LaTeX Tips for your Dissertation or 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 will focus on the actual write-up/content.

Comic from
Typesetting your dissertation is a perilous but satisfactory journey

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Presenting Your Work (Assignments/Dissertations)

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.

JP Presenting @
Presenting is fun. But it is your responsibility to make it so for the audience as well.

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Three Tips for a Successful Start to your Academic Project

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 first few weeks at least.

My projects are typically on the life sciences/computer science interface (but we’ve had many different ones – including intelligent automated sports betting).  But these three ingredients apply to any kind of project really.

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Computer Aided Drug Design (CADD) – Reading Lists

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 hierarchy of these fields (and the differences between them). I am including a reading list – which helps you  bootstrap the subject, and hopefully helps you determine if this is really something for you. The jargon will be daunting at first (especially if you are a computer scientist), but that is only an initial hurdle and hopefully you get familiar with the big words quickly. You do not need to understand everything, you just need to understand enough. Remember brick walls are there to show us how badly we want things! (Watch this: long and touching).

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Bioinformatics Starter Pack – Getting started in Bioinformatics

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 bioinformatics field is about.  Unfortunately, there currently is no undergraduate/postgraduate course with focus on Bioinformatics (in Malta*) – so attending a series of (local) lectures is not an option presently.  Do not despair, plenty of material to go around.

Note: This material is not specific to one area in bioinformatics, e.g. genomics, but aims to give a general (soft) introduction to the field!

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What’s in a progress report (FYP BSc/MSc dissertation)?

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.

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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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