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      Securing the future of research computing in the biosciences

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Author summary

          Improvements in technology often drive scientific discovery. Therefore, research requires sustained investment in the latest equipment and training for the researchers who are going to use it. Prioritising and administering infrastructure investment is challenging because future needs are difficult to predict. In the past, highly computationally demanding research was associated primarily with particle physics and astronomy experiments. However, as biology becomes more quantitative and bioscientists generate more and more data, their computational requirements may ultimately exceed those of physical scientists. Computation has always been central to bioinformatics, but now imaging experiments have rapidly growing data processing and storage requirements. There is also an urgent need for new modelling and simulation tools to provide insight and understanding of these biophysical experiments. Bioscience communities must work together to provide the software and skills training needed in their areas. Research-active institutions need to recognise that computation is now vital in many more areas of discovery and create an environment where it can be embraced. The public must also become aware of both the power and limitations of computing, particularly with respect to their health and personal data.

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          Most cited references50

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          VMD: Visual molecular dynamics

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            cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

            A software tool, cryoSPARC, addresses the speed bottleneck in cryo-EM image processing, enabling automated macromolecular structure determination in hours on a desktop computer without requiring a starting model.
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              Scalable molecular dynamics with NAMD.

              NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu. (c) 2005 Wiley Periodicals, Inc.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS Comput Biol
                PLoS Comput. Biol
                plos
                ploscomp
                PLoS Computational Biology
                Public Library of Science (San Francisco, CA USA )
                1553-734X
                1553-7358
                16 May 2019
                May 2019
                : 15
                : 5
                : e1006958
                Affiliations
                [1 ] School of Computing, University of Leeds, Leeds, United Kingdom
                [2 ] School of Pathology, Stanford University, Palo Alto, California, United States of America
                [3 ] Department of Physics, University of York, York, United Kingdom
                [4 ] Advanced Research Computing, University of Durham, Durham, United Kingdom
                [5 ] School of Business, University of Durham, Durham, United Kingdom
                [6 ] Information Services Division, UCL, London, United Kingdom
                [7 ] Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
                [8 ] School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
                [9 ] School of Physics and Astronomy, University of Leeds, Leeds, United Kingdom
                National Institutes of Health, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0001-9790-162X
                http://orcid.org/0000-0003-3278-296X
                http://orcid.org/0000-0001-5166-6329
                http://orcid.org/0000-0002-1027-0165
                http://orcid.org/0000-0002-2812-1651
                Article
                PCOMPBIOL-D-18-01128
                10.1371/journal.pcbi.1006958
                6521984
                31095554
                b18e37c9-7e24-4f2f-89d0-a037d36d3465
                © 2019 Leng et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Page count
                Figures: 1, Tables: 1, Pages: 15
                Funding
                JL would like to thank the UK Engineering and Physical Sciences Research Council (EPSRC, https://epsrc.ukri.org/) for her Research Software Engineering fellowship (EP/R025819/1). TCBM would also like to thank the EPSRC for his fellowship (EP/N031431/1). This work was supported in part through the EPSRC/BBSRC "Physics of Life" Network+ grant no. EP/P006639/1 ( https://bbsrc.ukri.org/). MS is grateful to the Arnold and Mabel Beckman foundation for her fellowship ( http://www.beckman-foundation.org/). MH acknowledges Creative Fuse North East, AHRC, AH/P005160/1 ( http://gtr.ukri.org/projects?ref=AH%2FP005160%2F1). Electron microscopy in the Astbury Biostructure Laboratory is supported by the University of Leeds and the Wellcome Trust ( https://wellcome.ac.uk/home) grants 108466/Z/15/Z and 208395/Z/17/Z. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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