Software Carpentry

Software Carpentry is an international collaboration to teach researchers software development skills to help them do more, in less time and with less pain. Software Carpentry training workshops, or boot camps, are highly-interactive two-day workshop which give researchers training in essential software development skills for research.

Rather than adopt a position of saying that these skills are good because software developers say they are, Software Carpentry teaches these skills in the context of how they contribute to correct, reproducible and reusable research.

Data Carpentry

Data Carpentry is a partner of Software Carpentry designed to teach basic concepts, skills and tools for working more effectively with data.

Data Carpentry is a partner of Software Carpentry designed to teach basic concepts, skills and tools for working more effectively with data. In many domains of research the rapid generation of large amounts of data is fundamentally changing how research is done. The deluge of data presents great opportunities, but also many challenges in managing, analyzing and sharing data.

Data Carpentry aims to teach researchers to retrieve, view, manipulate, analyze and store their's and other's data in an open and reproducible way. Researchers learn best when material is taught in their domain, so Data Carpentry workshops organized by ELIXIR tend to be domain-specific. Researchers are taught:

  • How to use spreadsheet programs (such as Excel)
  • How to get data out of spreadsheets and into more powerful tools - using R or Python
  • How to use databases, including managing and querying data in SQL
  • How to use workflows and automate repetitive tasks

Software and Data Carpentry Rollout by ELIXIR-UK for ELIXIR

ELIXIR UK is an official Software and Data Carpentry partner, with a long-term commitment to the growth and spread of Software and Data Carpentry mission. Together with the Software Sustainability Institute (SSI), which are the official coordinators of Software and Data Carpentry in the UK, ELIXIR UK have been working up and building the foundation for Data Carpentry and Software Carpentry within ELIXIR.

Aleksandra Pawlik (SSI's training lead based in Manchester with Carole Goble), has been working closely with Aleksandra Nenadic (ELIXIR UK's training lead for ICT and infrastructure technologies also based in Carole Goble's group) on rolling out the Software and Data Carpentry within ELIXIR under the umbrella of ELIXIR-UK.

The first part of the rollout has been covered by the SWC/DC Pilot project (officially ended in January 2016). The Pilot focused on the topics described below. We are now provide continued support for SWC/DC through ELIXIR EXCELERATE's 'Train the Researcher' and 'Train the Trainer' programmes and are negotiating a special partner status of ELIXIR with SWC/DC foundations.

Materials development

Building a foundation for materials specifically tailored to the life sciences by selecting and modifying existing ones from Software Carpentry and Data Carpentry.

Identifying the materials for the Data Carpentry and Software Carpentry which currently need further work and development, for example in the biocuration and standards areas.

Validating the materials with domain experts, prospective trainers and users who will provide feedback.

Tuning and adapting the content and delivery of the teaching.

Testing materials and collecting feedback

Test run of the foundation material in Data Carpentry events piloted by the ELIXIR-UK Node.

Test run of the foundation material in Data Carpentry events hosted by the other Elixir Nodes.

Assessment of the outcomes through follow-up surveys and interviews to determine what people actually adopt and what impact it has on their research.

Empowering ELIXIR Nodes to be able to develop Data and Software Carpentry workshops independently

Actively expanding the network of organisations within ELIXIR able to run Software and Data Carpentry events.

Expanding the network of organisations and groups contributing to both SWC and DC initiatives. The contributions consist of various effort. One of the key tasks is collaborative development and improvement of training materials. The contents needs to be updated and expanded depending on the community needs. These needs are best gauged by the community members (represented by organisations) themselves.

Expanding the pool of instructors within the ELIXIR Nodes

Train the trainer workshops, to train as many people within the Nodes to become trainers themselves, so that the Nodes can carry out the training work independently themselves.

Building the self-sustained network of instructors.

Software and Data Carpentry in NHS

In collaboration with Prof. Andy Brass from the University of Manchester, Software and Data Carpentry have been piloted in the NHS as part of the postgraduate studies (MSc in clinical bioinformatics for students based in NHS institutions across the UK):

Pilots have received excellent feedback, so much so that the demand for more workshops is predicted to grow very fast and there is a strong case for these courses being used for continuing professional development in the NHS.

Software and Data Carpentry materials will now also be used in the NHS Higher Specialist Scientist Training programme (HSST) in clinical bioinformatics (professional PhD for the NHS), as well as for the NHS Scientist Training programme in clinical bioinformatics (profession MSc for clinical scientist training) and clinical genomics MSc for the NHS (funded under 100k Genome project).