Software and research: the Institute's Blog

Latest version published on 7 October, 2016.

Tree.jpgBy Elisa Loza, Agent and and scientific statistician, Rothamsted Research.

Evolutionary biology is the branch of biology that studies the evolutionary processes that give rise to the diversity of life on Earth. Understanding these processes is essential to every aspect of our life including the development of crop varieties that are resistant to pests (and, therefore, food security); finding cures to human diseases (for example, there is some similarity between the way cancer develops in one person and the way genes evolve through billions of years); and measuring the impacts of pollution and climate change by studying the variation through time of microbial diversity in marine sediments or soil samples.

Modern evolutionary biology utilises the information from the components that make up all living organisms on Earth: our DNA. By comparing the DNA material of a set of organisms we can understand the relationships that hold amongst them and, ultimately, organise our biological knowledge into a model of ancestry and descent. The model of how all living organisms have evolved from ancestral forms into their present state is usually visualised as a tree of life: the root represents the common ancestor to all life (perhaps a primitive form of cell), the branches indicate the evolutionary paths that ancestors took when diversifying to become new species, and the tips correspond to the organisms that are alive today [1,…

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Latest version published on 7 October, 2016.

Crowd2.jpgBy Simon Hettrick and Neil Chue Hong.

We work with people who share two characteristics: they are involved with research, and that research relies on software. This incredibly diverse group is known as the research software community. It’s a convenient name, but what does it actually mean?

Identifying the people with a vested interest in the use of software in research is of obvious importance to the Institute: it’s our target market. But it’s also of use to the people in research software community. The different groups within the community are reliant on each other – even if they don’t know it. A better understanding of what other people are doing, and the better communication that entails, will help everyone to share ideas, results and solutions.

We’ve identified the three main groups of people (plus two other groups) that we think make up the research software community. Do you agree? Let us know.

The Researcher Who Uses Software

A researcher who uses software is someone whose primary goal is research. Their work is judged on the quality of their scientific output via traditional mechanisms like publications. This person sees the value in software, but only as a means to an end.

By software, we don’t mean the omnipresent variety, like word processing or email clients, because in today’s world that would cover almost everyone. We mean software that has been developed for performing a fundamental part of research. In fact, the software may have been…

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Latest version published on 6 October, 2016.

By Steve Crouch.

The SeIUCCR Summer SchoolCosnersHouse.jpg enables other researchers to learn about tools and techniques for e-Infrastructure, software development and data management to support and improve their science. So last week I made my way up to Oxford to host a session on sustainable software development at this year's Summer School, and based on feedback from participants, this year's School was even more successful than the one held last year.

Targeted at UK doctoral and postdoctoral researchers in the Engineering and Physical Sciences, demand for the School was high - only 30 out of 120 applicants were accepted for the course.

Building on the successful format from last year, attendees heard how e-Infrastructure was helping a number of SeIUCCR Community  Champions in their work. The participants were also taught approaches and practical skills for making the most out of Cloud and Grid infrastructures. For Cloud, these included Amazon's Web Services, Eduserv and Microsoft Azure, with Grid computing aspects provided by the NGS. Practical management of data was also covered by the Digital Curation Centre and the NGS, a topic of particular interest to…

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Latest version published on 30 September, 2016.

TwitterBirdy.jpgBy Simon Hettrick, Deputy Director.

There’s no questioning the success of Twitter. When you wake to John Humphrys telling you about the Today programme’s hashtag, you have to admit that social media is embedded in everyday life. There is an aspect of Twitter that fascinates me: the expert aspect. Can you be an expert in Twitter and, if you can, what does that mean? I haven’t been able to find an answer, so I decided to go back to my physicist roots and conduct an experiment.

My job is to let people know what’s going on here at the Software Sustainability Institute. Twitter is purpose built for this task. From the humble beginnings of a few followers, we’ve now got over 200 (not bad for a young institute, not so good if you’re Stephen Fry) and we are steadily accruing new followers each week. But I wanted more and, like so often in life, that is where my problems started.

The four tenets of Twitter (I reckon...)

There are lots of people out there who will tell you how to gain more followers – if you wish, you can even hire a Twitter consultant. Having looked at quite a few websites and talked to other Twitter users, it appears that the advice boils down to the four tenets of Twitter:

  1. Make tweets interesting
  2. Don’t send out too many tweets, or too few
  3. Retweet others and they will retweet you
  4. Direct message people with interesting content to show that you’re…
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Latest version published on 6 October, 2016.

ThoughtBubble_0.jpgBy Neil Chue Hong.

When you are putting together a proposal either for a new development, or to extend an existing piece of software, it can be useful to use infrastructure to support the writing process. In this post I discuss some tips that can help you whether you're part of an international collaboration or just people within a research group.

1. Use shared calendars and meeting schedulers to agree dates

A shared calendar and a meeting scheduler (e.g. Google Calendar, Doodle) can make it much easier to agree dates for meetings and teleconferences. 

2. Real-time communication is best for discussing ideas and overcoming issues

Whilst face-to-face communication is ideal, if you can't meet physically, tele- or videoconferencing is useful to discuss ideas and overcome problems that require rapid iteration towards a solution.

Real-time chat systems and instant messaging can be useful to initiate quick one-to-one conversations, or to get a quick answer to a question. Group chats (e.g. Skype chat, irc) are useful to keep the proposal writing group informed of progress as an alternative to email.

3. Make sure you can share and edit documents easily

Shared document editing platforms (e.g. Google Docs, wikis) allow many authors to work on a bid document at the same time. It’s important to choose one which keeps a revision history, so you can backtrack if necessary. However, you…

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