Software and research: the Institute's Blog
By Sam Relton PhD student, University of Manchester.
Reposted with permission from the original blog post.
The Software Sustainability Institute, Mathworks, and the Software Carpentry group recently collaborated to run a course at Manchester University. The event was designed to teach best practices in software engineering to young researchers and mainly focused on three points:
- the command line and shell scripting (mainly in Bash).
- version control, and in particular Git.
- data manipulation, unit testing, and performance considerations in MATLAB.
In this post I’ll highlight what I took away from the course and give links to some useful information.
Posted by s.hettrick on Monday 3 February 2014.
By Steve Crouch, Consultancy Leader.
The Institute's Open Call for projects helps researchers get the most out of the software they develop.
We are working the QuBIc research group at the University of Oxford to increase the uptake and transparency of their BASIL and FABBER MRI (magnetic resonance imaging) software. The Institute reviewed QuBIc's code, documentation and tutorials to find ways in which they could be improved. We advised on how to make the software more understandable to users, and how to make the code more configureable and maintainable, by improving the readability of the code and publishing its architecture. Working closely with the software's developers, the Institute will continue to help them refine these aspects, as well as the architecture of the code and its accessibility for others.
Posted by s.crouch on Friday 31 January 2014.
There’s a lot of talk about cloud computing, but what does it really mean for researchers? Of course, it’s not about the technology, but what we are trying to achieve with it. This varies enormously across disciplines, teams, and individual researchers, but the same stories come back time and time again: meeting paper deadlines, reproducible research, data sharing, and now big data.
What is cloud computing exactly? Well, it can be defined in different ways, but from a researcher’s perspective a nice way of summing it up is: getting what you need, when you need it.
Posted by s.hettrick on Thursday 30 January 2014.
This article is part of our series: a day in the software life, in which we ask researchers from all disciplines to discuss the tools that make their research possible.
Computer games are a big part of our lives. The size of the world games market is set to grow to $78 billion by 2017. In the UK, 40% of people have played games in the last twelve months. In other words, computer games and their role in society warrant serious research.
With this in mind, the University of Lincoln will launch the Games Research Group (CRG) on 13 March 2014 at the AHRC Creative Economy Showcase. The group's aim is to bring together staff and students to work on a wide range of research. For example, we will look into the role of social computing in how games are played, and how autonomous systems can be used to improve gameplay. We will also work on vision engineering, which is in the news right now thanks to the motion sensor design of the Xbox One.
Posted by a.hay on Wednesday 29 January 2014.
The ability to communicate your work is vital, whether you are a researcher, software developer or manager. Lightning talks are a popular way of allowing many people to talk about their work in a short time, and making it easy to work out who you should grab for a conversation at the coffee break. (They're popular at workshops, like our Collaborations Workshop.). For many, the idea of giving a talk under such strict timing can be terrifying. These top tips will help you become an electrifying lightning talk presenter.
1. Finish on time
This applies to all presentations, but is especially important for a lightning talk! If you don’t finish on time, the audience will have missed a part - a potentially fundamental part - of your talk. Rehearse your timings a number of times (you can even do this in front of a mirror or a friendly audience). Learn your style - most people speed up when presenting in front of an audience, but some slow down or elaborate more. Write a script if it helps to time the talk, but don't read from the script when you present for real.
Posted by n.chuehong on Tuesday 28 January 2014.
This article is part of our series, a day in the software life, in which we ask researchers from all disciplines to discuss the tools that make their research possible.
If Google were an artist, what would it paint? Perhaps it would be a vast landscape of connections, a world of “lines of light ranged in the nonspace of the mind, clusters and constellations of data. Like city lights, receding” as William Gibson put it.
Posted by a.hay on Monday 27 January 2014.
R is a well-established environment for statistical computing. It is often seen as an alternative to computing environments such as matlab or python. In this post, we give our five reasons for why we chose to use R for research.
R generates beautiful graphics with minimal effort. Publication-quality plots can be rendered in a wide range of vector- and raster-based formats. Recent extensions to the plotting system allow for complex visualisations to be expressed succintly. See R Graphics Gallery for example plots along with the code that generated the plots.
R comes with a robust packaging system to allow developers and domain experts to easily distribute their code. Packages come complete with documentation, vignettes (see point 3 below), and data files. Windows and Mac users can download packages in binary form, where C and Fortran code is pre-compiled. As of January 2013, the Comprehensive R Archive Network (CRAN) contains 5088 packages. The packaging build system is rigourous to ensure that packages will work for for other users. Within the field of Computational Biology, the Bioconductor project has 749 packages. Many packages accompany scientific papers within Computational Biology such that it typically takes under a minute between reading about a method in a paper and using it.
Posted by a.pawlik on Friday 24 January 2014.
By Simon Hettrick, Deputy Director.
During an in-depth discussion about the Institute, Mike Jackson (our Software Architect) summarised our raison d'être by saying "Better software, better research". A simple four-word phrase that perfectly describes the Institute's philosophy. Until that date, no one was aware of Mike's gift for poetry.
Of course, such a snappy phrase had to be emblazoned on a T-shirt. But it wasn't until we started wearing the T-shirts that we discovered that Better Software, Better Research chimed with a lot of people in the research community, and that many of them wanted a T-shirt for themselves. To fulfil this demand, we have now set up a T-shirt shop at Spreadshirt.
If you think that better software leads to better research, you can now buy a T-shirt and tell the world.
Posted by s.hettrick on Thursday 23 January 2014.
By Mike Jackson, Software Architect.
Software support can be a double-edged sword. On the one hand, requests for help prove your software has users. On the other hand, calls for assistance can come in at any time regardless of whether you’re busy or not. These top tips will help you manage support requests to the benefit of both your users and yourself.
1. Put yourself in the user's shoes
Users may have little, if any, software development knowledge or experience. Design your software and support materials from their perspective.
2. Treat each user as an individual
You can tell a lot about a user from what and how they compose their support request. Compare "I've got an error" to "I had a NullPointerException and here is my log file and parameter file". Tailor the advice you give to each individual and don’t rely on one size fits all responses.
Posted by m.jackson on Tuesday 21 January 2014.
The Software Sustainability Institute was asked to take part in the debate about the employability of computer scientists and the ideas that have been proposed to help the situation. For our next post on the issue, we wanted a perspective from a computer science department, so we are very pleased to publish this post from Joyce Lewis at the University of Southampton.
By Joyce Lewis, Senior Fellow for Partnerships and Business Development at the University of Southampton.
It all depends what you mean by computer scientists... The statistics collected by UK universities through the annual DHLE (Destinations of Leavers from Higher Education) appear to show that a number of graduates from courses that have the words Computer or IT in their titles are not in graduate-level jobs six months after graduation, and that this constitutes the highest proportion by subject of any graduates. However, a very large number of degree programmes are grouped under the Computer Science/Software/IT heading, and there is considerable variation in the employability figures between similar courses even at the same university.
Posted by s.hettrick on Friday 17 January 2014.