{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T02:04:47Z","timestamp":1762999487096,"version":"3.37.3"},"reference-count":63,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2019,5,16]],"date-time":"2019-05-16T00:00:00Z","timestamp":1557964800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1006958","type":"journal-article","created":{"date-parts":[[2019,5,16]],"date-time":"2019-05-16T17:26:33Z","timestamp":1558027593000},"page":"e1006958","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":5,"title":["Securing the future of research computing in the biosciences"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9790-162X","authenticated-orcid":true,"given":"Joanna","family":"Leng","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3278-296X","authenticated-orcid":true,"given":"Massa","family":"Shoura","sequence":"additional","affiliation":[]},{"given":"Tom C. B.","family":"McLeish","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5166-6329","authenticated-orcid":true,"given":"Alan N.","family":"Real","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1027-0165","authenticated-orcid":true,"given":"Mariann","family":"Hardey","sequence":"additional","affiliation":[]},{"given":"James","family":"McCafferty","sequence":"additional","affiliation":[]},{"given":"Neil A.","family":"Ranson","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2812-1651","authenticated-orcid":true,"given":"Sarah A.","family":"Harris","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2019,5,16]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"D794","DOI":"10.1093\/nar\/gkx1081","article-title":"The Encyclopedia of DNA elements (ENCODE): data portal update","volume":"46","author":"CA Davis","year":"2018","journal-title":"Nucleic Acids Research"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"D21","DOI":"10.1093\/nar\/gkx1154","article-title":"The European Bioinformatics Institute in 2017: data coordination and integration","volume":"46","author":"CE Cook","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"ref3","first-page":"7644","article-title":"Global Life Science Data Resources Working G.","volume":"543","author":"WP Anderson","year":"2017","journal-title":"Data management: A global coalition to sustain core data"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"D1","DOI":"10.1093\/nar\/gkx1235","article-title":"The 2018 Nucleic Acids Research database issue and the online molecular biology database collection","volume":"46","author":"DJ Rigden","year":"2018","journal-title":"Nucleic Acids Research"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"D649","DOI":"10.1093\/nar\/gkx1132","article-title":"The Reactome Pathway Knowledgebase","volume":"46","author":"A Fabregat","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1107\/S2059798317004181","article-title":"Trends in the Electron Microscopy Data Bank (EMDB).","volume":"73","author":"A Patwardhan","year":"2017","journal-title":"Acta Crystallogr D Struct Biol"},{"issue":"5","key":"ref7","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1038\/nmeth.3806","article-title":"EMPIAR: a public archive for raw electron microscopy image data","volume":"13","author":"A Iudin","year":"2016","journal-title":"Nat Methods"},{"issue":"10","key":"ref8","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1038\/nsmb.2897","article-title":"A 3D cellular context for the macromolecular world","volume":"21","author":"A Patwardhan","year":"2016","journal-title":"Nat Struct Mol Biol"},{"issue":"6178","key":"ref9","doi-asserted-by":"crossref","first-page":"1443","DOI":"10.1126\/science.1251652","article-title":"Biochemistry. The resolution revolution","volume":"343","author":"W Kuhlbrandt","year":"2014","journal-title":"Science"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1038\/s41592-018-0195-8","article-title":"A call for public archives for biological image data","volume":"15","author":"J Ellenberg","year":"2018","journal-title":"Nature Methods"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1038\/s41596-018-0084-8","article-title":"Collection, pre-processing, and on-the-fly analysis of data for high-resolution, single-particle cryo-electron microscopy","volume":"14","author":"RF Thompson","year":"2018","journal-title":"Nature Protocols"},{"issue":"3","key":"ref12","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1016\/j.jsb.2012.09.006","article-title":"RELION: implementation of a Bayesian approach to cryo-EM structure determination","volume":"180","author":"SH Scheres","year":"2012","journal-title":"J Struct Biol"},{"key":"ref13","unstructured":"Gatan [Internet]. c2018 [cited 2019 Apr 26]. K3 Camera. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.gatan.com\/k3-camera\" xlink:type=\"simple\">http:\/\/www.gatan.com\/k3-camera<\/ext-link>."},{"issue":"15","key":"ref14","doi-asserted-by":"crossref","first-page":"3871","DOI":"10.1021\/acs.jpcb.7b00672","article-title":"Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations","volume":"121","author":"TM Earnest","year":"2017","journal-title":"J Phys Chem B"},{"issue":"1","key":"ref15","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1111\/boc.201600044","article-title":"Mesoscale imaging with cryo-light and X-rays: Larger than molecular machines, smaller than a cell","volume":"109","author":"AA Ekman","year":"2017","journal-title":"Biol Cell"},{"issue":"5","key":"ref16","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1038\/nprot.2017.017","article-title":"Diverse protocols for correlative super-resolution fluorescence imaging and electron microscopy of chemically fixed samples","volume":"12","author":"BG Kopek","year":"2017","journal-title":"Nat Protoc"},{"issue":"2","key":"ref17","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1016\/j.celrep.2017.12.045","article-title":"True Molecular Scale Visualization of Variable Clustering Properties of Ryanodine Receptors","volume":"22","author":"I Jayasinghe","year":"2018","journal-title":"Cell Rep"},{"key":"ref18","first-page":"6386","article-title":"Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms","volume":"360","author":"TL Liu","year":"2018","journal-title":"Science"},{"key":"ref19","unstructured":"Thermo Fisher Scientific [Internet]. c2018 [cited 2018 Apr 15]. Amira Software for the Life Sciences. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.fei.com\/software\/amira-for-life-sciences\/\" xlink:type=\"simple\">https:\/\/www.fei.com\/software\/amira-for-life-sciences\/<\/ext-link>."},{"key":"ref20","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1038\/nmeth.4326","article-title":"Image Data Resource: a bioimage data integration and publication platform","volume":"14","author":"E Williams","year":"2017","journal-title":"Nature Methods"},{"issue":"10","key":"ref21","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/S0167-7799(01)01740-1","article-title":"The Virtual Cell: a software environment for computational cell biology","volume":"19","author":"LM Loew","year":"2001","journal-title":"Trends in Biotechnology"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1146\/annurev-bioeng-110915-114742","article-title":"The Virtual Physiological Human: Ten Years After.","volume":"18","author":"M Viceconti","year":"2016","journal-title":"Annu Rev Biomed Eng"},{"key":"ref23","unstructured":"Food and Drug Administration (FDA). Reporting of Computational Modeling Studies in Medical Device: Submissions Guidance for Industry and Food and Drug Administration Staff. FDA; 2010 [cited 2018 Jun 5]. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.fda.gov\/downloads\/MedicalDevices\/DeviceRegulationandGuidance\/GuidanceDocuments\/UCM381813.pdf\" xlink:type=\"simple\">https:\/\/www.fda.gov\/downloads\/MedicalDevices\/DeviceRegulationandGuidance\/GuidanceDocuments\/UCM381813.pdf<\/ext-link>."},{"key":"ref24","first-page":"23","article-title":"Recent progress in multi-scale models of the human atria.","volume":"14","author":"MA Colman","year":"2014","journal-title":"Drug Discovery Today: Disease Models"},{"issue":"9","key":"ref25","doi-asserted-by":"crossref","first-page":"2483","DOI":"10.1113\/JP270532","article-title":"How computer simulations of the human heart can improve anti-arrhythmia therapy","volume":"594","author":"NA Trayanova","year":"2016","journal-title":"J Physiol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1016\/j.cobme.2018.04.001","article-title":"The future is digital: in silico tissue engineering","volume":"6","author":"L Geris","year":"2018","journal-title":"Current Opinion in Biomedical Engineering"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1107\/S1399004714026777","article-title":"In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation","volume":"71","author":"A Gray","year":"2015","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"e1393","DOI":"10.1002\/wcms.1393","article-title":"Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity. Wiley Interdisciplinary Reviews","volume":"9","author":"DJ Huggins","year":"2018","journal-title":"Computational Molecular Science"},{"key":"ref29","unstructured":"Shaw DE, Dror RO, Salmon JK, Grossman JP, Mackenzie KM, Bank JA, et al. Millisecond-scale Molecular Dynamics Simulations on Anton. In: Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis. SC &apos;09. New York, NY, USA: ACM; 2009 [cited 2019 Apr 26]. p. 39:1\u201339:11. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.acm.org\/10.1145\/1654059.1654099\" xlink:type=\"simple\">http:\/\/doi.acm.org\/10.1145\/1654059.1654099<\/ext-link>."},{"key":"ref30","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1146\/annurev-biophys-042910-155245","article-title":"Shaw De. Biomolecular simulation: a computational microscope for molecular biology","volume":"41","author":"RO Dror","year":"2012","journal-title":"Annu Rev Biophys"},{"key":"ref31","first-page":"8","article-title":"Making biomolecular simulations accessible in the post-Nobel Prize era","volume":"10","author":"Q Cui","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12918-017-0484-3","article-title":"Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions","volume":"12","author":"I Vernon","year":"2018","journal-title":"BMC Syst Biol"},{"key":"ref33","first-page":"8","article-title":"Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning","volume":"12","author":"J Wu","year":"2017","journal-title":"PLoS ONE"},{"issue":"1","key":"ref34","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jsb.2014.03.001","article-title":"Automated particle picking for low-contrast macromolecules in cryo-electron microscopy","volume":"186","author":"R Langlois","year":"2014","journal-title":"J Struct Biol"},{"issue":"2","key":"ref35","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1016\/j.jsb.2017.12.015","article-title":"Convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation","volume":"202","author":"X Zeng","year":"2018","journal-title":"J Struct Biol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1016\/j.drudis.2018.01.039","article-title":"The rise of deep learning in drug discovery","volume":"23","author":"H Chen","year":"2018","journal-title":"Drug Discov Today"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/s40364-017-0082-y","article-title":"Machine learning and systems genomics approaches for multi-omics data","volume":"5","author":"E Lin","year":"2017","journal-title":"Biomark Res"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"1150","DOI":"10.1021\/acsmedchemlett.8b00500","article-title":"Artificial Intelligence in Drug Design-The Storm Before the Calm?","volume":"9","author":"AM Jordan","year":"2018","journal-title":"ACS Medicinal Chemistry Letters"},{"key":"ref39","first-page":"61","article-title":"cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets","volume":"2015","author":"M Le Muzic","year":"2015","journal-title":"Eurographics Workshop Vis Comput Biomed"},{"issue":"1","key":"ref40","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1109\/TVCG.2017.2744258","article-title":"Instant Construction and Visualization of Crowded Biological Environments","volume":"24","author":"T Klein","year":"2018","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"3","key":"ref41","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1021\/acs.accounts.6b00572","article-title":"A Multiscale Description of Biomolecular Active Matter: The Chemistry Underlying Many Life Processes","volume":"50","author":"GA Voth","year":"2017","journal-title":"Accounts of Chemical Research"},{"issue":"2","key":"ref42","article-title":"Patterns of Industrial Innovation","volume":"8","author":"WJ Abernathy","year":"1978","journal-title":"Technical Review"},{"year":"2017","author":"A Brett","key":"ref43"},{"issue":"16","key":"ref44","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1002\/jcc.20289","article-title":"Scalable molecular dynamics with NAMD","volume":"26","author":"JC Phillips","year":"2005","journal-title":"J Comput Chem"},{"issue":"1","key":"ref45","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: Visual molecular dynamics","volume":"14","author":"W Humphrey","year":"1996","journal-title":"Journal of Molecular Graphics"},{"key":"ref46","unstructured":"software.ac.uk [Internet]. The Software Sustainability Institute; c2018 [cited 2019 Apr 26]. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.software.ac.uk\/\" xlink:type=\"simple\">https:\/\/www.software.ac.uk\/<\/ext-link>."},{"key":"ref47","unstructured":"software-carpentry.org [Internet]. The Software Carpentry Foundation; c2018 [cited 2019 Apr 26]. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/software-carpentry.org\/\" xlink:type=\"simple\">https:\/\/software-carpentry.org\/<\/ext-link>."},{"key":"ref48","unstructured":"Microsoft Azure [Internet]. c2018 [cited 2019 Apr 26]. Import\/Export Pricing. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/azure.microsoft.com\/en-gb\/pricing\/details\/storage-import-export\/\" xlink:type=\"simple\">https:\/\/azure.microsoft.com\/en-gb\/pricing\/details\/storage-import-export\/<\/ext-link>."},{"key":"ref49","unstructured":"Microsoft Azure [Internet]. c2018 [cited 2019 Apr 26]. Big Compute: HPC &amp; Batch. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/azure.microsoft.com\/en-us\/solutions\/big-compute\/\" xlink:type=\"simple\">https:\/\/azure.microsoft.com\/en-us\/solutions\/big-compute\/<\/ext-link>."},{"key":"ref50","unstructured":"Gartner [Internet]. ResOps\u2014in Gartner IT Glossary. c2018 [cited 2019 Apr 4]. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.bit.ly\/resops_sept2017\" xlink:type=\"simple\">http:\/\/www.bit.ly\/resops_sept2017<\/ext-link>."},{"issue":"6","key":"ref51","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/S0969-2126(01)00187-3","article-title":"Where freedom is given, liberties are taken","volume":"3","author":"GJ Kleywegt","year":"1995","journal-title":"Structure"},{"issue":"4","key":"ref52","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1016\/S0969-2126(02)00743-8","article-title":"Homo Crystallographicus\u2014Quo Vadis?","volume":"10","author":"GJ Kleywegt","year":"2002","journal-title":"Structure"},{"issue":"6","key":"ref53","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1107\/S2059798316019276","article-title":"A pipeline approach to single-particle processing in <italic>RELION<\/italic>","volume":"73","author":"R Fernandez-Leiro","year":"2017","journal-title":"Acta Crystallographica Section D"},{"issue":"3","key":"ref54","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nmeth.4169","article-title":"cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination","volume":"14","author":"A Punjani","year":"2017","journal-title":"Nature Methods"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"e35383","DOI":"10.7554\/eLife.35383","article-title":"cisTEM, user-friendly software for single-particle image processing","volume":"7","author":"T Grant","year":"2018","journal-title":"eLife"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1021\/acs.biochem.8b00064","article-title":"New Opportunities Created by Single-Particle Cryo-EM: The Mapping of Conformational Space","volume":"57","author":"J Frank","year":"2018","journal-title":"Biochemistry"},{"issue":"6340","key":"ref57","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1126\/science.aan5955","article-title":"Whole cell maps chart a course for 21st-century cell biology","volume":"356","author":"R Horwitz","year":"2017","journal-title":"Science"},{"key":"ref58","unstructured":"Zooniverse [Internet]. c2018 [cited 2019 Apr 26]. Etch a cell. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.zooniverse.org\/projects\/h-spiers\/etch-a-cell\" xlink:type=\"simple\">https:\/\/www.zooniverse.org\/projects\/h-spiers\/etch-a-cell<\/ext-link>."},{"key":"ref59","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.jsb.2018.02.006","article-title":"Exploring applications of crowdsourcing to cryo-EM","volume":"203","author":"J Bruggemann","year":"2018","journal-title":"J Struct Biol"},{"key":"ref60","unstructured":"23andme.com [Internet]. 23 and Me; c2018 [cited 2019 Apr 26]. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.23andme.com\" xlink:type=\"simple\">https:\/\/www.23andme.com<\/ext-link>."},{"key":"ref61","unstructured":"uBiome.com [Internet]. uBiome; c2018 [cited 2019 Apr 26]. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/ubiome.com\/\" xlink:type=\"simple\">https:\/\/ubiome.com\/<\/ext-link>."},{"year":"2016","author":"D Lupton","key":"ref62"},{"year":"2014","key":"ref63"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006958","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T07:31:25Z","timestamp":1589009485000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006958"}},"subtitle":[],"editor":[{"given":"Anna R.","family":"Panchenko","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,5,16]]},"references-count":63,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2019,5,16]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006958","relation":{},"ISSN":["1553-7358"],"issn-type":[{"type":"electronic","value":"1553-7358"}],"subject":[],"published":{"date-parts":[[2019,5,16]]}}}