I see many students who struggle with LaTeX write-ups and who burn in typesetting hell for their mortal sins (hanging lists, anyone?). This post will focus on some of the more sophisticated details to publish a perfectly set document. This post is the first of a two-part series; focusing on LaTeX hints. The second part […]
Some presentation tips, based on my experience of the things which trouble students (and for which they lose marks) and the things which irked me in previous study-units’ presentations.
So, you have contacted me to undertake a project (Dissertation/FYP/Thesis) together. That is Great! I am enjoying it already. I always find myself repeating the same pointers to each student at the start (or throughout the project really). Thought I would write them down for posterity. So here comes my recipe for success, for the […]
I am always sending the same canned response to students who would like to do an FYP or a dissertation with me on the subjects I dabble in, Computer-Aided Drug Design (Discovery), Virtual Screening (VS), Ligand-based and Structure-Based methods, Cheminformatics, Bioinformatics and Computational Chemistry. Perhaps the first step for any student is to realize the […]
I often get the question “I’m interested in Bioinformatics but how do I get started?“. That question can typically be answered with “A google search“, but that is true for most of the non-existential questions nowadays. This post will give you pointers to material you need to cover to understand the basics of what this […]
It is that time of the year again. December, light drizzle, grey skies, Christmas presents lists, and of course progress reports for your final year project or MSc dissertation. So I get the blank stares when students sit in front of LaTeX, wondering what they should write.
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 […]
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 […]
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).
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 […]