{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,5]],"date-time":"2023-09-05T15:14:30Z","timestamp":1693926870437},"reference-count":18,"publisher":"Walter de Gruyter GmbH","issue":"2","license":[{"start":{"date-parts":[[2017,6,13]],"date-time":"2017-06-13T00:00:00Z","timestamp":1497312000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,6,13]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. <jats:italic>clubber<\/jats:italic> is our automated cluster-load balancing system developed for optimizing these \u201cbig data\u201d analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. <jats:italic>clubber<\/jats:italic>\u2019s goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC) resources. Notably, the latter can be added on demand, including cloud-based resources, and\/or featuring heterogeneous environments. The second goal of making HPCs user-friendly is facilitated by an interactive web interface and a RESTful API, allowing for job monitoring and result retrieval. We used <jats:italic>clubber<\/jats:italic> to speed up our pipeline for annotating molecular functionality of metagenomes. Here, we analyzed the Deepwater Horizon oil-spill study data to quantitatively show that the beach sands have not yet entirely recovered. Further, our analysis of the CAMI-challenge data revealed that microbiome taxonomic shifts do not necessarily correlate with functional shifts. These examples (21 metagenomes processed in 172 min) clearly illustrate the importance of <jats:italic>clubber<\/jats:italic> in the everyday computational biology environment.<\/jats:p>","DOI":"10.1515\/jib-2017-0020","type":"journal-article","created":{"date-parts":[[2017,6,13]],"date-time":"2017-06-13T10:01:32Z","timestamp":1497348092000},"source":"Crossref","is-referenced-by-count":5,"title":["clubber: removing the bioinformatics bottleneck in big data analyses"],"prefix":"10.1515","volume":"14","author":[{"given":"Maximilian","family":"Miller","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA"},{"name":"Department for Bioinformatics and Computational Biology, Technische Universit\u00e4t M\u00fcnchen, Boltzmannstr. 3, 85748Garching\/Munich, Germany"},{"name":"TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Technische Universit\u00e4t M\u00fcnchen, 85748Garching\/Munich, Germany, Tel.: +1 848 932 5638, Fax: +1 732 932 8965"}]},{"given":"Chengsheng","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA"}]},{"given":"Yana","family":"Bromberg","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA"},{"name":"Department of Genetics, Rutgers University, Human Genetics Institute, Life Sciences Building, Piscataway, NJ 08854, USA"},{"name":"Institute for Advanced Study at Technische Universit\u00e4t M\u00fcnchen (TUM-IAS), Garching\/Munich, Germany"}]}],"member":"374","reference":[{"key":"ref51","doi-asserted-by":"crossref","first-page":"032105","DOI":"10.1088\/1742-6596\/513\/3\/032105","article-title":"Accessing opportunistic resources with Bosco","volume":"513","year":"2014","journal-title":"J Phys Conf Ser"},{"key":"ref251","doi-asserted-by":"crossref","first-page":"032105","DOI":"10.1088\/1742-6596\/513\/3\/032105","article-title":"Accessing opportunistic resources with Bosco","volume":"513","year":"2014","journal-title":"J Phys Conf Ser"},{"key":"ref321","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","year":"1990","journal-title":"J Mol Biol"},{"key":"ref241","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1002\/cpe.938","article-title":"Distributed computing in practice: the Condor experience","volume":"17","year":"2005","journal-title":"Concurr Comp Pract Ex"},{"key":"ref181","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1128\/MMBR.68.3.518-537.2004","article-title":"Determination of the core of a minimal bacterial gene set","volume":"68","year":"2004","journal-title":"Microbiol Mol Biol Rev"},{"key":"ref151","doi-asserted-by":"crossref","first-page":"1928","DOI":"10.1038\/ismej.2015.5","article-title":"Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill","volume":"9","year":"2015","journal-title":"ISME J"},{"key":"ref161","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/BF02289694","article-title":"Nonmetric multidimensional scaling: a numerical method","volume":"29","year":"1964","journal-title":"Psychometrika"},{"key":"ref201","first-page":"745","article-title":"The DNA revolution","volume":"49","year":"2008","journal-title":"Canadian Vet J"},{"key":"ref351","doi-asserted-by":"crossref","first-page":"1928","DOI":"10.1038\/ismej.2015.5","article-title":"Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill","volume":"9","year":"2015","journal-title":"ISME J"},{"key":"ref171","first-page":"32","article-title":"A new method for non-parametric multivariate analysis of variance","volume":"26","year":"2001","journal-title":"Austral Ecology"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1111\/bjd.14362","article-title":"Rare inherited skin diseases and the Genomics England 100 000 Genome Project","volume":"174","year":"2016","journal-title":"Br J Dermatol"},{"key":"ref121","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","year":"1990","journal-title":"J Mol Biol"},{"key":"ref361","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/BF02289694","article-title":"Nonmetric multidimensional scaling: a numerical method","volume":"29","year":"1964","journal-title":"Psychometrika"},{"key":"ref371","first-page":"32","article-title":"A new method for non-parametric multivariate analysis of variance","volume":"26","year":"2001","journal-title":"Austral Ecology"},{"key":"ref01","first-page":"745","article-title":"The DNA revolution","volume":"49","year":"2008","journal-title":"Canadian Vet J"},{"key":"ref231","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1111\/bjd.14362","article-title":"Rare inherited skin diseases and the Genomics England 100 000 Genome Project","volume":"174","year":"2016","journal-title":"Br J Dermatol"},{"key":"ref381","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1128\/MMBR.68.3.518-537.2004","article-title":"Determination of the core of a minimal bacterial gene set","volume":"68","year":"2004","journal-title":"Microbiol Mol Biol Rev"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1002\/cpe.938","article-title":"Distributed computing in practice: the Condor experience","volume":"17","year":"2005","journal-title":"Concurr Comp Pract Ex"}],"container-title":["Journal of Integrative Bioinformatics"],"original-title":[],"link":[{"URL":"https:\/\/www.degruyter.com\/view\/journals\/jib\/14\/2\/article-20170020.xml","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2017-0020\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,4,22]],"date-time":"2021-04-22T01:57:34Z","timestamp":1619056654000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2017-0020\/html"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,6,13]]},"references-count":18,"journal-issue":{"issue":"2"},"URL":"https:\/\/doi.org\/10.1515\/jib-2017-0020","relation":{},"ISSN":["1613-4516"],"issn-type":[{"value":"1613-4516","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,6,13]]}}}