Software Sustainability Institute
Software Sustainability Institute
Vos R.A.,Naturalis Biodiversity Center |
Biserkov J.V.,Pensoft Publishers |
Balech B.,National Research Council Italy |
Beard N.,University of Manchester |
And 31 more authors.
Biodiversity Data Journal | Year: 2014
Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source "data enrichment" workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools and visualisation. Most use cases and exemplar data were provided by taxonomists. One goal of the meeting was to facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as taxonomists, systematists, ecologists, niche modelers, informaticians and ontologists. The suggested use cases resulted in nine breakout groups addressing three main themes: i) mobilising heritage biodiversity knowledge; ii) formalising and linking concepts; and iii) addressing interoperability between service platforms. Another goal was to further foster a community of experts in biodiversity informatics and to build human links between research projects and institutions, in response to recent calls to further such integration in this research domain. Conclusions: Beyond deriving prototype solutions for each use case, areas of inadequacy were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilising biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalisation of the concepts (and the links between them) that define the research domain, as well as increased interoperability between the software platforms that operate on these concepts. © Vos R et al.
Agency: GTR | Branch: EPSRC | Program: | Phase: Training Grant | Award Amount: 3.94M | Year: 2014
The achievements of modern research and their rapid progress from theory to application are increasingly underpinned by computation. Computational approaches are often hailed as a new third pillar of science - in addition to empirical and theoretical work. While its breadth makes computation almost as ubiquitous as mathematics as a key tool in science and engineering, it is a much younger discipline and stands to benefit enormously from building increased capacity and increased efforts towards integration, standardization, and professionalism. The development of new ideas and techniques in computing is extremely rapid, the progress enabled by these breakthroughs is enormous, and their impact on society is substantial: modern technologies ranging from the Airbus 380, MRI scans and smartphone CPUs could not have been developed without computer simulation; progress on major scientific questions from climate change to astronomy are driven by the results from computational models; major investment decisions are underwritten by computational modelling. Furthermore, simulation modelling is emerging as a key tool within domains experiencing a data revolution such as biomedicine and finance. This progress has been enabled through the rapid increase of computational power, and was based in the past on an increased rate at which computing instructions in the processor can be carried out. However, this clock rate cannot be increased much further and in recent computational architectures (such as GPU, Intel Phi) additional computational power is now provided through having (of the order of) hundreds of computational cores in the same unit. This opens up potential for new order of magnitude performance improvements but requires additional specialist training in parallel programming and computational methods to be able to tap into and exploit this opportunity. Computational advances are enabled by new hardware, and innovations in algorithms, numerical methods and simulation techniques, and application of best practice in scientific computational modelling. The most effective progress and highest impact can be obtained by combining, linking and simultaneously exploiting step changes in hardware, software, methods and skills. However, good computational science training is scarce, especially at post-graduate level. The Centre for Doctoral Training in Next Generation Computational Modelling will develop 55+ graduate students to address this skills gap. Trained as future leaders in Computational Modelling, they will form the core of a community of computational modellers crossing disciplinary boundaries, constantly working to transfer the latest computational advances to related fields. By tackling cutting-edge research from fields such as Computational Engineering, Advanced Materials, Autonomous Systems and Health, whilst communicating their advances and working together with a world-leading group of academic and industrial computational modellers, the students will be perfectly equipped to drive advanced computing over the coming decades.
Crouch S.,Software Sustainability Institute |
Crouch S.,University of Southampton |
Hong N.C.,Software Sustainability Institute |
Hong N.C.,University of Edinburgh |
And 16 more authors.
Computing in Science and Engineering | Year: 2013
To effect change, the Software Sustainability Institute works with researchers, developers, funders, and infrastructure providers to identify and address key issues with research software. © 2013 IEEE.
Contrastin M.,University of Cambridge |
Rice A.,University of Cambridge |
Danish M.,University of Cambridge |
Orchard D.,Imperial College London |
Orchard D.,Software Sustainability Institute
Computing in Science and Engineering | Year: 2016
The authors argue that they can increase confidence in Fortran programs with unit annotations and CamFort units-of-measure analysis. © 2016 IEEE.
MacLean D.,Norwich Research Park |
Aleksic J.,University of Cambridge |
Alexa A.,DNAdigest |
Attwood T.K.,University of Manchester |
And 14 more authors.
F1000Research | Year: 2015
One of the foundations of the scientific method is to be able to reproduce experiments and corroborate the results of research that has been done before. However, with the increasing complexities of new technologies and techniques, coupled with the specialisation of experiments, reproducing research findings has become a growing challenge. Clearly, scientific methods must be conveyed succinctly, and with clarity and rigour, in order for research to be reproducible. Here, we propose steps to help increase the transparency of the scientific method and the reproducibility of research results: specifically, we introduce a peer-review oath and accompanying manifesto. These have been designed to offer guidelines to enable reviewers (with the minimum friction or bias) to follow and apply open science principles, and support the ideas of transparency, reproducibility and ultimately greater societal impact. Introducing the oath and manifesto at the stage of peer review will help to check that the research being published includes everything that other researchers would need to successfully repeat the work. Peer review is the lynchpin of the publishing system: encouraging the community to consciously (and conscientiously) uphold these principles should help to improve published papers, increase confidence in the reproducibility of the work and, ultimately, provide strategic benefits to authors and their institutions. © 2015 Aleksic J et al.
Goble C.,University of Manchester |
Goble C.,Software Sustainability Institute
CEUR Workshop Proceedings | Year: 2016
Mismatches between users and producers of software, or indeed producers and funders of software, lead to misery. We propose a simple software project "reciprocity" framework from the perspective of the producer, covering 4 areas and 12 characteristics. By plotting the relative degree of some or all characteristics even subjective or rule of thumb values give project profiles. Such profiles can be useful tools for comparing projects against their own expectations and desires, to review and compare project types and identify user-producer reciprocity misalignments. © 2016, CEUR-WS. All rights reserved.
Sufi S.,Software Sustainability Institute
CEUR Workshop Proceedings | Year: 2016
Reproducibility, capability building, version control, testing, documentation, big data, data science, data management, expert coding, the list goes on. However it is the social side of software sustainability that allows the increase of capabilities and practices to permeate different research teams and domains thus supporting the culture change required for better computational research. In this paper we describe one of the mechanisms run by the author, who is the Community Lead at the Software Sustainability Institute, to help support the social side of research software; the Institute's Fellowship programme. © 2016, CEUR-WS. All rights reserved.
Agency: GTR | Branch: EPSRC | Program: | Phase: Fellowship | Award Amount: 488.45K | Year: 2016
Advances in High Performance Computing (HPC) and scientific software development will have increasingly significant societal impact through the computational design of new products, medicines, materials and industrial processes. However, the complexity of modern HPC hardware means that scientific software development now requires teams of scientists and programmers to work together, with different and non-overlapping skill-sets required from each member of the group. This complexity can lead to software development projects stalling. Investments in software development are in danger of being lost, either because key members of a team move on, or because a lack of planning or engagement means that a sustainable user and developer community has failed to gel around a particular code. Research Software Engineers (RSEs) can solve this problem. RSEs have the skills and training necessary to support software development projects as they move through different stages of the academic software lifecycle. Academic software evolves along this lifecycle, from being a code used by an initial team of researchers, through to a large multi-site community code used by academics and industrialists from across the UK and around the World. RSEs provide the training and support needed to help academic software developers structure their projects to support the sustainable growth of their user and developer communities. RSEs are also highly skilled programmers who can train software developers in advanced HPC techniques, and who can support developers in the implementation, optimisation and testing of complex and intricate code. Together with academic software developers, RSEs can support UK investment in HPC, and ensure that the potential of computational science and engineering to revolutionise the design of future products and industrial processes is realised. This project aims to develop sustainable RSE career pathways and funding at Bristol. This will support the growth of a sustainable team of RSEs at the University. Software development projects that will be supported include; the building of code to interface real biological cells with virtual simulated cells, so to support the rapid design of new biomanufacturing control processes; the development of code to more quickly model the behaviour of electrons in novel materials, to support the design of new fuel cells and batteries; code to improve our understanding of glass-like matter, so to help design new materials with exciting new properties; software to support modelling of the quantum interaction between laser light and microscopic nanoparticles, to support the design of optical tweezers and new optically driven nanomachines; and code to design new medicinal drugs and to understand why existing treatments are no longer working, thereby supporting the development of 21st century medicine. Finally, this project aims to create a coherent set of teaching materials in programming and research software engineering. These, together with the development of software to support science and programming lessons held in an interactive 3D planetarium, will help inspire and educate the next generation of scientists and RSEs. These materials will showcase how maths, physics, computing and chemistry can be used in the real world to create the high-tech tools and industries of the future.
PubMed | University of Würzburg, DNAdigest, Michigan State University, University of Manchester and 11 more.
Type: | Journal: F1000Research | Year: 2015
One of the foundations of the scientific method is to be able to reproduce experiments and corroborate the results of research that has been done before. However, with the increasing complexities of new technologies and techniques, coupled with the specialisation of experiments, reproducing research findings has become a growing challenge. Clearly, scientific methods must be conveyed succinctly, and with clarity and rigour, in order for research to be reproducible. Here, we propose steps to help increase the transparency of the scientific method and the reproducibility of research results: specifically, we introduce a peer-review oath and accompanying manifesto. These have been designed to offer guidelines to enable reviewers (with the minimum friction or bias) to follow and apply open science principles, and support the ideas of transparency, reproducibility and ultimately greater societal impact. Introducing the oath and manifesto at the stage of peer review will help to check that the research being published includes everything that other researchers would need to successfully repeat the work. Peer review is the lynchpin of the publishing system: encouraging the community to consciously (and conscientiously) uphold these principles should help to improve published papers, increase confidence in the reproducibility of the work and, ultimately, provide strategic benefits to authors and their institutions. Future incarnations of the various national Research Excellence Frameworks (REFs) will evolve away from simple citations towards measurable societal value and impact. The proposed manifesto aspires to facilitate this goal by making transparency, reproducibility and citizen-scientist engagement (with the knowledge-creation and dissemination processes) the default parameters for performing sound research.