{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,13]],"date-time":"2023-09-13T09:24:18Z","timestamp":1694597058722},"reference-count":38,"publisher":"Walter de Gruyter GmbH","issue":"2","license":[{"start":{"date-parts":[[2017,6,10]],"date-time":"2017-06-10T00:00:00Z","timestamp":1497052800000},"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":[[2017,6,10]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Docker virtualization allows for software tools to be executed in an isolated and controlled environment referred to as a container. In Docker containers, dependencies are provided exactly as intended by the developer and, consequently, they simplify the distribution of scientific software and foster reproducible research. The Docker paradigm is that each container encapsulates one particular software tool. However, to analyze complex biomedical data sets, it is often necessary to combine several software tools into elaborate workflows. To address this challenge, several Docker containers need to be instantiated and properly integrated, which complicates the software deployment process unnecessarily. Here, we demonstrate how an extension to Docker, Docker compose, can be used to mitigate these problems by providing a unified setup routine that deploys several tools in an integrated fashion. We demonstrate the power of this approach by example of a Docker compose setup for a drug target screening platform consisting of five integrated web applications and shared infrastructure, deployable in just two lines of codes.<\/jats:p>","DOI":"10.1515\/jib-2017-0016","type":"journal-article","created":{"date-parts":[[2017,6,10]],"date-time":"2017-06-10T10:01:30Z","timestamp":1497088890000},"source":"Crossref","is-referenced-by-count":4,"title":["Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform"],"prefix":"10.1515","volume":"14","author":[{"given":"Markus","family":"List","sequence":"first","affiliation":[{"name":"Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbr\u00fccken, Germany"}]}],"member":"374","reference":[{"key":"ref181","first-page":"274","article-title":"OpenLabNotes\u2013an electronic laboratory notebook extension for OpenLabFramework","volume":"12","year":"2015","journal-title":"J Integr Bioinform"},{"key":"ref351","doi-asserted-by":"crossref","first-page":"W98","DOI":"10.1093\/nar\/gkw373","article-title":"KeyPathwayMinerWeb: online multi-omics network enrichment","volume":"44","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/s13742-015-0092-3","article-title":"Enhanced reproducibility of SADI web service workflows with Galaxy and Docker","volume":"4","year":"2015","journal-title":"Gigascience"},{"key":"ref191","first-page":"643","article-title":"Simplified deployment of health informatics applications by providing docker images","volume":"228","year":"2016","journal-title":"Stud Health Technol Inform"},{"key":"ref131","doi-asserted-by":"crossref","first-page":"4278","DOI":"10.1038\/srep04278","article-title":"Efficient sample tracking with OpenLabFramework","volume":"4","year":"2014","journal-title":"Sci Rep"},{"key":"ref291","article-title":"Overview of high-throughput screening","year":"2009","journal-title":"Curr Protoc Pharmacol"},{"key":"ref301","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1146\/annurev-biochem-060408-092949","article-title":"Genomic screening with RNAi: results and challenges","volume":"79","year":"2010","journal-title":"Annu Rev Biochem"},{"key":"ref321","doi-asserted-by":"crossref","first-page":"4278","DOI":"10.1038\/srep04278","article-title":"Efficient sample tracking with OpenLabFramework","volume":"4","year":"2014","journal-title":"Sci Rep"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"2396","DOI":"10.1093\/bioinformatics\/btw120","article-title":"AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms","volume":"32","year":"2016","journal-title":"Bioinformatics"},{"key":"ref221","doi-asserted-by":"crossref","first-page":"1442","DOI":"10.12688\/f1000research.8935.1","article-title":"Bringing your tools to CyVerse discovery environment using Docker. 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