RiboViz: Understanding protein synthesis via analysis of ribosome profiling data
Latest version published on 24 July, 2019.
By Mike Jackson, Software Architect and Kostas Kavoussanakis, Group Manager, EPCC, The University of Edinburgh; Edward Wallace, Sir Henry Dale Fellow, School of Biological Sciences, The University of Edinburgh A multi-disciplinary team of biologists, bioinformaticians and research software engineers based at EPCC and The Wallace Lab at University of Edinburgh, The Shah Lab at Rutgers University and The Lareau Lab at University of California, Berkeley will enhance and extend a software suite, called RiboViz to extract biological insight from "ribosome profiling" data and drive forward…Talking with the next generation of psychologists about reproducibility and open research
Latest version published on 23 July, 2019.
By Andrew Stewart, University of Manchester and Software Sustainability Institute Fellow. Over the last month or so I’ve been fortunate to have given invited presentations to early career psychologists at the universities of Keele, Staffordshire and Lancaster. The combined Keele/Staffordshire Psychology Postgraduate Research Conference gave me the opportunity to provide some (recent) historical context to the current ‘replication crisis’ in the biosciences.Growing institutional support for RSEs across the UK
Latest version published on 12 July, 2019.
By Louise Chisholm, Jeremy Cohen, Jonathan Cooper, and Simon Hettrick. Most people who are looking to forge a career in research software engineering will come across barriers that are the result of outdated university policies put in place before software was such a critical element of research.Highlights of CarpentryConnect Manchester 2019
Latest version published on 12 July, 2019.
By Aleksandra Nenadic, Training Lead, Software Sustainability Institute CarpentryConnect Manchester 2019 took place from 25th to 27th June 2019. For the first two days, we were in a fantastic, modern, vibrant meeting venue – The Studio – at the very heart of Manchester.The challenges of running a workshop at a major conference (EGU General Assembly)
Latest version published on 8 July, 2019.
By Stuart Grieve, Software Sustainability Institute Fellow. In a previous post, I wrote about the process of and rationale for organising a workshop as part of a large international conference. To recap, as part of my Institute Fellowship, I, alongside colleagues ran a workshop in April at the EGU General Assembly in Vienna, the largest geoscience conference in Europe with over 16,000 attendees.Organising a workshop at the European Geosciences Union (EGU) General Assembly
Latest version published on 5 July, 2019.
By Stuart Grieve, Software Sustainability Institute Fellow Traditionally, geomorphologists have performed analysis of topographic data in an ad-hoc manner using commercially available GIS packages such as ArcGIS. Although many of the tools within these packages are useful for academic research, they are effectively black boxes, due to the closed source nature of the software and are typically controlled through a GUI. Open source variants such as WhiteboxGAT and QGIS, which provide methodological transparency, exist but do not resolve the challenges in documenting and sharing scientific…What does training in software sustainability look like?
Latest version published on 4 July, 2019.
By Mario Antonioletti, Daina Bouquin, Daniel S. Katz, Lucia Michielin, Colin Sauze, and Lucy Whalley. This post is part of the CW19 speed blog posts series. In this blog post, we address the idea of training in software sustainability in the form of questions and answers.How do you motivate researchers to adopt better software practices?
Latest version published on 30 July, 2019.
By Patrick McCann, Rachel Ainsworth, Jason M. Gates, Jakob S. Jørgensen, Diego Alonso-Álvarez, and Cerys Lewis. This post is part of the CW19 speed blog posts series. What are the challenges? For many researchers, the development of software is a means to an end—a chore that is necessary to allow them to get on with the real work of conducting research and publishing papers. They may not see themselves as programmers or recognise the code that they write as being software. Their supervisors or senior colleagues may not see the value of devoting perceived extra effort to following good…Software Metadata Creation and Curation
Latest version published on 2 July, 2019.
By Emily Bell, Radu Gheorghiu, Patricia Herterich, Daniel Hobley, and Sarah Stewart, British Library This post is part of the CW19 speed blog posts series. All attendees of the Software Sustainability Institute Collaboration Workshop 2019 are users or developers of research software, but may not recognise that the production and use of research software demands effective curation and attention to the metadata. We spent a breakout session thinking about where the community is in terms of effective curation of software and its metadata, what the problems still are, and where we can see…Reproducibility and Collaboration Challenges in interactive/exploratory research
Latest version published on 2 July, 2019.
By Adam Jackson, Dav Clarke, Becky Arnold, Ben Krikler, Joanna Leng. This post is part of the CW19 speed blog posts series. At the Software Sustainability Institute’s 2019 Collaborations Workshop, many discussions for the speed-blogging session focused on deposit of relatively fixed data and analysis code.