Monthly Archives: August 2017

Computational biology: an informal career path

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Geoffrey Siwo

Geoffrey Siwo{credit}Geoffrey Siwo{/credit}

Computational biology is one of the fastest growing areas in biomedical research but many biology students or researchers may not have time to study or access formal training. Geoffrey Siwo shares some tips on how to follow a less formal path.

When I started my undergraduate degree in biomedical science and technology 18 years ago, the idea of a student owning a personal computer would be the talk of campus, even if that student was studying computer science.

At the time internet access in many parts of Kenya, (and Africa at large), was still limited, with only about 200,000 of its 30m inhabitants online.

Here are some examples, based on my personal experience, on how a biologist can keep pace with computational biology. Continue reading →

ERC grants competition opens

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The European Research Council (ERC) in Brussels, an independent funding body supported by the European Commission, has announced €1.86 billion (US$2.2 billion) in four types of 2018 grants for early- and mid-career principal investigators (PIs).

piggybankApplications for two grant schemes open on 3 August, including ‘Starting’ grants of up to €1.5 million for up to 5 years for PIs who earned their PhD within 2-7 years ago; and a new collaborative programme, the ‘Synergy’ grant, which will fund 2-4 PIs in a cross-disciplinary project. The Synergy scheme, which awards up to €10 million for 6 years, was piloted in 2012 and 2013. The deadline is 17 October for Starting grant applications and 14 November for Synergy applications.

Applications for ‘Proof of Concept’ grants will be accepted starting in September, and for ‘Consolidator’ grants starting in October.

The 2018 grant programme will collectively fund about 900 PIs and is estimated to support 6,000 PhD students, postdocs and other lab members. ERC’s grant-success rate is 10-15%.

To apply for a Starting grant, click here . For a Synergy grant application, click here.  Good luck!

 

TechBlog: Jupyter Joins the Galaxy

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journal.pcbi.1005425.g001

{credit}PLoS Comput Biol 13(5):e1005425{/credit}

There’s a galaxy of tools in the Galaxy bioinformatics environment — 4,807 at last count. With them, researchers can do just about anything, computationally speaking. One thing they couldn’t do was work with their data programmatically. Now, thanks to a recent software update, that gap has been filled.

In a paper published on 25 May in PLoS Computational Biology, the Galaxy team describes a plug-in that provides access to both Jupyter (neé IPython notebook) and RStudio.

Continue reading →