{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:14:34Z","timestamp":1787008474319,"version":"build-2736575974"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Motivation: Biochemical modeling efforts now frequently take advantage of the possibility to automatically create reaction networks based on the specification of pairwise molecular interactions. Even though a variety of tools exist to visualize the resulting networks, defining the rules for the molecular interactions typically requires writing scripts, which impacts the non-specialist accessibility of those approaches. We introduce the Simmune Modeler that allows users to specify molecular complexes and their interactions as well as the reaction-induced modifications of the molecules through a flexible visual interface. It can take into account the positions of the components of trans-membrane complexes relative to the embedding membranes as well as symmetry aspects affecting the reactions of multimeric molecular structures. Models created with this tool can be simulated using the Simmune Simulator or be exported as SBML code or as files describing the reaction networks as systems of ODEs for import into Matlab.<\/jats:p>\n                  <jats:p>Availability: The Simmune Modeler and the associated simulators as well as extensive additional documentation and tutorials are freely available for Linux, Mac and Windows: http:\/\/go.usa.gov\/QeH (Note shortened case-sensitive URL!).<\/jats:p>\n                  <jats:p>Contact: \u00a0zhangfen@niaid.nih.gov or mms@niaid.nih.gov<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary Data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt134","type":"journal-article","created":{"date-parts":[[2013,3,18]],"date-time":"2013-03-18T20:40:12Z","timestamp":1363639212000},"page":"1229-1230","source":"Crossref","is-referenced-by-count":37,"title":["The Simmune Modeler visual interface for creating signaling networks based on bi-molecular interactions"],"prefix":"10.1093","volume":"29","author":[{"given":"Fengkai","family":"Zhang","sequence":"first","affiliation":[{"name":"Computational Biology Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bastian R.","family":"Angermann","sequence":"additional","affiliation":[{"name":"Computational Biology Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Meier-Schellersheim","sequence":"additional","affiliation":[{"name":"Computational Biology Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,3,17]]},"reference":[{"key":"2023012810390530400_btt134-B1","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1038\/nmeth.1861","article-title":"Computational modeling of cellular signaling processes embedded into dynamic spatial contexts","volume":"9","author":"Angermann","year":"2012","journal-title":"Nat. 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Bioeng."},{"key":"2023012810390530400_btt134-B5","doi-asserted-by":"crossref","first-page":"re6","DOI":"10.1126\/stke.3442006re6","article-title":"Rules for modeling signal-transduction systems","volume":"2006","author":"Hlavacek","year":"2006","journal-title":"Sci. STKE"},{"key":"2023012810390530400_btt134-B6","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1038\/nbt1054","article-title":"Automatic generation of cellular reaction networks with Moleculizer 1.0","volume":"23","author":"Lok","year":"2005","journal-title":"Nat. Biotechnol."},{"key":"2023012810390530400_btt134-B7","doi-asserted-by":"crossref","first-page":"e82","DOI":"10.1371\/journal.pcbi.0020082","article-title":"Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method","volume":"2","author":"Meier-Schellersheim","year":"2006","journal-title":"PLoS Comput. Biol."},{"key":"2023012810390530400_btt134-B8","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1038\/nmeth.1546","article-title":"Efficient modeling, simulation and coarse-graining of biological complexity with NFsim","volume":"8","author":"Sneddon","year":"2011","journal-title":"Nat. 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