Reproducibility

Better software, better COVID-19 research

Author: Mike Jackson
Posted: 30 Apr 2020 | 10:08

A friend recently forwarded me a tweet from Professor Neil Ferguson, director of J-IDEA and the MRC Centre for Global Infectious Disease Analysis at Imperial College London, concerning their COVID-19 pandemic modeller, used by the UK Government:

"I'm conscious that lots of people would like to see and run the pandemic simulation code we are using to model control measures against COVID-19. To explain the background - I wrote the code (thousands of lines of undocumented C) 13+ years ago to model flu pandemics..." @neil_ferguson - 22 Mar

Understanding protein synthesis via analysis of ribosome profiling data

Author: Mike Jackson
Posted: 8 Aug 2019 | 10:51

The molecular structure of a yeast ribosome, composed of 79 proteins

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.

Software deposit guidance for researchers

Author: Mike Jackson
Posted: 8 Aug 2018 | 10:55

Safe deposit boxes

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.

Software Deposit and Preservation Workshop

Author: Mike Jackson
Posted: 24 Jul 2018 | 16:50

Deposit button

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 We reviewed draft guidance on software deposit and preservation, discussed software deposit and preservation from the perspectives of the foregoing stakeholders, and explored ways in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.

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