Software and research: the Institute's Blog

The price of open-source software - a joint response

This viewpoint is published jointly on, (personal blog), (personal blog) under a CC-BY licence. It was written by Neil Chue Hong (Software Sustainability Institute), Simon Hettrick (Software Sustainability Institute), Andrew Jones (NAG), and Daniel S. Katz (University of Chicago & Argonne National Laboratory)

In their recent paper, Krylov et al. [1] state that the goal of the research community is to advance “what is good for scientific discovery.” We wholeheartedly agree. We also welcome the debate on the role of open source in research, begun by Gezelter [2], in which Krylov was participating. However, we have several concerns with Krylov’s arguments and reasoning on the best way to advance scientific discovery with respect to research software.

Gezelter raises the question of whether it should be standard practice for software developed by publicly funded researchers to be released under an open-source licence. Krylov responds that research software should be developed by professional software developers and sold to researchers.

We advocate that software developed with public funds should be released as open-source by default (supporting Gezelter’s position). However, we also support Krylov’s call for the involvement of professional software developers where appropriate, and support Krylov’s argument that researchers should be encouraged to use existing software where possible. We acknowledge many of Krylov’s arguments of the benefits of professionally written and supported software.

What is ORCID?

By Will Fyson (ORCID), University of Southampton.

Originally published on the Software Carpentry blog.

Part of being a successful researcher lies in the ability to stand out from your peers, which can be done through making and being acknowledge for valuable and original contributions. Once acknowledged for one discovery this can then act as a springboard to allow your peers to identify your other scholarly contributions, or alternatively identify potential for future collaboration, or be used as a proof of your research skills when applying for further funding. In short, making your work and accomplishments known is crucial to success in academia.

Yet whilst so many functions of the academic process hang on the concept of citations and as such the ability to identify the researchers behind a piece of work, the actual means of identifying a researcher is not without its problems. For example how to identify the discoveries and related work of a specific John Smith after coming across one of the author's particularly informative publications? How do we keep up to date with a researcher's publications if they change their name? How do we keep track of a successful researcher who works across a number of institutions over the course of their career or who engages in work across a range of disciplines?

Training update: workshop outreach, infrastructure improvements and solidifying partnerships

By Aleksandra Pawlik, Training Lead.

This is the last in this month's blog posts taking you around the different activities of the Institute. Today, we feature the Training team.

The training team has been travelling all over the UK and Europe to engage with learners from many different disciplines. We also report on an upcoming visit to the British Science Festival, and interesting new developments with Software Carpentry and Data Carpentry.

Supporting ELIXIR UK in training for bioinformatics

The Institute carries on its activities successfully supporting ELIXIR UK in delivering training to life science researchers. We are helping coordinate the pilot project to introduce and develop Software and Data Carpentry training within ELIXIR UK and across other international ELIXIR Nodes.

Policy update: surveys, jobs and diversity

By Simon Hettrick, Deputy Director and Policy Lead.

This is the third in a series of blog posts taking you behind the scenes at the Institute. Today, we here about the recent activities of the Policy team.

Thus far in 2015, the efforts of the policy team have mainly been focused on providing data and support for the Institute’s funding bid for a second phase. With this out of the way, July has seen the policy team re-focusing on research. We’ve also had time to catch up with our Research Software Engineer campaign and added a new member of staff.

Surveying further

In October 2014, we ran a nationwide survey to determine researchers’ views on software. We were keen to quickly analyse and publish these results and get the preliminary message out. Due to staff availability, we ended up conducting this first pass analysis in Excel. Although we published our analysis, Excel is not the best package for transparency, which is why we rightly received opprobrium from open-data advocates. But we reasoned that our approach would be acceptable as long as we repeated and extended the work in a more transparent manner in the future.

Our new starter this July, Olivier Philippe, arrived with some serious R skills and was immediately tasked with making the survey analysis transparent. He is using knitr to document both the results and the analysis in html. We will publish a paper later in the year about the analysis, and support this by publishing the data, the analysis and results in Zenodo.

Community update: open science, events and an opportunity to join the team

By Shoaib Sufi,Community Lead.

This is the second blog post highlighting the activities of the Institute over the last month. Today it's the turn of the Community team to talk about their work.

It’s been a busy time as ever in the Community team. We have interesting blog posts published from community members, informative workshops in the pipeline, and some exciting upcoming news about the team. Read on to find out more.

Community updates

We published an informative and reflective blog post by Institute Fellow Mike Croucher of Walking Randomly fame. Mike speaks about the dangers of thinking your software is correct and what you can do to feel more confident that it is. And if you have seen 2001 you know bad code can be quite dangerous...

Research Software Group update: software testing and a published paper

By Steve Crouch, Research Software Group lead.

This is the first in a series of blog posts by the Institute's Team Leads to provide an insight into the day-to-day work of the Institute.

The Institute is once again holding its Open Call for Projects, and we're starting to see applications rolling in. So if your project develops research software and you'd like some free expert help, why not consider submitting an application? We work with projects from any discipline, and in the last two months we've helped two groups in the fields of biomolecular simulation and data provenance develop the means to test their software, and had a paper published with one of our projects in the area of biological data visualisation.

The Institute's Research Software Group holds its Open Call about twice a year, and we've just opened the latest round of the call which closes on 30 September 2015. Since 2010, we've worked with over 50 projects to help improve their research software.

Congratulations to Data Carpentry on a Moore Foundation grant

Data Carpentry, one of our partners, has received $750,000 in funding from the Gordon and Betty Moore Foundation. Data Carpentry develops and provides training to researchers in fundamental data skills to enable more effective and efficient research progress. The Institute is excited by the success of Data Carpentry, because it provides the basis for further collaboration and allows us to help deliver the workshops across the UK.

The new grant will help support Data Carpentry for two years. It will allow the project to grow its core team, establish better infrastructure, work with the volunteer community to develop content, conduct more workshops in more scientific domains and plan for sustainability.

Should we change the way software skills are taught?

By Alexandra Simperler, Institute Fellow 2014 and NSCCS, Imperial College, and Katalin Phimister, Computational Chemist, UK.

In today's fast moving world, the number of electronic tools, programs and applications are ever increasing. People see them as a black box something that just works. They overlook the coding, configuration and setup that has been done by a team of developers. Does this prevent people from being proficient and effective users of the software? We want to start a discussion on this point by outlining some scenarios from our professional lives.

People are central to the way software skills are taught. Many users first come into contact with software tools during their university years, but others only start using them after working many years in industry. Those who are exposed to computational tools during their university years often have time to study it for years and familiarise themselves with the details of the algorithm. In industry the situation is different, time pressures often mean there is an immediate need to apply the software to real project work. This is why contemporary software training is focused on two questions:  how can we aid the users' research/analysis, and what is needed to just make it work?

New network to support Research Software Groups across the UK

By Simon Hettrick, Deputy Director.

If we want research to benefit from reliable software, we need to create a home in academia for Research Software Engineers (RSEs). In the long term, this means the creation of an RSE career path, but that involves a rather heavyweight shift in the way that universities deal with staff. Fortunately, there’s also a short-term solution: create more “research software groups”. This week, leaders of these groups met to discuss how they can work together, and how they can support the formation of new research software groups across the UK.

If you manage Research Software Engineers (even if they don’t use that job title) and want to benefit from the experience and resources of similar groups, research-software-group-leaders [at] googlegroups [dot] com (please get in touch). We are keen to include representatives from across the UK.

RSEs who work on their own tend to have a difficult relationship with their workload: there’s either too much work, or there isn’t enough to sustain their salary. By collecting RSEs into a Research Software Group, the demand for RSEs can be equalised, providing a more managed workload and an even income stream. This makes it easier to choose a career as an RSE, which means we get more RSEs working in academia - and more RSEs can only be good for research.

Interoperability test harness for Provenance Tool Suite

Family tree

By Mike Jackson, Software Architect.

In May I started a consultancy project with Trung Dong Huynh, Luc Moreau and Danius Michaelides of Electronics and Computer Science at the University of Southampton. As part of their research into provenance, they have developed the Southampton Provenance Tool Suite, a suite of software, libraries and services to capture, store and visualise provenance compliant with the World Wide Web Consortium (W3C) PROV standards. The goal of the consultancy was to develop an infrastructure, which systematically checks convertibility and round-trip conversions across combinations of Provenance Tool Suite packages and services operating collectively. Last week I completed development of an interoperability test harness which is now under review by Dong, Luc and Danius.

From ideas from Dong, Luc and Danius, I drafted an initial design which was reviewed by Dong, and then updated before implementation started (see the design prior to implementation). More detailed aspects of the design changed during implementation (see the design as implemented).