COBRA Toolbox
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- A multiscale agent-based model for the investigation of E. coli K12 metabolic response during biofilm formation
- Computational analysis of phenotypic space in heterologous polyketide biosynthesis -- applications to \textit{Escherichia coli}, \textit{Bacillus subtilis}, and \textit{Saccharomyces cerevisiae}
- Conditions for duality between fluxes and concentrations in biochemical networks
- \textit{In silico} predicted transcriptional regulatory control of steroidogenesis in spawning female fathead minnows (\textit{Pimephales promelas})
- Structural analysis of metabolic networks based on flux centrality
- Sbmltoolbox
- A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks
- iDynoR
- Metabolic impact assessment for heterologous protein production in \textit{Streptomyces lividans} based on genome-scale metabolic network modeling
- Metatool
- COBRApy
- Biomodel Engineering – From Structure to Behavior
- DFBAlab
- von Bertalanffy
- rBioNet
- VolEsti
- COMSTAT
- RKHSMetaMod
- meneco
- fastGapFill
- TensorLog
- BookIndRandSamplingMethods
- anNET
- Finding zeros of Hölder metrically subregular mappings via globally convergent Levenberg-Marquardt methods
- expa
- Hybrid metabolic network completion
- Polyrun
- \textit{In silico} genome-scale reconstruction and analysis of the \textit{Shewanella loihica} PV-4 metabolic network
- Billiard walk
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