Software and research: the Institute's Blog

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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MentoringBy Raniere Silva, Software Sustainability Institute, David Pérez-Suárez, University College London, Stian Soiland-Reyes, University of Manchester.

Ian Holmes said on Twitter:

"You can download our code from the URL supplied. Good luck downloading the only postdoc who can get it to run, though".

Ian's quote raises awareness that those working on research software need to use best practices, such as version control, testing and documentation, in their daily work because otherwise, other researchers, developers or even the authors themselves will have difficulty getting hold of the software or making it work. Keeping software effort in your research project for a long period of time can be challenging, especially if you don't have access to a big budget; this is also true for many open source projects.

To help the open source ecosystem, Google has a programme called Google Summer…

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key-concepts.pngBy Selina Aragon, Communications Officer, in conversation with Trung Dong Huynh, University of Southampton

This article is part of our series: Breaking Software Barriers, in which we investigate how our Research Software Group has helped projects improve their research software. If you would like help with your software, get in touch.

From concept to software

Provenance is traditionally the record of ownership of a work of art or an antique, used as a guide to authenticity or quality. Although mostly used to track the origins of a work of art, the term is now used in an array of fields ranging from palaeontology to science. It refers to having knowledge of all the steps involved in producing a scientific result, such as a figure, from experiment design through acquisition of raw data, and all the subsequent steps of data selection, analysis and visualisation. Such information is necessary for reproduction of a given result, and can serve to establish precedence. This concept also applies to the digital world; that is, data also originates from a particular point, and provenance provides evidence of its point of origin or discovery by establishing its ownership, custody, and transformations.

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RSE ConferenceBy Simon Hettrick, Deputy Director, Software Sustainability Institute

In a previous post, I discussed the success of the RSE Conference, but I’m hardly an impartial observer. To make sure that the conference improves every year, we ran a post-conference survey so that people could let us know what they thought.

We received 87 responses from the 202 attendees at the conference. That’s a response rate of 47% which is a phenomenal rate for this kind of survey. It’s best practice to offer a prize for feedback because it helps even out the balance of responses by providing an incentive to those who feel ambivalent or negative about the event. However, one £50 Amazon voucher doesn’t account for such a significant response, which means that people felt passionately about the conference. At this stage of the analysis, you’ve just got to cross your fingers and hope that this is good passion, rather than bad!

We asked whether people would attend the conference again—95% would—and whether they’d recommend the conference to others—100% would. That’s fantastic feedback, especially when we see that the conference was rated on average at 4.3 out of 5.

The majority of our attendees came from a background in Physical Sciences (30%), Computer Sciences (18%)…

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