gleeming1.pngBy Gary Leeming, University of Manchester.

The European Federation for Medical Informatics (EFMI) is the leading European organisation for medical informatics in Europe, representing 32 countries. Each year the Special Topic Conference (STC) is an opportunity to look in more detail at a specific area of research. Held in Tel Aviv, the 2017 conference's topic was "The practice of patient centered care: empowering and engaging patients in the digital era".

In their own words: "This conference will provide a platform for researchers, data scientists, practitioners, decision makers and entrepreneurs to discuss ways for sustainable and inclusive digital health innovations aimed at patient's/consumer's engagement and empowerment." Welcome Letter | STC 2017

In line with this objective the conference, held on a single day, was a fantastic opportunity to learn more about engaging patients in their own care and participating in research, and to present the work we have been doing here in Manchester with our own Public Experience Group (PEG).

The keynote presentation by Dr Kira Radinsky, chief scientist at eBay and a visiting professor…

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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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Supercomputer-promo.jpgToday’s supercomputers are the most powerful calculating machines ever invented, capable of performing more than a thousand million calculations every second. This gives scientists and engineers a powerful new tool to study the natural world—computer simulation.

This free 5-week online course will introduce you to what supercomputers are, how they are used and how we can exploit their full computational potential to make scientific breakthroughs. Register for the upcoming run on 15th January at Future Learn

This course was developed by EPCC at the University of Edinburgh and by SURFsara as part of the EC-funded PRACE project.

26215728419_e6bd12a04a_z.jpgBy Raniere Silva, Software Sustainability Institute, Yo Yehudi, InterMine, Cambridge University, David Pérez-Suárez, University College London.

The Mozilla Festival, or MozFest for short, is “an annual gathering of passionate thinkers and inventors from around the world who meet to learn from each other and help forge the future of the web" as described in the Mozilla Wiki. It started in 2010 in Barcelona but has been hosted in London since its second edition, in 2011. The event is a multi-massive-parallel session of debates and workshops. We attended the gathering to share ideas with Mozilla Open Leaders and other attendees interested in open science. Keep reading to find our top six highlights of MozFest 2017.

Open science public park

Some unconferences only have a open agenda, but others reinvent the whole space where it is happening. MozFest is in the second group, as you can see from the photo montage below. The photo in the right shows Naomi Penfold's activity, called…

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38449949554_d3c3ccd279_z.jpgBy Raniere Silva, Community Officer.

2018 started and my New Year resolutions are: using version control in all projects, commenting on my scripts, writing documentation for my packages, including tests for the code that I develop, taking advantage of continuous integration, providing virtual machine or containers for users, being more productive, and being more sustainable. Are any of those on your list too? If the answer is "yes", then our Collaborations Workshop 2018 (CW18) is a must go event for you this year. You can register now for CW18, which will take place on 26–28 March 2018 at Cardiff University.

Our Collaborations Workshop series is held in a unique ‘unconference’ style format that will definitely help you cross some of those New Year resolutions. The Hackday will be especially useful, as attendees form teams, get to know other, work for 24 hours in an idea using all sort of best practices and compete for generous prizes— in previous years we had Amazon Echo and Raspberry Pi 3 kits as prize.

The first two days…

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The Software Sustainability Institute are pleased to announce figshare as Platinum Sponsor of the Collaborations Workshop 2018 (CW18).

figshare is a repository to share and get credit for all of your research outputs including papers, data, media and code. They were a launch partner with Mozilla and Github in the ‘code as a research object’ project which promotes researchers getting credit for their code. figshare has an integration with Github that allows you to snapshot, archive, get a citable DOI for your code and track the online attention through Altmetric. Recent analysis of the figshare corpus shows that code is 8 of the top 10 cited items. figshare also supports preview of IPython Notebook/Jupyter Notebooks in browser!

Attendees of CW18 will have the opportunity to interact with figshare experts and learn new ways to be more productive when getting credit for their work. Register today for the Collaborations Workshop 2018, which will take place from Monday 26th to Wednesday 28th March 2018 at The School of Mathematics, Cardiff University.

By Edward Smith, Imperial College London.

The Research Software Engineer (RSE) 2017 conference started with an excellent keynote talk by Chris Woods, emphasising a number of issues. This set the tone for the conference, outlining the aspiration of developing the RSE community and changing perceptions. There seems to be clear progress in this area and a number of challenges still to face. One issue that came up was the misalignment of aspiration in the university selection processes for RSE fellowships candidates compared to those in the national RSE community. For me, the most interesting point was Chris’ emphasis on letting people use the technologies they feel most comfortable with, when working as an RSE. This was a theme from the conference that continued with no less than four talks by software engineers working at or with the MET office. Weather prediction is unique in that it is scientific software with a direct and constant validation, often by angry people without umbrellas. It is also an area where code and hardware reliability is crucial. They have an entire standby supercomputer in case the main one goes down and an extensive testing framework. In this context, it is therefore interesting that the MET RSEs are working on rewriting the entire HPC…

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cardforfellows(hols2018).jpgEveryone at the Software Sustainability Institute wishes our friends and colleagues all the best for the holiday season.

In a nutshell, this year has seen the announcement of a wonderful new set of Fellows, a second edition of the RSE conference, even more events, Software and Data Carpentry workshops, and Open Call projects.

After a busy year, we need a little break to get ready for everything we plan to do in  2018, like our Collaborations Workshop 2018. So please excuse us while we switch off our email and social media from the 23rd December to the 3rd January.  

Enjoy the festivities!

Assigning fellows applicationsBy Raniere Silva, Community Officer

A few people have asked us how we run certain processes at the Institute. This time, we will look at how we assigned Fellowship programme 2018 applications to our reviewers.

Data repository

We used Google Forms to collect applications as, from experience in previous editions, we know that Google Spreadsheet works well for reviewers as they are familiar with the platform and usually have a Google account. Google Drive then allows us to share the data the reviewers need and use "Microsoft Excel programming language" to summarise the result of the reviews.

On the master spreadsheet each reviewer has a sheet with their initials, where they will find all the information needed to assess the candidates, with relevant columns to mark their thoughts. Data validation helps reviewers input correct values.

Sheet generation

To generate each of the reviewers’ sheet we use pandas and PuLP, both Python libraries. Pandas allows us to interact with raw data stored in a tabular form as a Google Spreadsheet and to create local CSV files. PuLP is a linear optimisation

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Motivate Better Practice in Research SoftwareBy James Grant, University of Bath, Andrew Washbrook, University of Edinburgh, Louise Brown, University of Nottingham, Niels Drost, Netherlands eScience Center, and Andrew Bennett, European Centre for Medium-range Weather Forecasts

What can be termed as "coding" is a subset of wider software engineering practices such as version control, continuous integration and good software design. Coding is prevalent in academia but practices that allow sustainable software to be produced are frequently overlooked.  Motivating the uptake of the approaches, methods and tools, and highlighting the benefit they deliver, by engaging with researchers who develop software is the first step in spreading best practice in our community.

In discussions with researchers, we find that the use of version control is often highlighted as the first methodology that they would like to introduce into their workflow. We would therefore like to 1) identify approaches that can promote the use of version control by reducing barriers from textbook to full integration and 2) highlight the wider benefits of the methods beyond traditional software development.

Software related courses at an undergraduate level tend to focus on code syntax and functionality with limited time spent covering software management practices.  By including the use of version control as part of these training programs we can avoid much…

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