Bioinformatics

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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Typing BioJSby 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 best practices and the latest standards in JavaScript, inspiring the future technical roadmap for the BioJS community.

The Need for this Workshop

JavaScript has become the de facto language of the web. Console-like interactivity is now common place in most web applications and sites. Online collaboration plays an important role in research, enabling scientists to share and disseminate results regardless of geographical location. The data-intensive field of bioinformatics greatly benefits from JavaScript technologies applied to visualisation of biological datasets.…

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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 code, help with coding standards - ultimately making it easier to develop with BioJS.

BioJS, a multi-partner effort coordinated by TGAC, provides services such as infrastructure, guidelines and tools, to represent biological data on the Web that can be reused by anyone. It is an open-source, community-based project, with a modular, structured design that is ideal for data-intensive research. It allows users to build reusable, interactive applications which can be easily deployed on the web.

Components are the basic elements in the BioJS library, and are mainly written in JavaScript for the visualisation of biological data that can be easily used, shared and extended. They also allow developers to improve the user experience when browsing the community data…

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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 were also supported by Mike Cornell and course leader Professor Andy Brass who acted as helpers.

After a few discussions with Andy, we decided to embed the regular Software Carpentry workshop into a week-long training program that aimed to teach the students best practice in programming but also give them a higher level overview to help them in their future careers. With this in mind, we included a module on unit testing to demonstrate alternatives to regression testing.

We also added a brief introduction…

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

by Bruno Viera, PhD Student, School of Biological and Chemical Sciences, Queen Mary University London

attending on behalf of Yannick Wurm (SSI Fellow and Lecturer at QMUL), as one of his PhD students.

Highlights

  • Met Martin Page (@biodevops) and he became a Bionode contributor. Others that showed interest might become Bionode contributors later.
  • Met Toshiaki Katayama (@tktym) and he might contribute to a bionode-semantic module.
  • Saw Thomas Down (@dasmoth) again, and together with Martin Page we discussed collaboration between Bionode, Biodalliance and GeeFuTu.
  • I was asked to give a unplanned talk/demo at the end of the event about Bionode
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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 international institutions.

From a programming point of view, Bioconductor has all the benefits the R language brings, including a high-level, expressive language that allows users to easily and quickly prototype new computational methods. It also has a well-established system for packaging together software, data and

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