Software and research: the Institute's Blog

Software and reproducible research - best of the tweets

This year's Collaboration Workshop took place between March 26th and 28th at the Oxford e-Research Centre, was a great success. Its theme was software and reproducible research, and ended with a special Hackday where competing teams coded against the clock to create the best software.

Our sponsors this year were Microsoft, GitHub and the Oxford e-Research Centre itself, and we would in particular like to thank Kenji Takeda, Arfon Smith and the OeRC staff for all their help, not to mention all our attendees!

Naturally, lots of tweeting relating to the Workshop (and its hashtag, #CW14) took place before, during and after the event. So here are some of the best and most revealing tweets that resulted, including manatees, rabbits, pizza, writing on the walls and "hardcore Python deployment."

Top tips for writing a press release

Make sure your press release is a right 'ribbiting' read...By Simon Hettrick and Alexander Hay.

Whether you're researching a cure for cancer or the eating habits of the common toad, every now and then you'll want to tell the outside world about your research. It's time for a press release! Here are our five top tips on preparing one.

1. Do you need professional help?

Press releases need to be written in a journalistic style that will appeal to publishers. Most organisations will have press officers whose job it is to write press releases for researchers. This is typically a free service, because it's in your employer's interest to showcase your successes. To find a press officer, ask the faculty member responsible for marketing or contact the marketing department of your university or employer.

Exploring the integration of Subversion and Git with CVS

By Mike Jackson, Software Architect.

Michael Chappell leads the Quantitative Biomedical Inference (QuBIc) research group within the Institute of Biomedical Engineering at the University of Oxford. Michael has developed a method of processing functional magnetic resonance image (MRI) data that can be used to recognise blood flow patterns in the brain. I have been helping Michael through one of our consultancy projects, which he applied for through our open call. Part of our collaboration looked at issues around integrating Subversion or Git repositories with CVS.

QuBIc's method is implemented as part of a C++ code, FABBER, which can be used on its own or via BASIL (Bayesian Inference for Arterial Spin Labelling MRI), a shell-script that provides a richer command-line interface. Both FABBER and BASIL are distributed as part of FSL, the FMRIB Software Library, which is produced by The Oxford Centre for Functional MRI of the Brain, Nuffield Department of Clinical Neurosciences, University of Oxford and the John Radcliffe Hospital.

PyData London 2014

By Mark Basham, Senior Software Scientist, Diamond Light Source and 2014 Institute fellow.

As a scientist, the chance to glimpse inside the world of data analytics in the financial sector was something I was really keen on, and if nothing else, the setting for PyData London did not disappoint. Level 39 is the 39th floor of 1 Canada Square, at the heart of Canary Wharf. Its breath-taking views and modern layout and design made for a really good conference location, and set the mood for the conference well.

PyData is all about using Python to analyse data, and as such the delegates were a mix of academic and commercial programmers, which made for an interesting diversity of presentations and conversation. In addition to this, there was a two track program, the first generally targeted at novice Python users, and the other with more advanced talks.

Supporting and showcasing women in technology

By Catherine Breslin, Cam Women in Tech@CamTechWomen.

This article is part of our series Women in Software, in which we hear perspectives on a range of issues related to women who study and work with computers and software.

Just 17% of the UK’s technical workforce is female, and in many tech companies it’s still worthy of comment when there’s more than one woman in the room. That’s why we set up Cam Women in Tech, to showcase and support women who work in Cambridge’s tech industry.

The lack of diversity in the tech workforce has received increasing amounts of media attention in recent years. The general consensus is that there’s no one cause for the lack of diversity, but that a combination of factors work to steer girls away from the industry long before they leave school. Great initiatives like Lady Geek and Stemettes are working to address the gender imbalance by breaking down stereotypes, and are increasing future numbers by encouraging more girls to consider science and engineering careers.

How a photo from Playboy became part of scientific culture

By Hannah Dee, computer science lecturer, Aberystwyth University.

When I was approached to write a guest post on women in software, my first thought was to try and pull together another post about the leaky pipeline, school science, or girls toys. But that’s not the field in which I do most of my software development. It’s what I tend to pontificate on, but not what I research. I’m a vision researcher. So, could I come up with a computer vision topic that was somehow gendered? Easy!

When doing research in computer vision or image processing, it's useful to have a test image or two. Writing programs that reduce noise, alter brightness, or enhance edges is all very well and good, but without test images, we can't know if they work. Early on in vision science, the acquisition of images was hard, and there were a handful of images everyone used. This was partly due to expediency (not everyone had access to a scanner) and partly due to comparability (we want to be able to see the results of each algorithm on the same image or set of images). Today, nearly everyone has a digital camera as part of the device in their pocket, in the 70s and 80s such devices simply didn't exist.

Top tips for writing a case for a funding a software developer

By Mike Jackson, Software Architect.

You have been developing software that is becoming more popular. But now you are struggling to balance the need to develop and support your software, against the need to do your research. How do you convince funders to give you money to recruit a software developer to keep your users happy?

Here are our top tips in the form of four sets of questions that, by answering, will help you to convince funders.

Reproducible research – an impossible dream?

By Kenji Takeda, Microsoft Research.

Research results in peer-reviewed publications are reproducible, right? If only it was so clear cut. With high profile paper retractions and pushes for better data sharing by funders, publishers and the community, the spotlight is now focussing on the whole way research is conducted around the world.

While research software provides the potential for better reproducibility, most people agree that we are some way from achieving this. It’s not just a matter of throwing your source code online. Even though tools such as Github provide excellent sharing and versioning, it is down to the researcher and developer to make sure the code can not only be re-run, but also understood by others. There are still technical issues to overcome, but the social ones are even harder to tackle. The development of scientific software, choices by researchers, its use and reuse, are all intertwined. We at Microsoft Research are concerned with this: see Troubling Trends in Scientific Software.

"I am used to being in a male dominated classroom" - experiences of an A-level computing student

By Phoebe Chapman, A-level student, Barton Peveril College.

My journey into the unknown field of Computer Science started at an open day held at my college, Barton Peveril. I had not come across computing before and I (naively) thought it was pretty much the same as ICT (Information and Communications Technology), which I had studied at school and wasn’t very keen on. Computing has a lot more application than ICT. In ICT, all we did was take screen shots, hear about how to use Microsoft word and PowerPoint and access files and folders on a computer (all of which everyone knew how to do anyway). In my opinion, students should start learning programming skills at an earlier age, because it is too late to wait until A-level, when most of the important decisions on subjects have already been made.

I have always had an interest in maths and a logical approach to problems, and I was told that these skills would be very useful when studying computing. The idea of putting logic into practice is what encouraged me to try the subject. As I sat in my first-year classroom I was, at first, intimidated by the large number of guys who had been programming for years, and seemed to know a great amount about programming. This turned out not to be a problem, because the lessons were about getting everyone up to a certain standard, and I did not feel left behind. The lessons were interesting: we created programs to carry out all sorts of different functions. It quite quickly became my most enjoyable subject, despite my initial doubts. You really can make a program to do just about anything you want with knowledge of computer science.

Geeks who love the NHS: NHS Hack Days

By Helen Jackson and Carl Reynolds, academic clinical fellow and CEO, Open Healthcare UK.

The NHS Hack Day (NHSHD) series was the brainchild of Dr Carl Reynolds, an academic clinical fellow in respiratory medicine and founder and CEO of Open Healthcare UK. NHS Hack Day, London Edition 2014, will take place in May with the final date to be confirmed very soon. This will be the seventh event in a very successful series of hack events with a healthcare theme. 

On how he had the idea, Carl says "I was whinging about broken NHS IT, and Tom [Taylor] told me about the recent hack day he had participated in at the Cabinet Office and said why not have an NHS Hack Day? It seemed like a good idea, so when we got home we decided to make it happen...".