{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:45Z","timestamp":1772138085897,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2017,12,8]],"date-time":"2017-12-08T00:00:00Z","timestamp":1512691200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"NHGRI","doi-asserted-by":"publisher","award":["T32 HG002295"],"award-info":[{"award-number":["T32 HG002295"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000066","name":"National Institute of Environmental Health Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000066","name":"NIEHS","doi-asserted-by":"publisher","award":["R00 ES023504"],"award-info":[{"award-number":["R00 ES023504"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000066","name":"NIEHS","doi-asserted-by":"publisher","award":["R21 ES025052"],"award-info":[{"award-number":["R21 ES025052"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000041","name":"ADA","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000041","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Across biology, we are seeing rapid developments in scale of data production without a corresponding increase in data analysis capabilities.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present Aether (http:\/\/aether.kosticlab.org), an intuitive, easy-to-use, cost-effective and scalable framework that uses linear programming to optimally bid on and deploy combinations of underutilized cloud computing resources. Our approach simultaneously minimizes the cost of data analysis and provides an easy transition from users\u2019 existing HPC pipelines.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Data utilized are available at https:\/\/pubs.broadinstitute.org\/diabimmune and with EBI SRA accession ERP005989. Source code is available at (https:\/\/github.com\/kosticlab\/aether). Examples, documentation and a tutorial are available at http:\/\/aether.kosticlab.org.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx787","type":"journal-article","created":{"date-parts":[[2017,12,7]],"date-time":"2017-12-07T15:13:50Z","timestamp":1512659630000},"page":"1565-1567","source":"Crossref","is-referenced-by-count":5,"title":["Aether: leveraging linear programming for optimal cloud computing in genomics"],"prefix":"10.1093","volume":"34","author":[{"given":"Jacob M","family":"Luber","sequence":"first","affiliation":[{"name":"Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA"},{"name":"Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA"},{"name":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"},{"name":"Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA"}]},{"given":"Braden T","family":"Tierney","sequence":"additional","affiliation":[{"name":"Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA"},{"name":"Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA"},{"name":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"},{"name":"Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA"}]},{"given":"Evan M","family":"Cofer","sequence":"additional","affiliation":[{"name":"Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA"},{"name":"Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA"},{"name":"Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA"},{"name":"Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA"}]},{"given":"Chirag J","family":"Patel","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0837-4360","authenticated-orcid":false,"given":"Aleksandar D","family":"Kostic","sequence":"additional","affiliation":[{"name":"Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA"},{"name":"Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA"},{"name":"Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,12,8]]},"reference":[{"key":"2023012713022670500_btx787-B1","author":"Andrzejak","year":"2010"},{"key":"2023012713022670500_btx787-B2","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1016\/j.chom.2015.05.012","article-title":"Dynamics and stabilization of the human gut microbiome during the first year of life","volume":"17","author":"B\u00e4ckhed","year":"2015","journal-title":"Cell Host Microb"},{"key":"2023012713022670500_btx787-B3","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1038\/nbt.3780","article-title":"Reproducibility of computational workflows is automated using continuous analysis","volume":"35","author":"Beaulieu-Jones","year":"2017","journal-title":"Nat. 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