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 |