Software Carpentry

Software CarpentryBy Eilis Hannon, University of Exeter.

On Tuesday, 26th September we held a two day Software Carpentry workshop at the University of Exeter. 37 staff and students attended including a number of PhD students in their first week. The course covered the Unix Shell, Python and Git, and gave Jeremy Metz and me the opportunity to teach our first Software Carpentry workshop, alongside Andrew Walker from University of Leeds who was there to steady the ship and provide experience. This was particularly helpful when it came to debugging and resolving common issues.

I was impressed by the sustained enthusiasm over the two days and how much of the content we got through. Many attendees commented that they appreciated the slightly shorter days (from 10am to 4pm) and regular breaks, as these enabled them to remain focused and digest the content delivered. They were also grateful for the additional support provided by the helpers David Richards, Paul O’Neill, Ben Evans…

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digital humanititesBy Giacomo Peru

On 26th and 27th September, Oxford held one of the first Data Carpentry workshops for Humanities*. The workshop is fruit of a collaboration between Reproducible Research Oxford and the Software Sustainability Institute. Iain Emsley has undertaken the endeavour of porting the Ecology lessons to a Humanities version, using Early English Books Online Text Creation Partnership texts as the dataset. The choice has been to port Python but R will come next. The team of instructors was Iain (Python), Pip Willcox, from the Bodleian Libraries’ Centre for Digital Scholarship (Spreadsheets) and Lucia Michielin, from the University of Edinburgh (Open Refine and SQL).

According to the instructors, the dataset needs more cleaning (for example, multiple authors come in the same column!). The lessons need further revision but there is hope to submit them to Data Carpentry for consideration by the end of the year.

Contributions are therefore welcome!



Open Refine

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***This is now sorted as a couple of assistant instructors have been found***

The Software Sustainability Institute, on behalf of Reproducible Research Oxford, is looking for a second instructor for a Software Carpentry workshop in Oxford on 12th & 13th October 2017.

Please get in touch with if you'd like to help.

About the workshop

Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. This workshop is run by the Department of Biochemistry (Michal Gdula) and the Reproducible Research Oxford project. It will cover introduction to the UNIX shell, GitHub as well as programming and data visualization in R. 


Instructor trainingBy Amy Beeston, University of Sheffield.

I attended the instructor training course in Manchester last week. During one of the coffee breaks, we were sharing stories of how we first met these teachings, and how as new learners we first tried to put our freshly-acquired Software Carpentry skills to use. Following that conversation, our instructor Aleksandra Nenadic invited me to write this blogpost to share my experiences.

I was introduced to the concept of Software Carpentry by Greg Wilson during the week-long Sound Software Autumn School in late 2010. Heavily pregnant, I sat on the back row during most of Greg’s classes — the row with the extra leg/body room — and listened to the very best of my ability to every single word he said.

As a group of learners, we came from varied disciplines but all shared the need to focus our programming skills on developing tools that accessed data in the audio domain. Many of us were self-taught programmers, and some of us had relatively little text-based coding experience as we were used to thinking and working in real-time signal processing…

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CODATA-RDA Summer School in TriesteBy Mario Antonioletti, Research Software Engineer

Last week, thanks to the Software Sustainability Institute, I was lucky enough to go teach the R and SQL lessons from Software Carpentry at the The CODATA-RDA Research Data Science Summer School held near Trieste in Italy. The Summer School focuses on providing participants from all over the world, with six out of the seven continents represented, growing competence in accessing, analysing, visualising and publishing data. The School is open to participants from all disciplines and/or background from the sciences to humanities. The first week, which provides a basic framework, is followed by three applied workshops that focus on Extreme sources of data, bioinformatics, and IoT/Big Data analytics. So participants cover a lot of material over the two weeks of their attendance.

I was provided 1.5 days to do R and half a day to do SQL. This was done over three days. The typical modus operandi for the Carpentries is that you type and they follow, typing the same thing you do, as an instructor, to their own terminals. For R though, I previously found that it is hard to keep up and easy for the participants to lose contact with the commands…

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Library carpentryBy Julianne Schneider, Data Curator

This post was originally published at the Software Carpentry website.

In the space of a year, interest and participation in the Library Carpentry community has exploded like an amoeba who over-ate at an algae banquet and attempted one too many pseudopods.For Library Carpentry, though, this is a good thing; the pseudopods are propelling us forward across institutions, disciplines, and continents. The community, grounded in collaborative tools like Github and Gitter (I always want to type Glitter) is coalescing around lesson development and holding new workshops. Why is the buzz so strong? I think it’s a combination of relentless energy from people like Belinda Weaverand Tim Dennis (to name just a few), the acceptance and active encouragement of new people who want to contribute in some way, and the mutual recognition by all of us that in any one thing, we are all absolute beginners, and we all give each other permission to be terrible until we aren’t.

I am still terrible at Github and command line and use Tim’s Github workflow post every time I work with Github - seriously, this is Github workflow…

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CDT mapThe Software Sustainability Institute has gathered information on the Centres for Doctoral Training (CDTs) in a map, as some of them may require training in basic software development skills to help scientists improve or speed up their research, ensure that their results are more reliable and verifiable, encourage sharing code and collaboration with others and aid reproducibility overall. As the Institute already has multi-year training agreements with some CDTs relating to running and coordinating Software Carpentry (SWC) and Data Carpentry (DC) workshops, we were also interested to identify other centres, which may be interested in either helping with setting up regional training centres or setting up their own software training.

Centres for Doctoral Training (CDTs), also called Doctoral Training Centres (DTCs), are one of the several ways by which research councils in the UK provide support for advanced, high-level and increasingly interdisciplinary scientific training following undergraduate studies.

Go to the interactive map and find out more.


The Software Sustainability Institute, ELIXIR UK and the Department of Biochemistry at the University of Oxford are jointly organising a Bioinformatics Software Carpentry workshop in NGS data analysis. 

The workshop will be held at the Medical Sciences Teaching Center (MSTC) over 3 days, 5th-7th December 2016. The first two days will cover the standard Software Carpentry curriculum (introduction to the UNIX shell, GitHub as well as programming and data visualisation in R). The third day will involve hands-on next generation sequencing (NGS) data analysis in R. The aim is to make the course accessible to beginners, however some prior bioinformatics knowledge/skills will be an advantage. 

Please visit the workshop page for further information. The workshop is completely booked. However, if you are interested in attending, please get in touch with Aleksandra Nenadic in the case there are some cancellations and late availability.

Instructor TrainingBy Steve Crouch, Software Sustainability Institute, with Karin Lagesen, University of Oslo, and Laurent Gatto, University of Cambridge.

Last month, we held a Software and Data Carpentry Instructor Training workshop at the University of Cambridge, sponsored by the R Consortium. The demand for Carpentry events in the UK, and trained instructors to facilitate them, has always been very high, and I found this to be a very enjoyable event to increase the instructor pool in the UK.

The main organiser of the event was Laurent Gatto, a Software Sustainability Institute Fellow who has delivered numerous Carpentry courses since becoming a certified instructor in 2014. We also had the able helping hands of Paul Judge and Gabriella Rustici from the University of Cambridge Bioinformatics Training facility, who assisted greatly with the event and helped us make great use of the sophisticated presentation systems present in the training room.

The workshop was held on 19th and 20th of September, with myself and Karin Lagesen as instructors. We were delighted with the very high level of engagement from the 25 trainees - this was very much the kind of group we hope…

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SoftwareCarpentryNewcastle.jpgSoftware is of fundamental importance to most research, but many of the next generation of researchers will lack the skills they need to exploit it. A good understanding of software, and the confidence to develop it, allows researchers to get more work done in less time, and produce results that are both reliable and reproducible. The Software Sustainability Institute is an EPSRC-approved supplier of training for the Centres for Doctoral Training (CDT). 

Since 2012, over 1000 students have benefited from the training we deliver together with Software Carpentry and Data Carpentry - initiatives that have been developed for researchers from all disciplines. The Software Carpentry training covers a series of practical software engineering techniques and practices that provide the skills needed to harness the power of software and develop robust and maintainable code. The Data Carpentry training focuses on effective data management, analysis and sharing to support reproducible research.

Why Software and Data Carpentry?

The Software Carpentry initiative was founded in 1998, and is run by Software Carpentry Foundation. It has the backing of many leading figures in the scientific software community, and over 6000 students worldwide have benefited from the training. In 2012, we were made the UK…

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