Software and research: the Institute's Blog

Gaia artist's impresion
Gaia artist's impression. Credits: ESA/ATG MEDIALAB;
Background Image: ESO/S. Brunier, June 2013

By Francesca De Angeli, in collaboration with Marco Riello, Gregory Holland, Patrick Burgess and Paul Osborne.

This article is part of our series: A day in the software life, in which researchers from all disciplines discuss the tools that make their research possible.

On 19 December 2013, at 09:12:19 UTC, a spacecraft containing the Gaia satellite was launched from Europe's Spaceport in French Guiana. The Gaia satellite reached its stable operational orbit around L2 (approximately 1.5 million km from the Earth) about one month later. Since then, a continuous stream of data has been downloaded for further processing on ground. This data includes broad-band photometry and low-resolution spectra for all sources brighter than magnitude 20 and high-resolution spectra for sources brighter than magnitude 16.

The Gaia focal-plane assembly is the largest ever developed for a…

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Nasa picture of LondonBy Olivia Guest, Software Sustainability Institute Fellow

The Open Data Science Conference, ODSC, was held for the first time in London on October 8th and 9th. As far as I understand, it has its roots in the US and has only recently expanded to another continent. I’m not sure what I expected as I was still very much recovering from PyCon UK (yes, I’m a lightweight). However, I had noticed that quite a few talks were on packages I and/or colleagues use (e.g., TensorFlow, scikit-learn, etc.) so I was excited to see how and what they’re used for  by others.

The first talk was delivered by Gaël Varoquaux, a core developer of scikit-learn, joblib, and other Python packages. He touched on a number of important issues. Firstly, he defined what a data scientist is as  the combination of statistics and code, and,…

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Instructor TrainingBy Steve Crouch, Software Sustainability Institute, with Karin Lagesen, University of Oslo, and Laurent Gatto, University of Cambridge.

Last month, we held a Software and Data Carpentry Instructor Training workshop at the University of Cambridge, sponsored by the R Consortium. The demand for Carpentry events in the UK, and trained instructors to facilitate them, has always been very high, and I found this to be a very enjoyable event to increase the instructor pool in the UK.

The main organiser of the event was Laurent Gatto, a Software Sustainability Institute Fellow who has delivered numerous Carpentry courses since becoming a certified instructor in 2014. We also had the able helping hands of Paul Judge and Gabriella Rustici from the University of Cambridge Bioinformatics Training facility, who assisted greatly with the event and helped us make great use of the sophisticated presentation systems present in the training room.

The workshop was held on 19th and 20th of September, with myself and Karin Lagesen as instructors. We were delighted with the very high level of engagement from the 25 trainees - this was very much the kind of group we hope…

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Figure 1: Inspect your raw mass spectra and run tools from within the OpenMS visualisation tool TOPPView
Figure 1: Inspect your raw mass spectra and run tools
from within the OpenMS visualisation tool TOPPView

By Timo Sachsenberg and Oliver Kohlbacher, University of Tübingen

This article is part of our series A day in the software life, in which researchers from all disciplines discuss the tools that make their research possible.

High-throughput mass spectrometry has become a versatile technique to tackle a large range of questions in the life sciences. Being able to quantify diverse classes of biomolecules opens the way for improved disease diagnostics, elucidation of molecular structure and investigation of cellular pathways. In an interplay with other open-source software, OpenMS enables powerful workflows to transform biological data into meaningful knowledge.

In recent years, mass spectrometry has gained significant attention in the life sciences. The mass spectrometer determines the…

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Root-knot nematodes affect cropsBy Malcom Illingworth, Research Software Engineer.

The Software Sustainability Institute has been working with the School of Biological, Biomedical and Environmental Sciences at the University Of Hull to help improve the sustainability of their ReproPhylo software suite. The ReproPhylo developers applied for consultancy from the Institute via the Open Call.

Root-knot nematodes are parasitic roundworms whose larvae infect plant roots. These tiny parasites have a devastating impact on agriculture, causing 5% of crops to be lost worldwide each year. The Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, The University of Hull studies the genomes of these root-knot nematodes to understand how they have evolved and continue to evolve, their diversity, and the threat they pose to crops. This research involves applying both large-scale comparative genomics—comparing the genomes of different organisms—and phylogenomics—analysing genome data and evolutionary relationships. As part of their research, the group has developed ReproPhylo, a phylogenomics pipeline written…

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