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PMFA / Principal Metabolic Flux Mode Analysis
Allows analysis of metabolic networks. PMFA enables users to find metabolic flux modes that explains the variance in gene expression or fluxomic data collected from heterogeneous environmental conditions, without requiring a fixed set of predefined pathways to be given. The method combines stoichiometric flux analysis and principal component analysis. It can be applied to genome-scale metabolic network. The software includes a sparse variant of PMFA that favors flux modes containing a small number of reactions.
CGManalyzer
Provides functions for continuous glucose monitoring (CGM) studies. CGManalyzer is an analytic tool that can be used to analyze a CGM study from the very beginning to the end, including reading and displaying data, calculating regular statistics (e.g., mean, median, standard deviation, confidence interval) and nonlinear statistics, conducting group comparison and displaying results. The software can be applied to data measured by various existing CGM devices such as FreeStyle Libre, Glutalor, Dexcom, Medtronic CGM.
PSOMCS / Particle Swarm Optimization Constrained Minimal cut Set
Obtains optimal designs of metabolic networks satisfying multiple objectives. PSOMCS uses particle swarm optimization along with the direct calculation of concept of constrained minimal cut sets from the stoichiometric matrix. It finds competitive knockout strategies and designs compared to other current methods and is in some cases significantly faster. The tool can be used to identify knockouts which will force optimal desired behaviors in large and genome scale metabolic networks.
MC3 / Model & Constraint Consistency Checker
Performs model and constraint consistency checking. MC3 is useful for two operations: (1) identification of potential connectivity and topological issues for a given stoichiometric matrix and (2) description of issues that arise during constraint-based optimization. This tool is able to identify the conditions for dead-end metabolites. It can be useful for the scientist community for documenting and reporting issues with each published model.
Biomass
Returns the estimated biomass composition in amino acids, nucleotides (NTPs) and deoxynucleotides (dNTPs) for an organism, from files with selected sequences and transcriptomic data. Biomass is a java application that allows users to obtain results rapidly. The obtained data can be directly included in the biomass equation of a genome-scale metabolic model. The results obtained using this method and the described procedure are fairly close to experimental data, showing that the estimation of amino acid and nucleotide compositions from genome information and transcriptomic data are a good alternative when no experimental data is available.
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