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Publication for BioJADE
Evolving Robust Gene Regulatory Networks
[…] igm [, ]. Addressing this need an array of computational tools and software has been developed to aid the design, simulation and optimization process in synthetic biology. Many of these tools such as Biojade, ProMoT, TikerCell, Jarnac, GenoCAD etc. have become very popular and proven useful for the practitioners. Nevertheless, the issue of robustness in computer aided design of synthetic gene netw […]
A survey of enabling technologies in synthetic biology
[…] Thirty software tools, many of which have been recently reviewed , were listed in Question 10 throughout the duration of the survey: ApE (http://biologylabs.utah.edu/jorgensen/wayned/ape), BioJADE (http://web.mit.edu/jagoler/www/biojade), BioNetCAD (http://www.sysdiag.cnrs.fr/BioNetCAD), Cell Designer (http://celldesigner.org), ClothoCAD (http://www.clothocad.org), COPASI (http://www.co […]
Mathematical Modeling: Bridging the Gap between Concept and Realization in Synthetic Biology
[…] the modeling outcomes, thus relieving users of the burden of setting up and solving mathematical equations. A nonexhaustive listing of these software includes Athena (http://www.codeplex.com/athena), BioJade (http://web.mit.edu/jagoler/www/biojade), Gepasi (http://www.gepasi.org), SynBioSS (http://synbioss.sourceforge.net/), which reads and writes in SBML, and TinkerCell (http://www.tinkercell.com […]
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