Computational synthetic biology: Predicting DNA edits for bioengineering
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Updated
Mar 27, 2017 - Java
Computational synthetic biology: Predicting DNA edits for bioengineering
An R package to incorporate in a continuous way the gene-expression data as FBA flux boundaries in a metabolic model. Also, functions to calculate and plot the differences between model fluxes in different metabolic scenarios was included. This is an implementation of the algorithm described by Lee et al. (2012) in DOI: 10.1186/1752-0509-6-73.
Chemical reaction balancing web service
Code for Model-based Design of Bistable Cell Factories for Metabolic Engineering
Enumeration of biosynthetic pathways from metabolic networks
MNXref: Reconciliation of metabolites and biochemical reactions for metabolic networks
A study on multi-omic oscillations in Escherichia coli metabolic networks. Journal paper.
Compute minimal metabolic precursors sets that enable the production of target metabolites
Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae
Utility to simplify obtaining information from genome-scale models as well as their manipulation. This implementation is available only for working with COBRApy.
A GPU implementation of the sampling algorithm ACHR.
MOOMIN is a tool for analysing differential expression data
Enzymatic Link Prediction
An R package to find the gaps in metabolic networks, and fill it from the stoichiometric reactions of a reference metabolic reconstruction using a weighting function. Also include the option to download all the set of gene-associated stoichiometric reactions for a specific organism from the KEGG database.
Kinetic modeling of glucose and acetate metabolisms in E. coli
Bi-level regularized flux balance analysis of Synechococcus spp. PCC 7002
Trim, extract, and convert GEMs
A RMosek optimization interface for the Sybil package
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