Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action

ELIXIR Software and Data Carpentry Pilot action

The ELIXIR Hub strongly encourages interactions and collaborations between the Nodes. Such interactions are supported by short-term Pilot actions¹ that are funded by ELIXIR. The goal of these projects is to “tackle major European challenges in life science data access, high-performance computing and the interoperability of public biological and biomedical data resources”. Pilot actions usually involve several ELIXIR Nodes to build, test and demonstrate the value of the distributed infrastructure.

One of these collaborative activities is providing training in essential skills for life science researchers throughout ELIXIR. In part, these skills encompass computational and digital data manipulation and analysis skills. Even though there are a lot of materials available to teach these topics, they are scattered, hard to discover and access, or assume too much prior knowledge. Contrarily, there is a lack of training material in biocuration and for the development of content standards (terminologies, minimum information checklists, exchange formats) and their use (e.g. in annotation tools). Nevertheless, funders and researchers increasingly call for enhanced, standards-driven experimental annotation at the source, and for data sharing to maximise data reproducibility and reuse, in order to drive science and scientific discoveries (Wilkinson et al., 2016).

Training activities are one of the main focus areas of the ELIXIR UK Node, and the Training Theme that it leads. In 2014, the UK Node, in collaboration with and support from ELIXIR Finland, ELIXIR Netherlands, ELIXIR Switzerland and ELIXIR Sweden, proposed a Pilot action for “Working up and building the foundation for Data Carpentry and Software Carpentry within ELIXIR” to tackle this evident training gap.

The Pilot project had several overarching objectives. The first was to launch the Carpentry initiatives in the ELIXIR community and leverage the work of the Software Carpentry (SWC) and Data Carpentry (DC) initiatives from the US and Canada by reusing their existing training materials and well-tested, successful and popular model of hands-on teaching. Secondly, we wanted to tap into the international community built for years around the Carpentries, which included experienced researchers and trainers in life sciences who have been delivering and developing training on a regular basis. In the long run, the goal was to develop a self-sustainable pool of professional Carpentry instructors within ELIXIR who would deliver training across the Nodes, by incorporating the Instructor Training course, developed by the Carpentries. Finally, we wanted to join and help grow this international community by contributing the newly trained instructors, as well as further developing and adapting materials in the life sciences domain.

Software and Data Carpentry

SWC is an international collaboration aimed at teaching researchers (without prior knowledge or training in IT) basic software development skills. This initiative is very well established internationally and has been running since 1998.

SWC training courses are highly-interactive two-day workshops that give researchers training in essential software development skills, but in the context of how they contribute to improving research productivity and help produce robust and reproducible science. In other words, they look beyond just teaching people to code (i.e. syntax of a language or commands they can run) - teaching people how to code and coding best practices is as important (Wilson, 2016).

The materials used for both Carpentry workshops are openly available and developed by the community of experts and experienced instructors. The way workshops are delivered has been devised and perfected over the years of practice and is based on pedagogical approaches, taking into account learners’ backgrounds, reducing cognitive load, and giving and receiving constructive feedback. They employ techniques such as live coding, working in pairs and peer learning to make the training the most effective.

SWC training courses cover four core topics:

DC started in 2015 as a separate programme inspired by SWC. Both programmes maintain close ties, which help to build and share a community of practice among the instructors and expand the base of teaching materials and available trainers. DC aims to teach the skills that will enable researchers to be more effective and productive in working with data. As in SWC, teaching is delivered through intensive two-day workshops.

Contrary to SWC, DC designs the workshops to fit into needs of particular domains (e.g. life sciences, social sciences, digital humanities and library carpentries, etc.). The core DC workshop curriculum covers topics such as:

The instructors delivering the material are members of the SWC/DC instructor network and have completed training designed to prepare them to use “the Carpentry way” of teaching the skills for effective and productive work with research data. All instructors are volunteers and do not get remuneration for the workshops they teach - they do it because of their love of teaching or because they want to give back to the community. For that reason growing a large pool of instructors (primarily peer-researchers) allows for responding to the massive demand for the workshops.

Both Carpentries are aimed at providing researchers with the essential lab skills for computational science. They do this by focusing on the core skills and making sure that the best practices are passed on in a useful and effective way. Carpentries do not aim to teach audiences specific technical aspects of research - such an audience requires different training (within ELIXIR this type of training is covered by the Train the Developers Programme (van Gelder et al., 2016)). However, SWC/DC can act as an important connector between researchers and service providers, allowing both sides to communicate better and work more effectively.

Outreach

The delivery of the Pilot action was coordinated by the ELIXIR UK Node and started in late 2014 with outreach and engagement to ensure broad participation of the Nodes in the planned events. In order to streamline communication with other Nodes, we sent a request for volunteers (one per Node) to step in and become a SWC/DC Coordinator for their Nodes. The information about the planned Pilot activities would be passed on to the Coordinators who would then disseminate it within their Node. This was particularly important at the beginning of the Pilot, as SWC/DC workshops were relatively unknown among ELIXIR research organisations in 2014.

Reaching out to find the Coordinators was an iterative process. A number of people in ELIXIR were actively involved. We posted the call for Coordinators on the ELIXIR UK, as well as the main ELIXIR websites. The ELIXIR Training Coordinator Group (TrCG) was engaged from the very beginning and helped circulate announcements and facilitate communication with the Node members.

As a result, volunteers from 10 Nodes (out of 17 at the time) stepped in. Most of them did not know much about the SWC/DC workshops, but they all had strong interest in teaching. The call for Carpentry Coordinators specified that ideally their work responsibilities should be related to training so that the effort related to coordination would align with their regular responsibilities.

Workshops and hackathons

The Pilot was delivered as follows. Firstly, we ran four-day events that combined training material creation hackathon (two days) with a regular train-the-researcher workshop (two days). We ran two of these combined events - one in Finland and one in the Netherlands. These were then followed by an Instructor Training event, aimed at selected participants from the first two events who showed the most interest and enthusiasm about the programme and were willing to become instructors themselves.

The material creation hackathons consisted of two parts: the first one was to introduce the idea and running of SWC/DC workshops, curriculum and model of training; the second part was focused on improving existing and developing new training materials specifically focused on life sciences and its various sub-domains. Through these hackathons, we actually wanted to demonstrate another distinctive feature of SWC/DC - collaborative material development. All SWC and DC training materials, websites and other documents, are developed and shared by the community via GitHub. This approach has proven to be very successful, allowing for maximum inclusivity and production of high quality training materials avoiding redundancy in contents (Wilson et al., 2014; Wilson et al., 2016). As part of the hackathons, we wanted to train people to become proficient in this method of working, as well as create more materials.

Combined hackathon and workshop in Finland. The first combined event was held in Helsinki, Finland, in March 2015, hosted by ELIXIR Finland at the CSC IT Centre for Science.

The training material creation hackathon was advertised among the Nodes with the idea of bringing together 15 participants representing as many Nodes as possible to ensure wide representation and dissemination. Eventually 12 participants from 11 Nodes were present at the material creation hackathon (the first two days of the event).

The material development covered during the hackathon included:

The facilitators at the hackathon were two experienced Carpentry instructors - one of which was also among the Pilot proposers and a member of the DC Steering Committee at the time. After leading the hackathon, they also taught at the DC workshop that immediately followed (the last two days of the event). The workshop itself was attended by 29 researchers from the life sciences domain. The workshop was widely advertised across ELIXIR, so the attendees were not only the local researchers based in Finland, but also a few from other Nodes.

The attendees of the hackathon were strongly encouraged to stay for the last two days at the DC workshop as helpers and observers. We did not make it a requirement, since it would make the whole event almost a week long (including the time needed for travel), and may not be possible for some of them to commit to.

Combined hackathon and workshop in the Netherlands. The second event of the Pilot action, hosted by the ELIXIR Netherlands Node, was carried out similarly to the one in Finland. The hackathon and the workshop were co-located and run at the University Medical Centre Utrecht in June 2015. This time 19 participants represented 10 Nodes at the hackathon. To increase the outreach, we encouraged the Nodes to delegate a different representative to the one that was present in Finland - so we had an overlap of only five participants.

The material development took place in three groups:

One of the facilitators (and the Pilot proposer) was the same as in Finland. They were joined by another experienced instructor from the US, and a fellow member of the DC Steering Committee. This helped with providing background information to the participants about the workshops and both initiatives. After the hackathon, these instructors taught at the co-located DC workshop that followed and was attended by 30 researchers. Again, the workshop was advertised widely to allow representatives from all ELIXIR Nodes to receive the training. Similarly to the workshop in Finland, the one held at the University Medical Centre Utrecht was also mainly attended by local researchers.

The workshop received a lot of interest, not only from researchers based at universities in the Netherlands and nearby Nodes, but also from industry. One of the companies based in the Netherlands and focusing on bioinformatics contacted the organizers and asked if two of the company researchers could participate in the workshop. As the collaboration with this company is potentially beneficial for both the SWC/DC Foundations and the company, the researchers were welcome to attend. They had a very positive experience and as a result the company requested an internal workshop, which was delivered in December 2015 by two newly trained instructors from the Netherlands eScience Centre.

Instructor Training. The final event of the Pilot action was the SWC/DC Instructor Training. This covered the process and pedagogy of learning, as well as best practices in teaching, and was not just limited to teaching computational skills. The workshop was delivered over two days and was hosted by the ELIXIR Switzerland Node in Lausanne, Switzerland, in January 2016. Using the communication network we developed during the organisation of the preceding events, we reached out to the ELIXIR Nodes to fill the spaces for the workshop. Eight Nodes were represented at the event and 20 participants were trained as SWC/DC instructors (see Figure 1 below for the spread of participants per Node). As with the previous events, participants had financial support from the Pilot action budget.

Figure 1. Instructors trained per Node.

This Instructor Training was delivered by two trainers. One of them was the same instructor and facilitator who ran the events in Finland and the Netherlands. This helped with organisation and coordination of the workshop. The second trainer was the Executive Director of the Data Carpentry Foundation, which gave an excellent opportunity for the attendees to discuss various details of planned implementation of DC at their Nodes.

We explicitly advertised the Instructor Training as an event addressed at those representatives of the Nodes who were already interested in training and who aimed to become active Carpentry instructors engaging with the community and running workshops in the future. By the end of 2016, 17 attendees of the Instructor Training have completed the final “Carpentry Instructor Checkout Procedure” and became certified as SWC and/or DC Instructors (out of 20 trained in total - which is a high rate of 85%).