ArticleBioinformatics (Oxford, England)2010
BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- AutoAnalyze in Systems Biology.Bioinformatics and biology insights · 2019Article
- Computer-aided biochemical programming of synthetic microreactors as diagnostic devices.Molecular systems biology · 2018Article
- Elementary flux modes analysis of functional domain networks allows a better metabolic pathway interpretation.PloS one · 2013Article
- Genetic design automation: engineering fantasy or scientific renewal?Trends in biotechnology · 2012Review
- Computational tools for the synthetic design of biochemical pathways.Nature reviews. Microbiology · 2012Review
- Standard biological parts knowledgebase.PloS one · 2011Article
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Authors and funding
8 authors.
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Abstract
motivationSynthetic biology studies how to design and construct biological systems with functions that do not exist in nature. Biochemical networks, although easier to control, have been used less frequently than genetic networks as a base to build a synthetic system. To date, no clear engineering principles exist to design such cell-free biochemical networks.
resultsWe describe a methodology for the construction of synthetic biochemical networks based on three main steps: design, simulation and experimental validation. We developed BioNetCAD to help users to go through these steps. BioNetCAD allows designing abstract networks that can be implemented thanks to CompuBioTicDB, a database of parts for synthetic biology. BioNetCAD enables also simulations with the HSim software and the classical Ordinary Differential Equations (ODE). We demonstrate with a case study that BioNetCAD can rationalize and reduce further experimental validation during the construction of a biochemical network. AVAILABILITY AND IMPLEMENTATION: BioNetCAD is freely available at http://www.sysdiag.cnrs.fr/BioNetCAD. It is implemented in Java and supported on MS Windows. CompuBioTicDB is freely accessible at http://compubiotic.sysdiag.cnrs.fr/.
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Registered trials
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