{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T23:13:27Z","timestamp":1790723607041,"version":"4.1.0"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2018,6,27]],"date-time":"2018-06-27T00:00:00Z","timestamp":1530057600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000185","name":"Defense Advanced Research Projects Agency","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000185","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000185","name":"DARPA","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000185","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Big Mechanism Program"},{"DOI":"10.13039\/100000183","name":"US Army Research Office","doi-asserted-by":"crossref","award":["W911NF-14-1-0367"],"award-info":[{"award-number":["W911NF-14-1-0367"]}],"id":[{"id":"10.13039\/100000183","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000183","name":"US Army Research Office","doi-asserted-by":"crossref","award":["W911NF-14-1-0395"],"award-info":[{"award-number":["W911NF-14-1-0395"]}],"id":[{"id":"10.13039\/100000183","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>We present an overview of the Kappa platform, an integrated suite of analysis and visualization techniques for building and interactively exploring rule-based models. The main components of the platform are the Kappa Simulator, the Kappa Static Analyzer and the Kappa Story Extractor. In addition to these components, we describe the Kappa User Interface, which includes a range of interactive visualization tools for rule-based models needed to make sense of the complexity of biological systems. We argue that, in this approach, modeling is akin to programming and can likewise benefit from an integrated development environment. Our platform is a step in this direction.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We discuss details about the computation and rendering of static, dynamic, and causal views of a model, which include the contact map (CM), snaphots at different resolutions, the dynamic influence network (DIN) and causal compression. We provide use cases illustrating how these concepts generate insight. Specifically, we show how the CM and snapshots provide information about systems capable of polymerization, such as Wnt signaling. A well-understood model of the KaiABC oscillator, translated into Kappa from the literature, is deployed to demonstrate the DIN and its use in understanding systems dynamics. Finally, we discuss how pathways might be discovered or recovered from a rule-based model by means of causal compression, as exemplified for early events in EGF signaling.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The Kappa platform is available via the project website at kappalanguage.org. All components of the platform are open source and freely available through the authors\u2019 code repositories.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty272","type":"journal-article","created":{"date-parts":[[2018,4,16]],"date-time":"2018-04-16T19:11:48Z","timestamp":1523905908000},"page":"i583-i592","source":"Crossref","is-referenced-by-count":107,"title":["The Kappa platform for rule-based modeling"],"prefix":"10.1093","volume":"34","author":[{"given":"Pierre","family":"Boutillier","sequence":"first","affiliation":[{"name":"Department of Systems Biology, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mutaamba","family":"Maasha","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xing","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Harvard Medical School, Boston, MA, USA"},{"name":"Edgewise Networks, Burlington, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H\u00e9ctor F","family":"Medina-Abarca","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean","family":"Krivine","sequence":"additional","affiliation":[{"name":"IRIF, Universit\u00e9 Paris-Diderot \u2013 Paris Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00e9r\u00f4me","family":"Feret","sequence":"additional","affiliation":[{"name":"D\u00e9partement d\u2019informatique de l\u2019ENS (INRIA\/ENS\/CNRS), PSL Research University, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ioana","family":"Cristescu","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angus G","family":"Forbes","sequence":"additional","affiliation":[{"name":"Department of Computational Media, UC Santa Cruz, Santa Cruz, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Walter","family":"Fontana","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,6,27]]},"reference":[{"key":"2023051604334555000_bty272-B1","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1007\/978-3-319-40530-8_5","article-title":"A software package for chemically inspired graph transformation","volume":"9761","author":"Andersen","year":"2016","journal-title":"Lecture Notes Computer Sci"},{"key":"2023051604334555000_bty272-B2","doi-asserted-by":"crossref","first-page":"130.","DOI":"10.1038\/nmeth0211-130","article-title":"New approaches to modeling complex biochemistry","volume":"8","author":"Bachman","year":"2011","journal-title":"Nat. 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