Cheminformatics is hard. That is a great quote from Prof. Paul Finn. I think part of it is due to the nature of chemistry (e.g. which is the correct tautomer for this molecule?), and part of it is because of the lack of “standard” process definitions. So I am revisiting the standardization (of the molecule)/normalization(of… Continue reading Standardizing a molecule using RDKit
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… Continue reading Computer Aided Drug Design (CADD) – Reading Lists
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… Continue reading Upgrading R on Ubuntu
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… Continue reading Setting up a Bioinformatics Summer School
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… Continue reading Bioinformatics Big Data Hackathon
Welcome to WordPress. This is your first post. Edit or delete it, then start blogging!