Software and research: the Institute's Blog

Developing an industry-led mentoring scheme for software engineering undergraduates

By Robert Haines, Caroline Jay and Suzanne Embury, School of Computer Science, University of Manchester

ELIXIR UK Instructor Training at UCL

The Autumn 2015 series of Software and Data Carpentry Instructor Training workshops is in full swing. After two events run at the University of Leeds for the N8 Consortium and at the Imperial College London, the University College of London hosted Instructor Training supported by the ELIXIR UK.

Community update: Fellows 2016, Software Credit and PyCon UK 2015 Science track

By Shoaib Sufi, Community Lead

September was an active month. It’s funny as autumn enters in the UK, the academic world is in spring with new students, new projects and a re-invigoration after the traditional holiday period.

In this month's update read more about how Fellows 2016 is progressing, the rise of the Institute's Software Credit Workshop and other news from the Community.

However, before we start - the Community team is recruiting a Research Software Specialist. If you are keen to run events, support Fellows, build bridges to support research software and gain data about the community to analyse and publish, then this role is for you! Applications close 18 October 2015 - this post is also open to international applicants.

Jupyter Notebook workshop

By Aleksandra Pawlik, Training Lead.

Jupyter is an excellent solution for tacking problems with reproducible research. On 28 September in collaboration with ELIXIR UK, the Institute ran a workshop to introduce researchers to programmatic data manipulation using both tools.

The training was fully hands-on allowing the participants to try out on their own different Jupyter features. In short, Jupyter is an elaborated electronic lab book. It allows the user not only to take notes, embed images, link to resources but most importantly, provides a way to write interactive source code and capture and display the outputs within the notebook itself. Jupyter originated from the very popular IPython Notebook. Currently both, open source projects, are developed separately, albeit there is still a strong connection between them in terms of technology and communities.

Getting started with Travis CI

Automated assembly line

By Mike Jackson, Software Architect.

I have just completed developing an Interoperability test harness for Provenance Tool Suite. As part of this work, I used the TravisCI hosted continuous integration server for the first time. I've now written up walkthrough of Travis CI as part of our Build and test examples on GitHub.

Event for Research Software Engineers starts and ends with a bang at PyCon UK

By Sarah Mount, Research Associate King’s College London and Institute Fellow.

The first ever PyCon UK track for Research Software Engineers ended with a bang, when the conference venue was evacuated following the discovery of a one ton World War II bomb at a local building site! However, there was plenty of explosive material at the event, even before the bomb squad arrived.

You might be wondering, why another track for researchers in a Python conference? The answer isn’t simply that Python is popular in science and data analysis. PyCon UK is a community conference, it has no formal publication associated with it and most delegates come from industry, rather than academia. As such, the focus of the event is on writing high quality, robust, usable software. Research Software Engineers (RSEs) are often woefully under-supported in this area, and the problems posed by writing robust software are often deferred under pressure to produce the next paper or grant application. The Software Carpentry initiative aims to give RSEs a strong and broad grounding in computing skills. With the new PyCon UK track, we wanted to build a supportive community, where RSEs could continue learning beyond the classroom. Because PyCon UK is a community conference, we are in a strong position to provide a sympathetic environment where researchers could meet with professional software engineers to share skills and experiences.

My Software Carpentry work experience

By Jazib Askari, 6th form Student at Altrincham Grammar School for Girls, School’s Twitter feed.

My interest in computer science began when I realised how it acts as an integral part of my everyday life and shapes the world around me. Since I really enjoy studying Maths, I knew Computer Science would be the right path for me because both subjects require a systematic, lateral way of thinking.

In my first year of Sixth Form at Altrincham Grammar School for Girls I decided to undertake Computing as one of my A Level subjects and was surprised when I learned that only two other pupils had chosen it! In my Computing lessons I began learning Python and have gained considerable proficiency in the language. I was driven to constantly modify the code until I found the most efficient solution and enjoyed trying to find the most innovative ways of dealing with problems. Outside of school I decided to teach myself HTML and CSS and I loved to experiment by creating websites in website builders and turning them into my own work using HTML.

Software Carpentry taster sessions at the 5th Student Conference on Complexity Science

By Aleksandra Pawlik, Training Lead.

After running Data Visualisation and Manipulation workshops at the British Science Festival, we decided to run more taster sessions for our training. On 10 September we ran parallel short workshops at the 5th Student Conference on Complexity Science, organised by the University of Southampton, at a beautiful location in Granada. 

We covered version control with Git and an introduction to the command line. The taster sessions were based on the Software Carpentry materials and were fully hands-on, allowing the participants to try out the tools on their own machines. The command line module was taught by Jan Kim of The Pirbright Institute, and I ran the session on Git. 

Both sessions were well received. The groups were smaller than those at the standard workshops which allowed the instructors to answer individual questions from the audience and discuss selected topics in more detail. For Jan, who is a relatively new Carpentry instructor, it was also a great opportunity to gain some experience in delivering Software Carpentry workshops.

Training taster sessions at the British Science Festival

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.

Research Software Group update: improving the packaging of imaging and field theory software, and good feedback

By Steve Crouch, Research Software Group Lead.

During August, the Institute’s Research Software Group has helped developers in the areas of reflectance imaging and field theory to improve the usability and sustainability of their research software. We’ve also heard back from a previous project, where our work continues to realise a significant impact. Our Open Call is still open until 30 September - If you are looking for help with your own research software, why not submit an application?