{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T14:00:29Z","timestamp":1776175229029,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2016,12,5]],"date-time":"2016-12-05T00:00:00Z","timestamp":1480896000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"German Federal Ministry of Education and Research","award":["0316195"],"award-info":[{"award-number":["0316195"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>The goal of this project is to provide a simple interface to working with Boolean networks. Emphasis is put on easy access to a large number of common tasks including the generation and manipulation of networks, attractor and basin computation, model checking and trap space computation, execution of established graph algorithms as well as graph drawing and layouts.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>PyBoolNet is a Python package for working with Boolean networks that supports simple access to model checking via NuSMV, standard graph algorithms via NetworkX and visualization via dot. In addition, state of the art attractor computation exploiting Potassco ASP is implemented. The package is function-based and uses only native Python and NetworkX data types.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and Implementation<\/jats:title><jats:p>https:\/\/github.com\/hklarner\/PyBoolNet<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw682","type":"journal-article","created":{"date-parts":[[2016,10,25]],"date-time":"2016-10-25T11:05:33Z","timestamp":1477393533000},"page":"770-772","source":"Crossref","is-referenced-by-count":93,"title":["PyBoolNet: a python package for the generation, analysis and visualization of boolean networks"],"prefix":"10.1093","volume":"33","author":[{"given":"Hannes","family":"Klarner","sequence":"first","affiliation":[{"name":"Institut f\u00fcr Mathematik, Freie Universit\u00e4t Berlin, Berlin, Germany"}]},{"given":"Adam","family":"Streck","sequence":"additional","affiliation":[{"name":"Institut f\u00fcr Mathematik, Freie Universit\u00e4t Berlin, Berlin, Germany"}]},{"given":"Heike","family":"Siebert","sequence":"additional","affiliation":[{"name":"Institut f\u00fcr Mathematik, Freie Universit\u00e4t Berlin, Berlin, Germany"}]}],"member":"286","published-online":{"date-parts":[[2016,12,5]]},"reference":[{"key":"2023020204504970400_btw682-B1","doi-asserted-by":"crossref","first-page":"1.","DOI":"10.1186\/1751-0473-3-16","article-title":"Boolean network simulations for life scientists","volume":"3","author":"Albert","year":"2008","journal-title":"Source Code Biol. Med"},{"key":"2023020204504970400_btw682-B2","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1186\/1471-2105-12-490","article-title":"Antelope: a hybrid-logic model checker for branching-time Boolean GRN analysis","volume":"12","author":"Arellano","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023020204504970400_btw682-B3","volume-title":"Principles of Model Checking","author":"Baier","year":"2008"},{"key":"2023020204504970400_btw682-B4","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1186\/1752-0509-7-135","article-title":"SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools","volume":"7","author":"Chaouiya","year":"2013","journal-title":"BMC Syst. Biol"},{"key":"2023020204504970400_btw682-B5","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1007\/3-540-45657-0_29","volume-title":"Proceedings of the 14th International Conference on Computer Aided Verification, CAV \u201902","author":"Cimatti","year":"2002"},{"key":"2023020204504970400_btw682-B6","first-page":"483","volume-title":"Graph Drawing","author":"Ellson","year":"2001"},{"key":"2023020204504970400_btw682-B7","first-page":"11","volume-title":"Proceedings of the 7th Python in Science Conferences (SciPy 2008)","author":"Hagberg","year":"2008"},{"key":"2023020204504970400_btw682-B8","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1109\/TCBB.2011.62","article-title":"Multiscale binarization of gene expression data for reconstructing boolean networks","volume":"9","author":"Hopfensitz","year":"2012","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinf. (TCBB)"},{"key":"2023020204504970400_btw682-B9","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780195079517.001.0001","volume-title":"The Origins of Order: Self Organization and Selection in Evolution","author":"Kauffman","year":"1993"},{"key":"2023020204504970400_btw682-B10","doi-asserted-by":"crossref","first-page":"130","DOI":"10.3389\/fbioe.2015.00130","article-title":"Approximating attractors of Boolean networks by iterative CTL model checking","volume":"3","author":"Klarner","year":"2015","journal-title":"Front. Bioeng. Biotechnol"},{"key":"2023020204504970400_btw682-B11","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1007\/s11047-015-9520-7","article-title":"Computing maximal and minimal trap spaces of Boolean networks","volume":"14","author":"Klarner","year":"2015","journal-title":"Nat. Comput"},{"key":"2023020204504970400_btw682-B12","doi-asserted-by":"crossref","first-page":"1529","DOI":"10.1093\/bioinformatics\/btr166","article-title":"Inferring Boolean network structure via correlation","volume":"27","author":"Maucher","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020204504970400_btw682-B13","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1093\/bioinformatics\/btq124","article-title":"Boolnet \u2013 an R package for generation, reconstruction, and analysis of boolean networks","author":"M\u00fcssel","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020204504970400_btw682-B14","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.biosystems.2009.04.008","article-title":"Logical modelling of regulatory networks with ginsim 2.3","volume":"97","author":"Naldi","year":"2009","journal-title":"Biosystems"},{"key":"2023020204504970400_btw682-B15","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1093\/bioinformatics\/btv013","article-title":"Cooperative development of logical modelling standards and tools with CoLoMoTo","volume":"31","author":"Naldi","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020204504970400_btw682-B16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0022-5193(05)80350-9","article-title":"Regulatory networks seen as asynchronous automata: a logical description","volume":"153","author":"Thomas","year":"1991","journal-title":"J. Theor. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/5\/770\/49038018\/bioinformatics_33_5_770.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/5\/770\/49038018\/bioinformatics_33_5_770.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,20]],"date-time":"2024-06-20T05:00:20Z","timestamp":1718859620000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/5\/770\/2725550"}},"subtitle":[],"editor":[{"given":"Cenk","family":"Sahinalp","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2016,12,5]]},"references-count":16,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2017,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw682","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,3,1]]},"published":{"date-parts":[[2016,12,5]]}}}