It is that time of the year again. December, light drizzle, grey skies, Christmas presents lists, and of course progress reports for your B.Sc. final year project (FYP) or M.Sc. dissertation. So I understand the blank stares when students sit in front of LaTeX, wondering what they should write.
(more…)Author: jp
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Upgrading R on Ubuntu
During our DataX course, we recently had an issue where installing the tm package had a dependency on the slam package (that’s Sparse Lightweight Arrays and Matrices for you). This package requires R >3.3.1, which is a shame as I asked students to install 3.2 at the beginning of the course. Don’t despair; keep calm and upgrade R.
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Setting up a Bioinformatics Summer School
As part of the TrainMALTA EU project activities, I volunteered/was tasked with setting up the IT infrastructure for the HTS (or NGS) bioinformatics summer school. It has been quite an experience, and the whole setup is far from trivial – so I thought I’d document parts of it here. Habitually, I turned to google to search what others in my shoes have done and nothing turned up. Nothing on google – this setup must be worth documenting!
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Installing Cufflinks (RNA-Seq) on Ubuntu
So, you have a ton of hard-disks spinning with RNA Seq data you need to analyse? Excellent. But first you need some software to do that. This post follows the nature protocol described by Trapnell et el. described here (something freely accessible from nature publishing group – must be my lucky day today).
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Bioinformatics Big Data Hackathon
Note: I should have written this ages ago, but only now has the cold weather caught up with my nocturnal habits.
As part of the first keystone summer school we organised a summer school over four days in July 2015 at the University of Malta. The summer school was titled Keyword Search over Big Data and I was asked to help with organising the one-and-a-half-day big data hackathon. With my bioinformatics hat on, it was easy to fish for “big data” for the event.
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