MOTIVATION: The SBML Render Extension enables coloring and shape information of biochemical models to be stored in the Systems Biology Markup Language (SBML). Rendering of this stored graphical information in a portable and well supported system such as TeX would be useful for researchers preparing documentation and presentations. In addition, since the Render Extension is not yet supported by many applications, it is helpful for such rendering functionality be extended to the more popular CellDesigner annotation as well. RESULTS: SBML2TikZ supports automatic generation of graphics for biochemical models in the popular TeX typesetting system. The library generates a script of TeX macro commands for the vector graphics languages PGF/TikZ that can be compiled into scalable vector graphics described in a model. AVAILABILITY: Source code, documentation and compiled binaries for the SBML2TikZ library can be found at http://www.sbml2tikz.org. In addition, a web application is available at http://www.sys-bio.org/layout
MOTIVATION: The SBML Render Extension enables coloring and shape information of biochemical models to be stored in the Systems Biology Markup Language (SBML). Rendering of this stored graphical information in a portable and well supported system such as TeX would be useful for researchers preparing documentation and presentations. In addition, since the Render Extension is not yet supported by many applications, it is helpful for such rendering functionality be extended to the more popular CellDesigner annotation as well. RESULTS: SBML2TikZ supports automatic generation of graphics for biochemical models in the popular TeX typesetting system. The library generates a script of TeX macro commands for the vector graphics languages PGF/TikZ that can be compiled into scalable vector graphics described in a model. AVAILABILITY: Source code, documentation and compiled binaries for the SBML2TikZ library can be found at http://www.sbml2tikz.org. In addition, a web application is available at http://www.sys-bio.org/layout
Authors: M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang Journal: Bioinformatics Date: 2003-03-01 Impact factor: 6.937
Authors: Nicolas Le Novère; Michael Hucka; Huaiyu Mi; Stuart Moodie; Falk Schreiber; Anatoly Sorokin; Emek Demir; Katja Wegner; Mirit I Aladjem; Sarala M Wimalaratne; Frank T Bergman; Ralph Gauges; Peter Ghazal; Hideya Kawaji; Lu Li; Yukiko Matsuoka; Alice Villéger; Sarah E Boyd; Laurence Calzone; Melanie Courtot; Ugur Dogrusoz; Tom C Freeman; Akira Funahashi; Samik Ghosh; Akiya Jouraku; Sohyoung Kim; Fedor Kolpakov; Augustin Luna; Sven Sahle; Esther Schmidt; Steven Watterson; Guanming Wu; Igor Goryanin; Douglas B Kell; Chris Sander; Herbert Sauro; Jacky L Snoep; Kurt Kohn; Hiroaki Kitano Journal: Nat Biotechnol Date: 2009-08-07 Impact factor: 54.908
Authors: Natalie J Stanford; Martin Scharm; Paul D Dobson; Martin Golebiewski; Michael Hucka; Varun B Kothamachu; David Nickerson; Stuart Owen; Jürgen Pahle; Ulrike Wittig; Dagmar Waltemath; Carole Goble; Pedro Mendes; Jacky Snoep Journal: Methods Mol Biol Date: 2019