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Foreman: Manage Procfile-based applications;. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/ddollar\/foreman\" xlink:type=\"simple\">https:\/\/github.com\/ddollar\/foreman<\/ext-link>."},{"key":"ref18","unstructured":"V PHB. Phusion Passenger: a fast and robust web server and application server for Ruby, Python and Node.js;. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/phusion\/passenger\" xlink:type=\"simple\">https:\/\/github.com\/phusion\/passenger<\/ext-link>."},{"key":"ref19","unstructured":"Perham M. Sidekiq: Simple, efficient background processing for Ruby.;. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/mperham\/sidekiq\" xlink:type=\"simple\">https:\/\/github.com\/mperham\/sidekiq<\/ext-link>."},{"key":"ref20","unstructured":"The PostgreSQL Global Development Group. PostgreSQL: a powerful, open source object-relational database system.;. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.postgresql.org\" xlink:type=\"simple\">https:\/\/www.postgresql.org<\/ext-link>."},{"key":"ref21","unstructured":"Docker: A Better Way to Build Apps;. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.docker.com\" xlink:type=\"simple\">https:\/\/www.docker.com<\/ext-link>."},{"key":"ref22","doi-asserted-by":"crossref","first-page":"e0165129","DOI":"10.1371\/journal.pone.0165129","article-title":"Model Based Analysis of Clonal Developments Allows for Early Detection of Monoclonal Conversion and Leukemia","volume":"11","author":"C Baldow","year":"2016","journal-title":"PloS one"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"W443","DOI":"10.1093\/nar\/gkv315","article-title":"PLIP: fully automated protein-ligand interaction profiler","volume":"43","author":"S Salentin","year":"2015","journal-title":"Nucleic acids research"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"e56","DOI":"10.1093\/nar\/gku081","article-title":"Multiplexing clonality: combining RGB marking and genetic barcoding","volume":"42","author":"K Cornils","year":"2014","journal-title":"Nucleic acids research"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"e1002815","DOI":"10.1371\/journal.pcbi.1002815","article-title":"Parameter identifiability and sensitivity analysis predict targets for enhancement of STAT1 activity in pancreatic cancer and stellate cells","volume":"8","author":"K Rateitschak","year":"2012","journal-title":"PLoS computational biology"},{"issue":"11","key":"ref26","doi-asserted-by":"crossref","first-page":"1474","DOI":"10.1093\/bioinformatics\/btt157","article-title":"LibSBMLSim: a reference implementation of fully functional SBML simulator","volume":"29","author":"H Takizawa","year":"2013","journal-title":"Bioinformatics"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","article-title":"The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models","volume":"19","author":"M Hucka","year":"2003","journal-title":"Bioinformatics (Oxford, England)"},{"key":"ref28","first-page":"96","article-title":"Improving collaboration by standardization efforts in systems biology","author":"A Dr\u00e4ger","year":"2014","journal-title":"Frontiers in Bioengineering and Biotechnology"},{"issue":"13","key":"ref29","doi-asserted-by":"crossref","first-page":"2143","DOI":"10.1093\/bioinformatics\/bth200","article-title":"Web-based kinetic modelling using JWS Online","volume":"20","author":"BG Olivier","year":"2004","journal-title":"Bioinformatics"},{"issue":"3","key":"ref30","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1177\/030631289019003001","article-title":"Institutional ecology,translations\u2019 and boundary objects: Amateurs and professionals in Berkeley\u2019s Museum of Vertebrate Zoology, 1907-39","volume":"19","author":"SL Star","year":"1989","journal-title":"Social studies of science"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1005898","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,12,29]],"date-time":"2017-12-29T00:00:00Z","timestamp":1514505600000}},{"DOI":"10.1371\/journal.pcbi.1006083","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2018,3,26]],"date-time":"2018-03-26T00:00:00Z","timestamp":1522022400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005898","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,7]],"date-time":"2019-10-07T23:14:55Z","timestamp":1570490095000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005898"}},"subtitle":[],"editor":[{"given":"Timoth\u00e9e","family":"Poisot","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2017,12,15]]},"references-count":30,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2017,12,15]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005898","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,12,15]]}}}