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Searches through every possible set of chemical reaction, enzyme pairs to create metabolite pathways from the input chemical to the output chemical. Used to find the optimal DNA sequences to add to a cell for a given input chemical, output chemical and cell.
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.
The aim of this repository is to assist in further improving and expanding the genome-scale human metabolic reconstruction through the use of issues. Please note that pull requests will be automatically closed.
Utility to simplify obtaining information from genome-scale models as well as their manipulation. This implementation is available only for working with COBRApy.
"Maps for when the living gets tough: Maneuvering through a hostile energy landscape" | Mondeel, Thierry D.G.A. Rehman, Samrina Zhang, Yanfei Verma, Malkhey Dürre, Peter Barberis, Matteo Westerhoff, Hans V. | 2016 | IFAC-PapersOnLine |