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
This post is written with some tongue-in-cheek; I do not mean for you to take these points as unassailable. No doubt there are some omissions here, but I had to pick my top ten (plus). These are things that looking back at my M.Sc. (Imperial) and D.Phil. (University of Oxford) experiences have forged the way… Continue reading The 10+ Commandments of Undertaking Postgraduate Research
These tips are mostly focused at writing an academic (and scientific) dissertation. But I think most of these suggestions are sensible enough they should feature in any lengthy document. Based on my experience as an examiner and a supervisor, these are the most common things I notice each time I pick a project write-up.
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… Continue reading LaTeX Tips for your Dissertation or Project Write-up
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… Continue reading Three Tips for a Successful Start to your Academic Project
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
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… Continue reading Bioinformatics Starter Pack – Getting started in Bioinformatics
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.
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