|
|
| Name |
Description |
Version |
Minimum Galaxy Version |
|
|
Create a compound to reactions distance matrix. |
2.0.1 |
16.01 |
|
|
Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity. |
2.0.1 |
16.01 |
|
|
Compute the Choke points of a metabolic network. |
2.0.1 |
16.01 |
|
|
Provides tabulated compound graph edge list, with one column with target's degree. |
2.0.1 |
16.01 |
|
|
Create a compound to compound distance matrix. |
2.0.1 |
16.01 |
|
|
Extract pathway(s) from a SBML file and create a sub-network SBML file |
2.0.1 |
16.01 |
|
|
Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. |
2.0.1 |
16.01 |
|
|
Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds of interests ids, one per row. |
2.0.1 |
16.01 |
|
|
Create a subnetwork from a metabolic network in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. |
2.0.1 |
16.01 |
|
|
Convert FBC package annotations to sbml html notes |
2.0.1 |
16.01 |
|
|
Get gene lists from a list of reactions and a SBML file. |
2.0.1 |
16.01 |
|
|
Get reactant lists from a list of reactions and a SBML file. |
2.0.1 |
16.01 |
|
|
Build a SBML file from KEGG organism-specific pathways. Uses Kegg API. |
2.0.1 |
16.01 |
|
|
Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets. |
2.0.1 |
16.01 |
|
|
Compute the MetaboRank, a custom personalized PageRank for metabolic network. |
2.0.1 |
16.01 |
|
|
This tool runs edit-distance based fuzzy matching to perform near-similar name matching between a metabolic model and a list of chemical names in a dataset. A harmonization processing is performed on chemical names with substitutions of common patterns among synonyms, in order to create aliases on which classical fuzzy matching can be run efficiently. |
2.0.1 |
16.01 |
|
|
Create a report summarizing several graph measures characterising the structure of a metabolic network. |
2.0.1 |
16.01 |
|
|
Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test. |
2.0.1 |
16.01 |
|
|
Perform a network expansion from a set of compound targets to create a precursor network. |
2.0.1 |
16.01 |
|
|
Create a reaction to reaction distance matrix. |
2.0.1 |
16.01 |
|
|
Create a graph representation of a SBML file content, and export it in graph file format. |
2.0.1 |
16.01 |
|
|
Create a tabulated file listing reaction attributes from a SBML file |
2.0.1 |
16.01 |
|
|
Check balance of all the reactions in a SBML. |
2.0.1 |
16.01 |
|
|
Perform a network expansion from a set of compound seeds to create a scope network |
2.0.1 |
16.01 |
|
|
Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology |
2.0.1 |
16.01 |
|
|
Scan a network to identify side compounds. |
2.0.1 |
16.01 |
|
|
Create a Sbml File from a tabulated file that contains the reaction ids and the formulas |
2.0.1 |
16.01 |
|
|
Run a Topological Pathway Analysis (TPA) to identify key pathways based on topological properties of its constituting compounds. |
2.0.1 |
16.01 |
|
|
Create a Meta-Network from two sub-networks in SBML format. |
2.0.1 |
16.01 |
|
|
Extract databases' references from SBML annotations or notes. |
2.0.1 |
16.01 |
|
|
Get proteome in fasta format of a model present in the BIGG database |
2.0.1 |
16.01 |
|
|
Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others. |
2.0.1 |
16.01 |
|
|
Create a tabulated file with metabolite attributes from a SBML file |
2.0.1 |
16.01 |
|
|
Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam) |
2.0.1 |
16.01 |
|
|
Advanced creation of a compound graph representation of a SBML file content |
2.0.1 |
16.01 |
|
|
Creation of a Pathway Network representation of a SBML file content |
2.0.1 |
16.01 |
|
|
General SBML model processing |
2.0.1 |
16.01 |
|
|
Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges |
2.0.1 |
16.01 |
|
|
Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas |
2.0.1 |
16.01 |
|
|
Set EC numbers to reactions in a SBML file from a tabulated file containing the reaction ids and the EC numbers |
2.0.1 |
16.01 |
|
|
Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way |
2.0.1 |
16.01 |
|
|
Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids |
2.0.1 |
16.01 |
|
|
Set names to network objects in a SBML file from a tabulated file containing the object ids and the names |
2.0.1 |
16.01 |
|
|
Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways |
2.0.1 |
16.01 |
|
|
Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references |
2.0.1 |
16.01 |
|
|
Extract pathway(s) from a SBML file and create a sub-network SBML file |
2.0.1 |
16.01 |
|
|
Get gene lists from a list of reactions and a SBML file. |
2.0.1 |
16.01 |
|
|
Get reactant lists from a list of reactions and a SBML file. |
2.0.1 |
16.01 |
|
|
Extract databases' references from SBML annotations or notes. |
2.0.1 |
16.01 |
|
|
Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others. |
2.0.1 |
16.01 |
|
|
Create a tabulated file with metabolite attributes from a SBML file |
2.0.1 |
16.01 |
|
|
Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges |
2.0.1 |
16.01 |
|
|
Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas |
2.0.1 |
16.01 |
|
|
Set EC numbers to reactions in a SBML file from a tabulated file containing the reaction ids and the EC numbers |
2.0.1 |
16.01 |
|
|
Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way |
2.0.1 |
16.01 |
|
|
Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids |
2.0.1 |
16.01 |
|
|
Set names to network objects in a SBML file from a tabulated file containing the object ids and the names |
2.0.1 |
16.01 |
|
|
Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways |
2.0.1 |
16.01 |
|
|
Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references |
2.0.1 |
16.01 |
|
|
Get proteome in fasta format of a model present in the BIGG database |
2.0.1 |
16.01 |
|
|
Convert FBC package annotations to sbml html notes |
2.0.1 |
16.01 |
|
|
Build a SBML file from KEGG organism-specific pathways. Uses Kegg API. |
2.0.1 |
16.01 |
|
|
Create a graph representation of a SBML file content, and export it in graph file format. |
2.0.1 |
16.01 |
|
|
Create a tabulated file listing reaction attributes from a SBML file |
2.0.1 |
16.01 |
|
|
Create a Sbml File from a tabulated file that contains the reaction ids and the formulas |
2.0.1 |
16.01 |
|
|
Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam) |
2.0.1 |
16.01 |
|
|
Advanced creation of a compound graph representation of a SBML file content |
2.0.1 |
16.01 |
|
|
Creation of a Pathway Network representation of a SBML file content |
2.0.1 |
16.01 |
|
|
General SBML model processing |
2.0.1 |
16.01 |
|
|
This tool runs edit-distance based fuzzy matching to perform near-similar name matching between a metabolic model and a list of chemical names in a dataset. A harmonization processing is performed on chemical names with substitutions of common patterns among synonyms, in order to create aliases on which classical fuzzy matching can be run efficiently. |
2.0.1 |
16.01 |
|
|
Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test. |
2.0.1 |
16.01 |
|
|
Create a compound to reactions distance matrix. |
2.0.1 |
16.01 |
|
|
Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity. |
2.0.1 |
16.01 |
|
|
Compute the Choke points of a metabolic network. |
2.0.1 |
16.01 |
|
|
Provides tabulated compound graph edge list, with one column with target's degree. |
2.0.1 |
16.01 |
|
|
Create a compound to compound distance matrix. |
2.0.1 |
16.01 |
|
|
Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. |
2.0.1 |
16.01 |
|
|
Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds of interests ids, one per row. |
2.0.1 |
16.01 |
|
|
Create a subnetwork from a metabolic network in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. |
2.0.1 |
16.01 |
|
|
Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets. |
2.0.1 |
16.01 |
|
|
Compute the MetaboRank, a custom personalized PageRank for metabolic network. |
2.0.1 |
16.01 |
|
|
Create a report summarizing several graph measures characterising the structure of a metabolic network. |
2.0.1 |
16.01 |
|
|
Perform a network expansion from a set of compound targets to create a precursor network. |
2.0.1 |
16.01 |
|
|
Create a reaction to reaction distance matrix. |
2.0.1 |
16.01 |
|
|
Perform a network expansion from a set of compound seeds to create a scope network |
2.0.1 |
16.01 |
|
|
Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology |
2.0.1 |
16.01 |
|
|
Scan a network to identify side compounds. |
2.0.1 |
16.01 |
|
|
Run a Topological Pathway Analysis (TPA) to identify key pathways based on topological properties of its constituting compounds. |
2.0.1 |
16.01 |
|
|
Check balance of all the reactions in a SBML. |
2.0.1 |
16.01 |
|
|
Create a Meta-Network from two sub-networks in SBML format. |
2.0.1 |
16.01 |