Software and research: the Institute's Blog

Latest version published on 15 August, 2017.

Learning programming for non-programmersBy Thomas Etherington, Senior Research Leader, Royal Botanic Gardens, Kew, and Institute Fellow.

One of the Software Sustainability Institute’s missions is to increase programming skills through training. So as part of my Software Sustainability Institute Fellowship, and with support from the Royal Geographical Society, I am organising an introductory programming workshop targeted at geographers. However, as well as telling people what they need to know from the perspective of someone with programming skills, I also think it is important to understand how learning computer programming is viewed from the non-programmer's perspective so that the training can be made as effective as possible. Therefore, the application process for attending the workshop involved a survey that asked non-programmers questions about their perceptions of computer programming.  I’ve summarised here what I think are some interestingly consistent themes and how these will affect the design of my workshop.

I had a total of 18 applicants for the workshop, the majority of whom had interests in human geography, so the following does need…

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Latest version published on 11 August, 2017.

Computational NeuroscienceBy Stephen Eglen, University of Cambridge.

The annual Computational Neuroscience meeting was held this July in Antwerp, Belgium. This is a well-established meeting for researchers to discuss matters around computational modelling and analysis of neuronal systems. Although computational simulation and analysis is at the heart of this field, historically there has been little evidence of sharing of code. I was pleasantly surprised, however, to discover at the meeting that many leading labs now embrace open science. Below I outline my key observations based on observing and presenting at two workshops.

Workshop 1: Recent methods and analyses for neuronal population recordings

Recent technological developments mean that it is now possible to record the spiking activity of many hundreds or thousands of neurons simultaneously. This workshop described some of these recent techniques and the challenges for data analysis. Two themes of general interest emerged in my view from the first day:

  1. People are now sharing their computational methods; most speakers at the workshop already made…

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Latest version published on 9 August, 2017.

Berlin summer schoolBy Ben Marwick, University of Washington and University of Wollongong.

Recently we concluded the 2017 Summer School on Reproducible Research in Landscape Archaeology at the Freie Universität Berlin (17th–21th July), funded and jointly organised by Exc264 Topoi, CRC1266, and ISAAKiel. With a group of 15 archaeologists and geographers from Berlin, Kiel and Cologne, we spent a week learning advanced geostatistics and how to make our research more reproducible.

Reproducibility is a relatively new concept for archaeology; it has only recently received some attention, and so we encountered many challenges in teaching and learning this unfamiliar subject. The general idea is that a piece of research, such as a publication, should contain enough information for another researcher to reproduce the results in that paper. In former times, when archaeology was simpler than today, this was relatively straightforward. However, that is not the case nowadays, with computers and complex software and algorithms…

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Latest version published on 17 August, 2017.

MONC By Selina Aragon, Communications Officer, in conversation with Adrian Hill, Met Office

This article is part of our series: Breaking Software Barriers, in which we investigate how our Research Software Group has helped projects improve their research software. If you would like help with your software, get in touch.

Adrian Hill, the project’s primary contact, talked to us about the usefulness of the Institute’s collaboration with the Met Office and EPCC to promote the uptake and development of MONC. Adrian especially highlighted the invaluable help he received from Mike Jackson, Research Software Engineer, in setting up the basis for what has progressed into successful software with unexpected benefits and long-term value, used by researchers as well as PhD and masters' students.

Collaborative efforts

In collaboration with EPCC (Edinburgh Parallel Computing Centre) and the Met Office, the Institute provided help to rewrite the Large Eddy simulation model (LEM) as its successor, the Met Office NERC cloud (MONC). MONC is a complete re-engineering of LEM, which preserves LEM's underlying science. MONC has been developed to provide a flexible community model that can exploit modern supercomputers…

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Latest version published on 11 August, 2017.

Video and Reproducibility in the Behavioural SciencesBy Joy Lorenzo Kennedy (Scientific Support Specialist), Karen Adolph (Principal Investigator), & Rick O. Gilmore (Principal Investigator)

Behavioural researchers are under fire due to low levels of reproducibility; more than half of the findings from psychological studies cannot be replicated. On the reasonable assumption that both the original researchers and the replication team are competent, why are they getting different results? Inability to replicate findings might be a side effect of the inability to reproduce methods and procedures with sufficient fidelity. In fact, as behavioural research expands beyond its traditional white, middle-class participant base, one of the most notable findings is the extent to which small differences in context create differences in behaviour and development. As such, slight variations in instructions, stimuli, procedures, experimenters, testing room, and so on can lead to different outcomes. No matter how detailed the method section in published works, full explication of a methodology is impossible due to the limitations of text and static images to convey the full richness of the testing situation. This makes it difficult to ensure that researchers can truly…

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