{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,31]],"date-time":"2024-07-31T02:13:54Z","timestamp":1722392034814},"reference-count":13,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2006,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>The analysis of biochemical networks using a logical (Boolean) description is an important approach in Systems Biology. Recently, new methods have been proposed to analyze large signaling and regulatory networks using this formalism. Even though there is a large number of tools to set up models describing biological networks using a biochemical (kinetic) formalism, however, they do not support logical models.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Herein we present a flexible framework for setting up large logical models in a visual manner with the software tool ProMoT. An easily extendible library, ProMoT's inherent modularity and object-oriented concept as well as adaptive visualization techniques provide a versatile environment. Both the graphical and the textual description of the logical model can be exported to different formats.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>New features of ProMoT facilitate an efficient set-up of large Boolean models of biochemical interaction networks. The modeling environment is flexible; it can easily be adapted to specific requirements, and new extensions can be introduced. ProMoT is freely available from <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.mpi-magdeburg.mpg.de\/projects\/promot\/\" ext-link-type=\"uri\">http:\/\/www.mpi-magdeburg.mpg.de\/projects\/promot\/<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-7-506","type":"journal-article","created":{"date-parts":[[2006,11,17]],"date-time":"2006-11-17T22:34:01Z","timestamp":1163802841000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Visual setup of logical models of signaling and regulatory networks with ProMoT"],"prefix":"10.1186","volume":"7","author":[{"given":"Julio","family":"Saez-Rodriguez","sequence":"first","affiliation":[]},{"given":"Sebastian","family":"Mirschel","sequence":"additional","affiliation":[]},{"given":"Rebecca","family":"Hemenway","sequence":"additional","affiliation":[]},{"given":"Steffen","family":"Klamt","sequence":"additional","affiliation":[]},{"given":"Ernst Dieter","family":"Gilles","sequence":"additional","affiliation":[]},{"given":"Martin","family":"Ginkel","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2006,11,17]]},"reference":[{"key":"1245_CR1","volume-title":"Biological Feedback","author":"R Thomas","year":"1990","unstructured":"Thomas R, D'Ari R: Biological Feedback. 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