Eilis Hannon

Software CarpentryBy Eilis Hannon, University of Exeter.

On Tuesday, 26th September we held a two day Software Carpentry workshop at the University of Exeter. 37 staff and students attended including a number of PhD students in their first week. The course covered the Unix Shell, Python and Git, and gave Jeremy Metz and me the opportunity to teach our first Software Carpentry workshop, alongside Andrew Walker from University of Leeds who was there to steady the ship and provide experience. This was particularly helpful when it came to debugging and resolving common issues.

I was impressed by the sustained enthusiasm over the two days and how much of the content we got through. Many attendees commented that they appreciated the slightly shorter days (from 10am to 4pm) and regular breaks, as these enabled them to remain focused and digest the content delivered. They were also grateful for the additional support provided by the helpers David Richards, Paul O’Neill, Ben Evans…

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Coding RetreatBy Dr Eilis Hannon, University of Exeter, Software Sustainability Fellow.

On Friday 30th June, the first Coding Retreat was trialled at the University of Exeter.  The idea originated from a Writing Retreat I attended, where the focus was to clear all distractions and use the time not just to write but to produce high quality output. This parallels many of the challenges that researchers face when writing software and the idea that there is no time to consider making the code nice or think about how someone else would use it. So it struck me that a Coding Retreat could be a mechanism to provide the discipline to promote good practise. 

Based on the Writing Retreat I attended, the premise was to develop a similar event providing researchers with the time and space to focus and prioritise writing high quality, sustainable software. The workshop was designed to be inclusive; open to any programming language, any discipline and any project. The only requirement was that attendees had a project to work on, either improving or finishing ongoing work or starting something new.

The day started with refreshments and an overview of what the day would involve. The primary objective of the workshop is to use the time, cleared from the usual daily distractions, to produce high-quality code putting into practice all the principles acknowledged…

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Seductive Data

By Eilis Hannon, University of Exeter, Martin Callaghan, University of Leeds, James Baldwin, Sheffield Hallam University, Mario Antonioletti, Software Sustainability Institute, David Pérez-Suárez, University College London.
 

This post is part of the Collaborations Workshops 2017 speed blogging series.

In our daily work we may, at some point, need to access data from third parties that we wish merge or compare with some data that we have generated or obtained. Invariably we may turn to Google to find pertinent data sources. Domain experts may be able to refer us to data sources or in part there are keywords that can unlock what you are trying to find on the web. Alongside, we can filter results using advanced Boolean operators.  In order to make sense of the results, we can consider a number of factors, such as top links and domains that are most relevant to the topic. For specific domains, there will be known and trusted data providers, e.g. the Gene Expression Omnibus (GEO) or the…

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Open sourceBy Alice Harpole, University of Southampton, Danny Wong, Royal College of Anaesthetists, and Eilis Hannon, University of Exeter, Software Sustainability fellows

There has been a collective push in recent years to make all empirical data open access, and this is often a requirement where it has been funded by taxpayers. One reason for this is to improve the overall quality of research and remove any barriers from replicating, reproducing or building on existing findings with the by-product of promoting a more collaborative style of working. In addition to making the data available, it is important to make it user-friendly by providing clear documentation of what exactly it is and how the data was generated, processed and analysed. There are a number of situations, where the key contribution from the research is not simply the underlying data but the software used to produce the findings or conclusions, for example, where a new methodology is proposed, or where the research is not based on any experimental data but instead on simulations. Openly sharing software is as critical here as sharing the raw data for experimental studies. What’s more, there are likely many projects where both the data and software are equally as important, and while there is an expectation to provide the data, this currently…

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DiversityBy Eilis Hannon, Research Fellow in Bioinformatics, in the Complex Disease Epigenetic Group at the University of Exeter.

This post summarises a discussion with Lawrence Hudson, Roberto Murcio, Penny Andrew and Robin Long as part of the Fellow Selection Day 2017.

The question of how to improve diversity is suitably broad and vague to initially induce silence in a group, but eventually, true to its name, it promotes a wide-ranging discussion. Sometimes the task is divided up to target particular under-represented groups, as it starts to become a bit of a minefield to develop a scheme that improves diversity in general. What opens the door to some parts of society can simultaneously close the doors to others. Hackathon events are a common and successful method of attracting young people to computer science; however, if they take place over the weekend and are marketed as providing beer and pizza for sustenance, you start to exclude anyone with caring responsibilities or discourage anyone who doesn’t drink.

Before we can think about trying to improve diversity, it is helpful to consider what exactly do we mean and what are the benefits…

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Bioinformatics Research Fellow, University of Exeter Medical School, University of Exeter

Interests

My research focuses on integrating epigenetic, transcriptomic and genetic data to aid the understanding of the molecular aetiology of brain disorders. I am interested in understating how genetic risk factors for these disorders influence molecular variation in the brain. 

My work

For the last 3 years I have worked as a Bioinformatics Research Fellow in the Epigenetics Group at the University of Exeter. At the end of my undergraduate degree in Mathematics at Cardiff University I wanted to take the knowledge that I had developed and apply it in other contexts. Genetics appealed to me as an opportunity to apply my skills to a cutting edge area of research with the potential to have benefit to patients. 

During my PhD in Bioinformatics at Cardiff University, I gained knowledge in psychiatric genetics and experience of applied statistics by modelling gene expression across brain development. This led to my current position where I am involved in a wide range of research projects primarily focused on integrating different types of ‘omics data to understand the regulation of gene expression in the brain by adapting existing methodologies. 

Increasingly I am involved in teaching programming and bioinformatics skills to staff and students at the University, primarily making use of the Software Carpentry materials. As bioinformatics analyses become more bespoke and complex, there…

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