Serverless computing in omics data analysis and integration

Piotr Grzesik, Dariusz R Augustyn, Łukasz Wyciślik, Dariusz Mrozek
<span title="2021-09-09">2021</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
A comprehensive analysis of omics data can require vast computational resources and access to varied data sources that must be integrated into complex, multi-step analysis pipelines. Execution of many such analyses can be accelerated by applying the cloud computing paradigm, which provides scalable resources for storing data of different types and parallelizing data analysis computations. Moreover, these resources can be reused for different multi-omics analysis scenarios. Traditionally,
more &raquo; ... ers are required to manage a cloud platform's underlying infrastructure, configuration, maintenance and capacity planning. The serverless computing paradigm simplifies these operations by automatically allocating and maintaining both servers and virtual machines, as required for analysis tasks. This paradigm offers highly parallel execution and high scalability without manual management of the underlying infrastructure, freeing developers to focus on operational logic. This paper reviews serverless solutions in bioinformatics and evaluates their usage in omics data analysis and integration. We start by reviewing the application of the cloud computing model to a multi-omics data analysis and exposing some shortcomings of the early approaches. We then introduce the serverless computing paradigm and show its applicability for performing an integrative analysis of multiple omics data sources in the context of the COVID-19 pandemic.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbab349">doi:10.1093/bib/bbab349</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34505137">pmid:34505137</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8499876/">pmcid:PMC8499876</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lqlrhoycnbg3xdygxpfejn6xvu">fatcat:lqlrhoycnbg3xdygxpfejn6xvu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210922013949/https://watermark.silverchair.com/bbab349.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAtgwggLUBgkqhkiG9w0BBwagggLFMIICwQIBADCCAroGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM0j0Xwbw7pksjO3enAgEQgIICi3x6fVHpM_4zCANE4jeBDnRdLEmUioacGYCTKBkC8eWx9TqTWt1lMkFq6B7L9Q9Zeh7cHX25L6TTZMQ4EFopwhvK64R_LPbRaH3n_R3fcDjUYU1BgfTbVifeS42SYVPqef_kerfFplOSzvNyTUU6lJSRu5QGgchLA-wqelt5xeLewyFgni7Y3mVodhxt8-6bKnMgW1qk3f2pco3w5tk_QRMPKapVYN5aCrvWvnLCXDN00T2EmUVURFRJkci8ZygXMysDPtIybtbqic5rMqrMOXwxYrdQYx-xU-T15qfQgTye49icucjxk2Hvy7Ke1iEOPcVNi1vEq1LT_SugL8OifZHQhon7BKH2Vlu8hvJhCTu6-iwJIqotZW7n9Vr3dvECb49w3NAh_kQO8gQXTK894urQP2eulrIeZh2pKKv2PK-8vKQShwwLjiK-umwR6mxr5941YFSI30u02DNKOFjuwAQRyXrwli9X8AXWg6zzrKIZRbu26gOPGRCh_-gbdnggbSnyLlTAUarwaYwmf4bhcDZkSjkbG92bMnpoTUXfDbnhrSFQvEDObpwUEMO2d49-_m9IkADh0jrHZ1NY7cdQcF5IFN8FtUjy7x8k-eAxNjpjr9kgs7rxFx4doh8ncJCSijn4IYaNA4Q18s-gSSS2Irs5Uc6zrb34c-0lFKDzCIg7T9xCXiN1KLrHA5GU4Y605M_9yD4RGxHQ4kNgjJ5PIUsfhu42gFUUaSDtSfpZ9OyEesOAT6GBAv17EgjuYik0BShOEwpDRcJqtpf36X8rmT7L04fOmKnx3KbWc2vTkKNJrHhGyePGxwebmcR6lbX0E7e1WiDrzxRYW9JbVtUwI4Ip5I2w8Psa2TekIg" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/40/e1/40e12041dc9baf9f4a1c209856ab458ae58a64d1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbab349"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8499876" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>