing to imaging. She believes that some areas of the imaging community are failing to fully pick up on the potential of computing, and Leng hopes to transform the use of technology in the field to accelerate scientific discovery.  

Leng will develop software on campus at the University of Leeds for three new imaging techniques, collaborating with Sven Schroeder for spectral X-ray imaging, Rik Drummond-Brydson for spectral electron microscopy imaging and Michelle Peckham for super-resolution light microscopy, in partnership with Diamond Light Source, SuperSTEM and the SCI Institute in Utah, USA.

With 20 years of experience in imaging, visualisation and High Performance Computing (HPC), Leng brings a broad network of contacts to her fellowship, having been interested in imaging and visualisation since her undergraduate degree in biophysics at the University of Leeds. After university, she retrained in computer science, looking for a better paid career, only to “realise at the last minute that I couldn’t face working for one of the banks!” That moment of clarity “brought her to her senses”, and she moved to work in visualisation at the University of Manchester at the Computer Graphics Unit that shortly afterwards hosted an academic…

Continue Reading