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)

University of Birmingham meeting: Visualisation Workshop

The University of Birmingham hosted a Remote Visualisation Workshop earlier this week, which had an interesting variety of folk talking about interesting things.

Despite the disparity of the topics – ranging from using consumer grade Virtual Reality equipment to visualise and manipulate Molecular Dynamics simulation data (only 600 pounds! fun watching someone trying to tie a
knot in a long string peptide!), alternative methods to interact with HPC machines such as Jupyter notebook and JupyterHub, the pros and cons of various technical means to achieve or improve remote graphical access, and an overview of how visualisation fits into the scientific method – it was clear how they all had the same aim:

Reducing the friction involved in using a computer and working with it results.

The length of the list of technologies covered by the end of the day was pretty impressive and I’d say that the award for best-name-of-technology-I’ve-not-heard-of-before goes to Apache Guacamole. Technology with the most promise might go to Jupyter notebook / JupyterHub – not because I think it will replace SSH access with an interface bearing a strong resemblance to Mathematica which I was using in the 1990’s – but due to the way it provides an alternative method focused on being able to develop, collaborate and present work.

The slides for my bit are here.

Introduction to reproducible research workflows in Python

Are you using Python for research purposes or data analysis? Are you interested in learning how to make your computational workflows more reproducible?
ARC (Advanced Research computing) at Leeds is offering a one-day introductory workshop on reproducible workflows with Python on the 14th of June 2018,  running from 10:00 to 16:00.

⚠ Please note that this is not a course to learn Python but for Python users wanting to learn more about how to introduce reproducibility practices into their data analysis workflows.

More details can be found at

Registration link:

Open to all staff and students at The University of Leeds

University of Surrey meeting: What is Research Software Engineering?

I recently attended an event at The University of Surrey called What is Research Software Engineering? Along with many institutions, Surrey are considering some sort of central Research Software Engineering function so they invited a few people from the national community to give talks on the topic.

The first talk was by Simon Hettrick, deputy director of the Software Sustainability Institute who presented the history of research software engineers.  We’ve been around forever of course but we didn’t rally around a name until 2012. Simon’s talk is essential viewing for someone who has never heard of the RSE movement and he is more than happy to come to a university near you.

My talk was called So you wanna build an RSE group? where I discussed the history and lessons learned when we built the RSE group at The University of Sheffield.  Developing this talk was useful reflection for me since it allowed me to consider what should be in the strategy for the RSE group that we will be building at Leeds (Hiring soon!…join the national RSE group to ensure that you are notified of all RSE career opportunities)

Next up was our host, Evren Imre who gave a very open and frank talk about his personal experiences of working as a vision researcher — much of which was spent developing software.

Finally, we heard from Christian Kroos: In his talk, Here be dragons he presented some considerations on research software design based on his experiences developing research software, both as a researcher and as a research software developer.