Software and research: the Institute's Blog

What do you tell your PhD student Three Years Before They Leave …

By Vince Knight, Cardiff University, Olivia Wilson, University of Southampton, Shoaib Sufi, Software Sustainability Institute, Steve Crouch, Software Sustainability Institute, and Ian Gent, University of St Andrews.

A speed blog from the Collaborations Workshop 2016 (CW16).

"Congratulations Dr Smith"

The words every PhD student dreams of hearing, at least if your name is Smith. First from your examiners, and then soon afterwards from your supervisor. And then those words every PhD student dreads of hearing from your supervisor…

"Just before you go to your super-rich quant futures job on Wall Street, could you just …

…. hand over your code to my new PhD student please?"

The inevitable abyss: find mentors who will help you get out

A view through my glasses. Image by UnknownNet Photography. Heather Ford, University of Leeds, Jonah Duckles, Software Carpentry Foundation, Angus Maidment, STFC, Martin Callaghan, University of Leeds, Terhi Nurmikko-Fuller, University of Oxford e-Research Centre, and Amy Beeston, University of Sheffield.

A speed blog from the Collaborations Workshop 2016 (CW16).

We are all continually entering and exiting the constant cycle of the hero’s journey. It’s the story of learning.

The question of best practices for the mentoring of a range of people from various different backgrounds is multi-faceted and complex. There are three main aspects that proved particularly fruitful for conversation:

9 steps for quality research software

Pipettes on shelf by Jean-Etienne Minh-Duy Poirrier. Laurence Billingham, British Geological Survey, Steven Lamerton, Science and Technology Facilities Council, Nick Rees, Square Kilometre Array Organisation, Mike Croucher, University of Sheffield, Richard Domander, Royal Veterinary College, and Carl Wilson, Open Preservation Foundation.

A speed blog from the Collaborations Workshop 2016 (CW16).

Researchers, we need to talk about software.

The research community has a problem, some still see talking about it as taboo. Hiding from the problem and hoping it goes away will not make it go away. We are going to have to deal with it sometime, we can only put off dealing with it, and do so by borrowing time from our future selves.

How do we improve research software usability for non-developers?

Xerox Alto mouse by Michael Hicks. Swithun Crowe, University of St Andrews, Mike Jackson, Software Sustainability Institute, Karen Porter, University of Oxford, Neil Chue Hong, Software Sustainability Institute, Mayeul d' Avezac, UCL, and Oliver Laslett, University of Southampton.

A speed blog from the Collaborations Workshop 2016 (CW16).

The communities affected by a piece of software are many and varied. There will be some who care about each bowel movement in the code, and others who really just want to know what needs to be put in and what comes out. This blog post describes four different communities from the cognoscenti to the would-be users, and the tools that make it easy for the community to emerge and work together.

Reproducible Research: Citing your execution environment using Docker and a DOI

By Robert Haines, Institute Fellow & Research Software Engineering Manager, IT Services, University of Manchester and Caroline Jay, Institute Fellow & Lecturer, School of Computer Science, University of Manchester.

As we move into a world where (hopefully) more and more people are trying to make their research as reproducible as possible, a lot of us are turning to Docker to help out with the task of distributing our research software in a way in which it is as accessible as possible to others. As we move in this direction we need to be able to cite the software environments that we are executing, not just the source code itself.


Top tips for using a wiki

Tantalus Road through Hawaiian jungle - wiki is a Hawaiian word

By Mike Jackson, Software Architect.

My EPCC colleague, George Beckett, recently e-mailed me to comment that "I'm conscious that wikis typically deteriorate into a mess of conflicting/out-dated materials, if not managed closely". George asked whether the Institute had advice on good practices for using a wiki. So, for George and others with wiki worries, here are our top tips on using a wiki for a software project...

Promoting uptake and development of MONC


By Mike Jackson, Software Architect.

We're helping EPCC and the Met Office promote the uptake, and ongoing development, of the Met Office NERC cloud (MONC) model within the atmospheric sciences community. We're assessing how easy it is to deploy MONC, helping set up a MONC virtual machine and advising on setting up resources for engaging with and supporting researchers.

Do you want a research time machine? Apply for the Azure for Research award

By Kenji Takeda, Microsoft Research

One thing that most of us never have enough of is time. Developing skills through Software Carpentry, software reusability, open data, open research, and growing the cohort of Research Software Engineers can really help reduce the time taken for us to do our research. The Software Sustainability Institute is leading the charge with this, and increasing people’s capabilities is a recipe for success. But when it comes down to it, eventually we have to run some code, a processing pipeline, big data computation, or share massive amounts of data.

How many women should you expect at an academic event?

By Simon Hettrick, Deputy Director.

I’ve attended a lot of events during my time in academia, but I can think of only one where women outnumbered men (one of the BSA’s Science Communication Conferences). This is not a revelation, of course. It's well known that women are poorly represented at events: as keynote speakers, on expert panels, or just as attendees in general. When I've discussed this issue in the past, I've often been asked "How many women do you expect to see?". It’s a practical question, but not one I've yet seen answered.

Should the first target for an academic event be to simply mirror the population within the event's discipline? I’ve written this blog post with this principle in mind, but also to start a discussion about whether this is indeed a helpful target.​ It occurs to me that people must have already tried this, so I'd also welcome any data on these attempts and whether they successfully improved representation.

We're looking for equality of opportunity throughout academia, but this is a distant proposition in some disciplines. If we aim for representation as a first step, we provide a target that's easy to measure and possible to achieve. If an organiser can prove success at this first target - in other words, that they are representing the gender split in their community - it would help raise awareness of the event and this could help to further improve representation at later events. I realise that targets are fraught with complication, but they also give you something simple and quantitative to aim for. It's all too easy to lose sight of the bigger picture​ during the nerve-jangling panic of event organisation.

"Supporting Research Software Community Though Training"

The Institute's training activities have received a lot of interest from various international projects and institutions focusing on supporting research.