Mike Jackson's blog

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 understanding of protein synthesis.

EPCC is providing ongoing technical support to Edinburgh-based property management company DJ Alexander as it expands across the UK in conjunction with the release of its revolutionary software platform, Apropos. It has been very rewarding to work with DJ Alexander, helping them develop a software solution that facilitates rather than constrains their expansion and helps contribute to their continued success.

In our role as members of the Research Engineering Group of the Alan Turing Institute, Anna Roubickova and I worked with Efi Tsamoura and Benjamin Spencer (Department of Computer Science at the University of Oxford) on PDQ, a proof-driven query planner that has great potential within the realm of data science for medical research. 

PickCells is image analysis software developed by the Centre for Regenerative Medicine (CRM) at The University of Edinburgh. PickCells allows biologists to explore multidimensional biological images of stem cell niches, organoids, and embryos. In late October, with the assistance of six researchers, we evaluated the usability of PickCells to help guide its future development.

To run our usability evaluation, we followed Steve Krug's highly-recommended and very readable book "Rocket Surgery Made Easy: The Do-It-Yourself Guide to Finding and Fixing Usability Problems". This book describes a practical way to carry out usability evaluations with minimal overhead.

PickCells is an image analysis platform developed by the Centre for Regenerative Medicine (CRM) at The University of Edinburgh. It combines generic image analysis algorithms, visualisation modules and data mining functionality within a stand-alone Java application.

The Software Sustainability Institute has published a set of guides to depositing research software into digital repositories. The guides, development of which was funded by Jisc, are intended for researchers, principal investigators and research leaders, and research data and digital repository managers.

Research software is an integral part of the modern research ecosystem. Taken together, research software – alongside data, facilities, equipment, and an overarching research question – can be viewed as a research activity or experiment, worthy to be published. Conversely, a publication can be considered as a narrative that describes how the research objects are used together to reply to the research question.

On the 11th July, the Software Sustainability Institute and Jisc ran a Software Deposit and Preservation Workshop at St Anne's College, Oxford. This workshop brought together twelve research data managers, digital repository vendors, publishers, policymakers and researchers. We reviewed draft guidance on software deposit and preservation, discussed software deposit and preservation from the perspectives of the foregoing stakeholders, and explored ways in which to drive forward the adoption of best practices in software deposit and preservation.

In October I attended GRADnet's "Moving Forward for 2nd Year PGRs" day in London for physics post-graduates, and ran two sessions on "Writing better software to research".

SEPnet, the South East Physics Network, is a consortium of universities in the south east of England. It promotes excellence in physics in both academia and industry via research, collaboration, training, and outreach. GRADnet is SEPnet's collaborative graduate school which provides professional skills training to PhD students.

GRADnet's "Moving Forward for 2nd Year PGRs" day offered attendees a choice of 5 sessions both morning and afternoon, on 'Creating impact', 'How to write a successful Fellowship application', 'Research data management', 'Unconscious Bias', and 'Writing better software for research'. Sixty-six students attended the event.

The Software Sustainability Institute’s Collaborations Workshop 2015 (CW15) will be held from 25-27 March 2015 in Oxford, UK.

CW15 focuses on software, best practice and the social side of working past the boundaries of traditional disciplines and roles to accelerate research outcomes. Or, put differently, interdisciplinarity done right!

EPCC helped lead the way in creating the standardised Message-Passing Interface (MPI) programming system to enable faster, more powerful, problem solving using parallel computing. It is now the ubiquitous de-facto standard among both hardware and software vendors.

Mike Jackson and Dan Holmes explain how EPCC continues to be involved in its development and use.