Software Carpentry

4982558043_06968b80f1_z.jpgBy Mike Jackson, Software Architect

Early March saw us deliver our annual Software Carpentry workshop for the Regenerative Medicine Centre for Doctoral Training at The University of Manchester. I was joined by co-instructors Peter Smyth and David Mawdsley and helpers Nicolas Gruel and Nilani Ganeshwaran from The University of Manchester. Our course was run within the impressive redbrick edifice that is the Sackvile Street Building.

We gave the attendees an introduction to the bash shell, good programming practice using Python, and version control with Git. We started with 20 attendees and ended with 16, which is one of the lower rates of attrition I've seen.

There were the inevitable setup problems arising from attendees having Linux, Windows and Mac OS, and different flavours of Python. This meant that for some attendees, as one commented, "my Anaconda software and what was on the projector was different" and that the course was "sometimes hard to follow."

Of the concepts covered, loops seemed to be the most challenging, for both bash shell and Python, attendees questioning why they are used and in what circumstances. One attendee commented that "Some of the coding vocab is a bit lost on me!" which coincidentaly relates to a recent thread on the Software Carpentry…

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carpentrycon2018Registrations are now open for CarpentryCon 2018 in Dublin. The event will take place from 30th May to 1st June 2018. 

CarpentryCon 2018 is the key networking and community building event in the Software and Data Carpentries' (now The Carpentries') annual calendar. This three-day event will help develop the next generation of research leaders by providing practical skill-ups, networking, workshops and all kinds of discussions.

60-years-of-Computing_badge-artwork.pngBy Blair Archibald, Software Sustainability Institute Fellow

How do you bring research domains together?

This is a difficult question to answer, fields have their own focuses, terminology and idiosyncrasies; what appeals to a researcher in one field may not appeal to a researcher in another. However, with over 92% of researchers suggesting they make use of computational science in their research is it possible that computational techniques could be used to help bridge domains? This post documents my experiences in organising an event aimed specifically at trying to exploit this idea within a single University environment.

60 Years of Computing at Glasgow

Although we have been computing for many decades, Computing Science and the use of electronic computing machines is relatively recent. This year, the School of Computing Science at the University of Glasgow has been celebrating 60 years of Computing at the University of Glasgow. In 1957 they became the first University in Scotland to order a computing machine, an English Electrics DEUCE machine.

As part of these celebrations, myself and a group of fellow Ph.D. students,…

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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.


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