Author: Martin Callaghan

The Carpentries and Research Computing

I’m pleased to announce that we’ve renewed our membership of The Carpentries for another year.

For those of you that don’t know what ‘The Carpentries’ are, they (we) are an international organisation of volunteer instructors, trainers, organisations and staff who develop curricula and teach coding and data science skills to researchers worldwide.

We’re pleased to be able to support the aims of the Carpentries and in conjunction with other UK partner organisations (and especially our friends at the Software Sustainability Institute ) help the wider UK research community develop their skills.

Here at Leeds, we organise and run two and three-day workshops as part of our training programme. We have a new group of instructors on board, so do keep an eye on the training calendar for upcoming workshops. We run workshops using R, Python and occasionally Matlab.

In conjunction with out colleagues at the University of Huddersfield, we’ve also attracted some BBSRC STARS to run another set of workshops. You’ll find more information about this at the Next Generation Biologists website.

In previous years we have run a number of workshops in conjunction with our colleagues in the School of Earth and Environment funded by a number of NERC ATSC awards.

If you’re interested in finding out more, perhaps to be a helper at a workshop, a future instructor or you’d like to find out more about the content of a typical workshop then please get in touch.

Programming for Evolutionary Biology conference

I thought I’d update you on a conference I’m presenting at in September.  It’s Programming for Evolutionary Biology 2018, taking place in Buttermere in the beautiful Lake District from September 2-6th 2018.

It’s organised by our colleagues (and BBSRC STARS partners) at the University of Huddersfield, Jarek Bryk (@jarekbryk), Maria Luisa Martin Cerezo and Marina Soares da Silva.

PEB’s aim is to bring 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.

It’s a fantastic programme, please check it out.  The organisers are still able to accept applications, so if you are interested then get in touch.

My session is on Cloud Computing.  We’ll be looking at how to use Cloud services for genomics analyses, including setting up our own server in the Cloud, how to store and manage our data and an introduction to the Cloud Genomics services: Microsoft Genomics and Google Genomics.

Summer training workshops

The summer months are a great opportunity to catch up on training and development and we’ve got two workshops coming up at the University of Leeds in July.

To keep up to date with our training workshops, keep an eye on our training pages.  Courses for the new academic year will be advertised in late August.

On to the workshops:

Software Carpentry with Python

Dates: July 9th and 10th 2018

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

In this workshop, you will learn the basics of Python, the Linux command line shell and version control using Git and Github.

Workshop website:

Instructors for this workshop are: Martin Callaghan; Harriet Peel and James O’Neill (all University of Leeds)

If you prefer R to Python, there’ll be an R based Data Carpentry workshop coming up in August, just before the start of the new academic year.

HPC Carpentry

Dates:  July25th and 26th 2018

This workshop is run in conjunction with our colleagues at EPCC (Edinburgh University) through ARCHER training. It’s an introductory workshop and will use one of the new EPSRC funded ‘Tier 2’ clusters, Cirrus ,rather than our local HPC facilities.

This course is aimed at researchers who have little or no experience of using high performance or high throughput computing but are interested to learn how it could help their research, how they could use it and how it provides additional performance. You need to have previous experience working with the Unix Shell.

You don’t need to have any previous knowledge of the tools that will be presented at the workshop.

After completing this course, participants will:

  • Understand motivations for using HPC in research
  • Understand how HPC systems are put together to achieve performance and how they differ from desktops/laptops
  • Know how to connect to remote HPC systems and transfer data
  • Know how to use a scheduler to work on a shared system
  • Be able to use software modules to access different HPC software
  • Be able to work effectively on a remote shared resource

Workshop website:

Instructors for this workshop are: Andy Turner (EPCC), Martin Callaghan (University of Leeds) and Chris Bording (IBM Research, Hartree)