Bioinformatics

By Mike Jackson, Software Architect, The Software Sustainability Institute. PickCells is an image analysis platform developed by the Centre for Regenerative Medicine (CRM) at The University of Edinburgh.
Figure 1: Inspect your raw mass spectra and run tools from within the OpenMS visualisation tool TOPPViewFigure 1: Inspect your raw mass spectra and run tools

by Manuel Corpas, Project Leader, ELIXIR-UK Technical Coordinator, CorpasLab, The Genome Analysis Centre (TGAC).

In this blog entry we discuss the outcomes of the recently held JavaScript for Visualisation Workshop, The Genome Analysis Centre (TGAC), Norwich, UK, April 21-22. This workshop brought 26 attendees from around the UK and the continent. The event was open to both core technical members and developers not currently involved in the BioJavaScript (BioJS) project. The workshop was facilitated by Software Sustainability Institute 2016 fellow Manuel Corpas to promote software…

By Devasena Inupakutika, Software Consultant.

With the advent of data-driven research in the life sciences, researchers have relied on data visualisations to generate hypotheses. Many bioinformatics services providers, such as EMBL-EBI or the NCBI, provide a browser-based environment to do this, as well as new ways to visualise biological data. It is important that the software is both high quality and user friendly, which helps researchers compare and contrast, as well as develop, well grounded conclusions. The Software Sustainability Institute worked with BioJS to review their…

By Aleksandra Pawlik, Training Leader.

Last month saw us run a special Software Carpentry course for students undertaking the MSc in Clinical Bioinformatics course at the University of Manchester. This combines an academic curriculum with a work-based programme.

The students are already qualified professionals and based at various clinical units throughout the UK, with teaching take place during short, intense training sessions.

The instructors at the Software Carpentry workshop were the Institute’s Aleksandra Nenadic, who taught for the first time, and myself. We…

18-21 September 2014, at EMBL-EBI, Cambridge

Last month saw the BioC 2014 conference take place at the Dana-Farber Cancer Institute, Boston, MA. Starting with a Developer Day on July 30th, it continued with a series of talks and workshops until August 1st.

Bioconductor is an R-based open-source, open-development software project. It  provides tools for the analysis and comprehension of high-throughput genomics data. First developed in 2001 by Robert Gentleman, who also co-founded R with Ross Ihaka, it is overseen by a core team based at the Fred Hutchinson Cancer Research Center, alongside several other American and…

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