{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T10:56:08Z","timestamp":1767178568262,"version":"build-2238731810"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1013819","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,12,26]],"date-time":"2025-12-26T00:00:00Z","timestamp":1766707200000}}],"reference-count":23,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2025,12,19]],"date-time":"2025-12-19T00:00:00Z","timestamp":1766102400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000943","name":"Commonwealth Scientific and Industrial Research Organisation","doi-asserted-by":"publisher","award":["No grant number available"],"award-info":[{"award-number":["No grant number available"]}],"id":[{"id":"10.13039\/501100000943","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["DP210103401"],"award-info":[{"award-number":["DP210103401"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Organisations are challenged when meeting the computational requirements of large-scale bioinformatics analyses using their own resources. Cloud computing has democratised large-scale resources, and to reduce the barriers of working with large-scale compute, leading cloud vendors offer serverless computing, a low-maintenance and low-cost model that provides ample resources for highly scalable software applications. While serverless computing has broad use, its adoption in bioinformatics remains poor. Here, we demonstrate the most extensive use of high-performance serverless computing for bioinformatics by applying the available technologies to CRISPR-Cas9 guide RNA (gRNA) design. Our adaptation of the established gRNA design tool, named Crackling, implements a novel, cloud-native and serverless-based, high-performance computing environment using technologies made available by Amazon Web Services (AWS). The architecture, compatible with technologies from all leading cloud vendors, and the AWS implementation, contributes to an effort of reducing the barrier to large computational capacity in bioinformatics and for CRISPR-Cas9 gRNA design. Crackling Cloud can be deployed to any AWS account, and is freely available on GitHub under the BSD 3-clause license:\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/bmds-lab\/Crackling-AWS\" xlink:type=\"simple\">https:\/\/github.com\/bmds-lab\/Crackling-AWS<\/jats:ext-link>\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1013819","type":"journal-article","created":{"date-parts":[[2025,12,19]],"date-time":"2025-12-19T18:44:46Z","timestamp":1766169886000},"page":"e1013819","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Democratising high performance computing for bioinformatics through serverless cloud computing: A case study on CRISPR-Cas9 guide RNA design with Crackling Cloud"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3619-5682","authenticated-orcid":true,"given":"Jacob","family":"Bradford","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Divya","family":"Joy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mattias","family":"Winsen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicholas","family":"Meurant","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mackenzie","family":"Wilkins","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laurence O.W.","family":"Wilson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Denis C.","family":"Bauer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dimitri","family":"Perrin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2025,12,19]]},"reference":[{"issue":"2","key":"pcbi.1013819.ref001","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1038\/s41587-018-0010-1","article-title":"Ultrafast search of all deposited bacterial and viral genomic data","volume":"37","author":"P Bradley","year":"2019","journal-title":"Nat Biotechnol."},{"issue":"6","key":"pcbi.1013819.ref002","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giaa063","article-title":"The democratization of bioinformatics: A software engineering perspective","volume":"9","author":"B Lawlor","year":"2020","journal-title":"Gigascience."},{"issue":"1","key":"pcbi.1013819.ref003","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbab349","article-title":"Serverless computing in omics data analysis and integration","volume":"23","author":"P Grzesik","year":"2022","journal-title":"Brief Bioinform."},{"key":"pcbi.1013819.ref004","doi-asserted-by":"crossref","unstructured":"Crespo-Cepeda R, Agapito G, Vazquez-Poletti JL, Cannataro M. Challenges and opportunities of Amazon serverless lambda services in bioinformatics. In: Proceedings of the 10th ACM international conference on bioinformatics, computational biology and health informatics; 2019. p. 663\u20138. https:\/\/doi.org\/10.1145\/3307339.3343462","DOI":"10.1145\/3307339.3343462"},{"key":"pcbi.1013819.ref005","first-page":"578","article-title":"Serverless nanopore basecalling with AWS lambda. In:","volume":"2021","author":"P Grzesik","year":"2021","journal-title":"Computational science\u2013ICCS"},{"key":"pcbi.1013819.ref006","doi-asserted-by":"crossref","unstructured":"Arjona A, Gabriel-Atienza A, Lanuza-Orna S, Roca-Canals X, Bourramouss A, Chafin TK, et al. Scaling a variant calling genomics pipeline with FaaS. In: Proceedings of the 9th international workshop on serverless computing; 2023. p. 59\u201364. https:\/\/doi.org\/10.1145\/3631295.3631403","DOI":"10.1145\/3631295.3631403"},{"issue":"7","key":"pcbi.1013819.ref007","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0254363","article-title":"Evaluation of serverless computing for scalable execution of a joint variant calling workflow","volume":"16","author":"A John","year":"2021","journal-title":"PLoS One."},{"key":"pcbi.1013819.ref008","doi-asserted-by":"crossref","unstructured":"Niu X, Kumanov D, Hung L-H, Lloyd W, Yeung KY. Leveraging serverless computing to improve performance for sequence comparison. In: Proceedings of the 10th ACM international conference on bioinformatics, computational biology and health informatics; 2019. p. 683\u20137. https:\/\/doi.org\/10.1145\/3307339.3343465","DOI":"10.1145\/3307339.3343465"},{"key":"pcbi.1013819.ref009","article-title":"DNAvisualization.org: A serverless web tool for DNA sequence visualization","volume":"47","author":"BD Lee","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"pcbi.1013819.ref010","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkac417","article-title":"AutoESD: A web tool for automatic editing sequence design for genetic manipulation of microorganisms","volume":"50","author":"Y Yang","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"pcbi.1013819.ref011","volume-title":"Accessible and interactive RNA sequencing analysis using serverless computing","author":"L-H Hung","year":"2019"},{"issue":"2","key":"pcbi.1013819.ref012","doi-asserted-by":"crossref","first-page":"98","DOI":"10.3390\/bdcc7020098","article-title":"Massive parallel alignment of RNA-seq reads in serverless computing","volume":"7","author":"P Cinaglia","year":"2023","journal-title":"BDCC."},{"issue":"6213","key":"pcbi.1013819.ref013","doi-asserted-by":"crossref","first-page":"1258096","DOI":"10.1126\/science.1258096","article-title":"Genome editing. The new frontier of genome engineering with CRISPR-Cas9","volume":"346","author":"JA Doudna","year":"2014","journal-title":"Science."},{"issue":"8","key":"pcbi.1013819.ref014","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1007274","article-title":"A benchmark of computational CRISPR-Cas9 guide design methods","volume":"15","author":"J Bradford","year":"2019","journal-title":"PLoS Comput Biol."},{"key":"pcbi.1013819.ref015","doi-asserted-by":"crossref","unstructured":"Bo C, Dang V, Sadredini E, Skadron K. Searching for potential gRNA off-target sites for CRISPR\/Cas9 using automata processing across different platforms. In: 2018 IEEE international symposium on high performance computer architecture (HPCA); 2018. p. 737\u201348. https:\/\/doi.org\/10.1109\/hpca.2018.00068","DOI":"10.1109\/HPCA.2018.00068"},{"key":"pcbi.1013819.ref016","unstructured":"Li W. GitHub repository: davidliwei\/awesome-CRISPR. GitHub; 2024. 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Fast and scalable off-target assessment for CRISPR guide RNAs using partial matches. In: 2024 IEEE international conference on bioinformatics and biomedicine (BIBM); 2024. p. 1649\u201354. https:\/\/doi.org\/10.1109\/bibm62325.2024.10822812","DOI":"10.1109\/BIBM62325.2024.10822812"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1013819","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,12,26]],"date-time":"2025-12-26T00:00:00Z","timestamp":1766707200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1013819","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,26]],"date-time":"2025-12-26T18:51:14Z","timestamp":1766775074000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1013819"}},"subtitle":[],"editor":[{"given":"Mark","family":"Ziemann","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2025,12,19]]},"references-count":23,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2025,12,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1013819","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,19]]}}}