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.

Library CarpentryWhat is Library Carpentry?

Library Carpentry introduces librarians to the fundamentals of computing and provides them with a platform for further self-directed learning, based on similar initiatives Software Carpentry and Data Carpentry.

Library Carpentry is made by librarians, for librarians to help them:

  • automate repetitive, boring, error-prone tasks

  • create, maintain and analyse sustainable and reusable data

  • work effectively with IT and systems colleagues

  • better understand the use of software in research

  • and much more…

How it started?

Library Carpentry was started by James Baker, Software Sustainability Institute Fellow 2015. James used his Fellowship funds to launch initial Library Carpentry workshops, which attracted 59 participants from 14 institutions in London and reached 200-250 librarians. Since then, a number of workshops have run in various countries across four continents.

Find out more about the Library Carpentry activities.


There are still some places left at the Data Carpentry for Social Scientists and Humanities workshop organised by the SSI Fellow 2016 Heather Ford at the University of Leeds on 21-22 November 2016. 

This two-day event is aimed at researchers in the social sciences, humanities and other disciplines who want to learn how to use popular tools for data cleaning, management and visualisation in a hands-on, interactive workshop. 

James Baker accepts British Library Labs awardLibrary Carpentry (lead by the James Baker, Software Sustainability Institute Fellow 2015) wins the British Library Labs 2016 award for Teaching and Learning on 7th November 2016.

James is using the award fund to run even more Library Carpentry workshops (see the Library Carpentry workshop call).

What is Library Carpentry?

Library Carpentry is made by librarians, for librarians to help you:

  • automate repetitive, boring, error-prone tasks
  • create, maintain and analyse sustainable and reusable data
  • work effectively with IT and systems colleagues
  • better understand the use of software in research
  • and much more…

Library Carpentry introduces you to the fundamentals of computing and provides you with a platform for further self-directed learning. Find out more about Library Carpentry activities.

British Library Labs Awards 2016

The annual BL Labs Awards, introduced in 2015, recognises outstanding and innovative work that has been carried out using the British Library’s digital collections and data. This year, they commend work…

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Data Carpentry is programme inspired by Software Carpentry. Both programmes maintain close ties which helps to build a community of practice among the instructors and expand the base of teaching materials. Data Carpentry aims to teach the skills that will enable researchers to be more effective and productive in working with data.

As an official Data Carpentry Foundation Partner, we coordinate Software Carpentry activities in the UK by helping organise workshops for the UK research community. For more information about our collaboration with Data Carpentry or organising a Data Carpentry workshop in the UK, email us at

What is Data Carpentry

Data Carpentry Foundation is a sister organisation of Software Carpentry Foundation designed to teach researchers skills to retrieve, view, manipulate, analyse and store their or other people's data in an open and reproducible way.

Data Carpentry workshops have been running since 2014. As in Software Carpentry, teaching is delivered through intensive two-day workshops. Contrary to Software Carpentry, Data Carpentry designs the…

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aleksandra_1.jpgTraining Lead

Aleksandra leads the Institute's training activities. She holds a PhD in Computing from the Open University and her PhD research focused on documentation in scientific software.

Outside of academia, Aleksandra has worked as a researcher for NHS Lothian projects and as a freelance IT consultant in the commercial sector.

Aleksandra supports the development of Software and Data Carpentry initiatives. She is one of Software and Data Carpentry certified instructors and taught at a number of workshops in the UK, other European countries and US. Aleksandra is a member of the Data Carpentry Steering Committee and served as a member of Software Carpentry Steering Committee in 2015. She's also supporting the Institute's collaboration with the Centers for Doctoral Training in the UK.

Read posts on this website by Aleksandra.

EPCC's Andy Turner developed some JavaScript to visualise the usage of applications running on ARCHER, the UK national super-computing service. The visualisation of data in this way reminded me of how the Institute had visualised research data for a poster. I decided to spend a bit of time making Andy's scripts more general, so they could also be used to present Institute data including how much effort we've spent on consultancy, and who with, and how many researchers we've trained via Software Carpentry workshops.

At present, these scripts are prototypes and render sample data from static CSV files. We'd hope, in time, to have these CSV files dynamically updated weekly or monthly from the Google spreadsheets where we record our data. 

Please contact us if you have any suggestions on what data on our activities you think we should visualise and how best we could visualise it. Alternatively add your suggestions as issues on its GitHub repository.

(Please note that we're trying out these visualisations based on a static data set, so they're not up to date).

Updated: (07/03/16) the visualisations are now available HERE!

By Aleksandra Pawlik, Training Lead.

Last week the Institute ran workshops on Data Visualisation and Manipulation at the British Science Festival. The workshops were based on Software and Data Carpentry, providing an introduction to the computational lab skills and tools essential for modern research.

The Data Visualisation session focused on using Jupyter Notebook and Python together with two of its very popular scientific libraries: NumPy and matplotlib for analysing and plotting data. The training materials were from the Software Carpentry Python Novice materials. The afternoon session covered structured data manipulation using SQL. For this session we used the Data Carpentry materials Structured data - SQL for ecology. All of these materials are available for reuse under the CC-BY licence.

The sessions were held as a part of the British Science Festival which this year was hosted at the University of Bradford. Thanks to the organisers, the sessions were run in a top-notch computer laboratory (although the lack of a projector caused some problems for this kind of hands-on workshop).

I ran the training on the first day, whilst the day two sessions were run by two Software Carpentry volunteers: Anthony Harrison and Dave Jones.…

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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.

After running two hackathons and workshops hosted by ELIXIR Finland and ELIXIR Netherlands Aleksandra Pawlik, the Institute’s Training Lead, co-ran a Data Carpentry workshop hosted by ELIXIR Slovenia. The workshop for 30 attendees was delivered at the Faculty of Medicine, University of Ljubljana and the National Institute of Biology in Ljubljana. The other instructors were Aleksandra Nenadic (ELIXIR-UK Training Coordinator for Infrastructure Technology and University of Manchester) and Peter Juvan (Faculty of Medicine, University of Ljubljana, ELIXIR SI).…

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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?


Thus, a typical user training session often comprises a journey through the user interface using a simple input, running a calculation and analysing the output. An input (in our field) is usually graphical in nature and…

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