Other resources

A list of projects we are involved in and activities we run.

Ongoing activities

Northern Bioinformatics User Group

Also known as NorthernBUG. This is a network of bioinformaticians and users or bioinformatics services in the north of England. Inspired by the Scottish NextGenBUG we hold quarterly meetings to build a community of researchers and others using big data in biology. Since 2019 NorthernBUG is a Sectional Interest Group, officially supported by The Genetics Society.

Synthetic biology

We have been developing a series of DNA parts and protocols to facilitate teaching about synthetic biology in higher education. The website at practicalsyntheticbiology.net presents the current set of parts and other resources, but they have been overhauled - thanks to the work of Alex Siddall in my group and Jason Sanders from the School of Arts and Design here at Huddersfield, we are expanding the number of parts available and preparing a new set of printed and digital materials to go with them. The preprint is now available on biorxiv: UNIGEMS: plasmids and parts to facilitate teaching on assembly, gene expression control and logic in E. coli.

Coding Club

Coding club is an informal series of meetings for postgraduate students and interested staff with the aim of introducing command-line coding and R programming. We meet every week for two hours in a small group to learn and practice shell scripting and R data analysis. In 2021-22 the coding club has been reshaped as an R course for PGRs and staff.

Below is the set of websites where I maintain a list of resources about which students ask again and again. Each of the websites is maintained at Github and everybody is welcome to contribute to expanding and improving them.

Computational biology FTW

My ever-growing list of resources to get into computational biology. I am a big fan of R and use it both in my teaching and research and am always on the lookout for good approaches to teach and learn it. Shell is another must-have in computational biology (see above) and so I am trying to stay on top of it all by following a bunch of excellent people on Twitter and collecting good resources on this list.

How to run a local BLAST

This is a short tutorial on how to install and run BLAST on your local computer. I provide example input file and a database and a copy of BLAST options from the NCBI website (which I find is not very easy to follow). It’s now over a year old but is still accurate (although do pay attention to a sneaky option -max_target_seqs).

Stats for students

List of online resources about statistics, aimed at undergraduates but useful to anyone :-)

Career advice, placements and funding opportunities

This is my collection of links about sources of funding and career advice, mostly relevant to undergraduates and graduate students. I needed them in a single place so that I am able to direct students there who ask me about this quite often. I also tried to make it a bit more UK-centred compared to what is available on the web already.

Past activities

Next Generation Biologists workshops

This is a BBSRC STARS-programme-funded project that I am involved in alongside Dr Mary J. O’Connell, formerly at the University of Leeds and currently at the University of Notingham) and Martin Callaghan from the University of Leeds. We run a series of workshops to introduce and train researchers in the skills and best practices in scientific computing and bioinformatics. You can read all about the project and the workshops on the website nextgenbiologists.org. This project ended in February 2020

Programming for Evolutionary Biology 2018 conference

The Programming for Evolutionary Biology (PEB) conference brings together scientists broadly interested in applying bioinformatic tools to answer evolutionary and ecological questions. Unlike other conferences featuring mostly talks and poster sessions, it aims to serve as a platform for discussing common programming pitfalls encountered during research and features workshops to further develop participants’ bioinformatic skills. This project happened and was really nice :-)