{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T07:01:11Z","timestamp":1791270071167,"version":"4.1.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: BIOCHAM (the BIOCHemical Abstract Machine) is a software environment for modeling biochemical systems. It is based on two aspects: (1) the analysis and simulation of boolean, kinetic and stochastic models and (2) the formalization of biological properties in temporal logic. BIOCHAM provides tools and languages for describing protein networks with a simple and straightforward syntax, and for integrating biological properties into the model. It then becomes possible to analyze, query, verify and maintain the model with respect to those properties. For kinetic models, BIOCHAM can search for appropriate parameter values in order to reproduce a specific behavior observed in experiments and formalized in temporal logic. Coupled with other methods such as bifurcation diagrams, this search assists the modeler\/biologist in the modeling process.<\/jats:p>\n               <jats:p>Availability: BIOCHAM (v. 2.5) is a free software available for download, with example models, at<\/jats:p>\n               <jats:p>Contact: \u00a0Sylvain.Soliman@inria.fr<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl172","type":"journal-article","created":{"date-parts":[[2006,5,4]],"date-time":"2006-05-04T00:30:37Z","timestamp":1146702637000},"page":"1805-1807","source":"Crossref","is-referenced-by-count":199,"title":["BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge"],"prefix":"10.1093","volume":"22","author":[{"given":"Laurence","family":"Calzone","sequence":"first","affiliation":[{"name":"Projet Contraintes, INRIA Rocquencourt \u00a0 BP105, 78153 Le Chesnay Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fran\u00e7ois","family":"Fages","sequence":"additional","affiliation":[{"name":"Projet Contraintes, INRIA Rocquencourt \u00a0 BP105, 78153 Le Chesnay Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sylvain","family":"Soliman","sequence":"additional","affiliation":[{"name":"Projet Contraintes, INRIA Rocquencourt \u00a0 BP105, 78153 Le Chesnay Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2006,4,10]]},"reference":[{"key":"2023012409011320700_b1","doi-asserted-by":"crossref","first-page":"3289","DOI":"10.1093\/bioinformatics\/bth378","article-title":"BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains","volume":"20","author":"Blinov","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012409011320700_b2","first-page":"85","article-title":"Using hybrid concurrent constraint programming to model dynamic biological systems","author":"Bockmayer","year":"2002"},{"key":"2023012409011320700_b3","article-title":"Machine learning biochemical networks from temporal logic properties","author":"Calzone","year":"2006","journal-title":"Trans. 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