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Table 2 Description of all tools available with MetaNET

From: MetaNET - a web-accessible interactive platform for biological metabolic network analysis

Tool sub-category Tool name Tool description Source
Upload Data Upload file To upload file on MetaNET. Galaxy
Tool category: Format Converter
Import to MetaNET BiGGSBML Reader Converts BIGG SBML Format to reactions file. SBRT
PalssonSBML Reader Converts Palsson SBML Format to reactions file. SBRT
Metatool Input File Reader Converts input files of Metatool into reactions File. SBRT
Export to MetaNET Metatool Input File Writer Converts reaction Files into input files of Metatool. SBRT
Tool category: Network Information Retriever
Fetch IDs Fetch Objective function Retrieves reaction ID of objective function from SBML file. In-house
Fetch Gene IDs Retrieves list of all gene Ids from SBML file. In-house
Fetch Reaction IDs Retrieves list of reaction Ids from reactions file. SBRT
Fetch Catalyst IDs Retrieves list of all catalysts from SBML file. In-house
Fetch Chemical Species (Metabolites) Retrieves list of chemical species Ids from reactions file. SBRT
Fetch Reaction attributes Fetch Flux Constraints Retrieves flux bounds from SBML file In-house
Fetch Reactions-Genes Associations Retrieves reaction-gene reactions associations from SBML file. SBRT
Fetch Reactions-Catalysts Associations Retrieves reaction-catalyst associations from SBML file. SBRT
Fetch Other Info Generate Stochiometric Matrix Generates stoichiometry matrix. SBRT
Generate Linear Equations Generates system of linear equations. SBRT
Fetch Reactions Retrieves reactions without Ids. In-house
Fetch Reactants Retrieves list of all reactants from the given reactions file. In-house
Fetch Products Retrieves list of all products from the given reactions file. In-house
Fetch Equivalent Reactions Retrieves names of all stoichiometric equivalent reactions. SBRT
Fetch Flux Vectors Retrieves flux vectors from SBML file. SBRT
Tool category: Flux Balance Analysis
Single Objective Optimizer Single Objective Optimizer Computes optimal value of fluxes in a stoichiometric network using multiple constraints. SBRT
Multiple Objectives Optimizer Multiple Objectives Optimizer Computes optimal value of multiple objectives in a stoichiometric network using multiple constraints. SBRT
Tool category: Perturbation Analysis
Single Entity Knock-outs Reaction knock-out Optimizer Computes effects of deleting sets of reactions from a stoichiometric network. SBRT
Catalyst knock-out Optimizer Computes effects of deleting sets of catalysts from a stoichiometric network. SBRT
Gene Knock-out Optimizer Computes effects of deleting sets of genes from a stoichiometric network. SBRT
Pairwise Entity Knock-outs Pairwise Genes Knock-out Computes effects of deleting pairs of genes from a chemical reaction network for multi-target drug identification. SBRT
Pairwise Catalysts knock-out Computes effects of deleting pairs of catalysts from a chemical reaction network for multi-target drug identification. SBRT
Pairwise Reactions knock-out Computes effects of deleting pairs of reactions from a chemical reaction network for multi-target drug identification. SBRT
Tool category: Essentiality Test
Find Essential Reactions Essential Reactions Reporter Finds essential reactions of a network. In-house
Find Essential Catalysts Essential Catalysts Reporter Finds essential catalysts of a network. In-house
Find Essential Genes Essential Genes Reporter Finds essential genes of a network. In-house
Tool category: Flux Variability Analysis
Constraint Variations Create Constraint Variation file Creates constraint variation file for Flux Variability Analysis. In-house
Flux Variability Optimizer Computes optimal value of a single objective function for multiple set of flux constraints. SBRT
Find Flux caps Flux Cap Identification Creates caps for each unbounded flux in a stoichiometric network. SBRT
Tool category: Other Utilities
File Operations Remove beginning Removes constraints or objectives from a file. Galaxy
Select First Selects first n objectives or constraints from a file. Galaxy
Select Last Selects last n constraints or objectives from a file. Galaxy
Add constraint Adds constraint in a constraint file. Galaxy
Replace constraint Replaces constraint of particular reaction. In-house
Make pairs Makes all possible pairs of genes or catalysts or reactions IDs. In-house
Tool category: Flux Comparisons
Flux Distribution Comparison Flux Distribution Comparison Compares flux distributions for equality within a given tolerance. SBRT
Flux Intervals Comparison Flux Interval Comparison compares intervals for equality within a given tolerance. SBRT
Tool category: Random Generator
Random Generator Random Objectives Generator Generates random objective functions. SBRT
Random Constraints Generator Generates random constraints. SBRT
Tool category: Flux Distribution Plots
Flux Optimizer Plot Flux Optimization Plotter Plots result of FBA optimization. In-house
Essentiality Plots Reactions Essentiality Plotter Plots result of deleting sets of reactions versus objective function. In-house
Genes Essentiality Plotter Plots result of deleting sets of genes versus objective function. In-house
Catalysts Essentiality Plotter Plots result of deleting sets of catalysts versus objective function. In-house
Knock-Out Plots Reactions knock-out Plotter Plots the results of deleting sets of reactions or genes in a stoichiometric network. In-house
Genes knock-out Plotter Plots the results of deleting sets of genes in a stoichiometric network. In-house
Catalysts knock-out Plotter Plots the results of deleting sets of catalysts in a stoichiometric network. In-house
Tool category: Chemical Species participation
Grouping Chemical Species Chemical Species Participation as Reactants Groups chemical reactions based on the given chemical species as reactants. SBRT
Chemical Species Participation as Product Groups chemical reactions based on the given chemical species as products. SBRT
Single Species participation Single Chemical species Participation Finds chemical reactions containing given chemical species. In-house
Chokepoint Analysis Find Chokepoint Reactions finds chokepoint reactions of biological network. In-house
Tool category: Network Reducer
Reversible Reactions Breaker Reversible Reactions Breaker Breaks reversible reactions into pairs of irreversible “forward” and “reverse” reactions. SBRT
Redundant Reactions Remover Redundant Reactions Remover Removes redundant reactions from stoichiometric networks. SBRT
WW Network Reducer WW Network Reducer Reduces size of stoichiometric networks for the purpose of identifying the cycles they contain. SBRT
MS Network Reducer MS Network Reducer Reduces size of stoichiometric networks for the purpose of identifying the cycles they contain. SBRT
Tool category: Cycles/Paths Identifier
SLP Cycles SLP Cycle Identifier Identifies cycles in stoichiometric networks. SBRT
Extreme Paths Extreme Path Identifier Identifies extreme currents in stoichiometric networks. SBRT