Software developed by our group
ANSEP Astrocyte Neuron Simulation Environment Platform
The Simulation Environment Platform, was created under the need to operate metabolic reconstructions with omic data, obtained experimentally, over the last years at the Pontificia Universidad Javeriana, in the context of neurodegenerative diseases (EN).
The platform is available and free of charge for the scientific community, offering tools that contribute to a better understanding of neurodegeneration processes, as well as the development of therapeutic or pharmacological strategies that reduce the impact and consequences of these diseases.
G2F Find and Fill Gaps in Metabolic Networks
The G2F package finds the gaps (metabolites not produced or not consumed in any other reaction), and fills it from the stoichiometric reactions of a reference metabolic reconstruction using a weighting function. Also the option to download all the set of gene-associated stoichiometric reactions for a specific organism from the KEGG database is available.
Minval: An R package for MINimal VALidation of Stoichiometric Reactions
The Minval package was designed as a tool to identify orphan metabolites and evaluate the mass and charge balance of stoichiometric reactions. The package also includes functions to characterize and write models in TSV and SBML formats, extract all reactants, products, metabolite names and compartments from a metabolic reconstruction.