met4j merge requestshttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests2023-07-25T17:43:56+02:00https://forgemia.inra.fr/metexplore/met4j/-/merge_requests/31ORA2023-07-25T17:43:56+02:00Clement FrainayORAAdd app for "traditional" pathway enrichment analysis (ORA)Add app for "traditional" pathway enrichment analysis (ORA)Clement FrainayClement Frainayhttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/27Implementation of topological pathway analysis2023-07-25T16:01:20+02:00Clement FrainayImplementation of topological pathway analysisAn alternative to over-representation analysis for pathway analysis. This shifts from the simplistic view of pathways as "bag of reactions" and takes pathway connectivity into account, using centrality measure to gauge the impact of each...An alternative to over-representation analysis for pathway analysis. This shifts from the simplistic view of pathways as "bag of reactions" and takes pathway connectivity into account, using centrality measure to gauge the impact of each measured individual on the whole pathway.Clement FrainayClement Frainayhttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/29add ReactionDistanceMatrix app2023-07-10T17:34:55+02:00Louison Fresnaisadd ReactionDistanceMatrix appAdd a Met4j_toolbox app to compute the pairwise distance matrix on the reaction graph.
This reaction graph can be pruned with a list of side compounds and a list of reactions to exclude.Add a Met4j_toolbox app to compute the pairwise distance matrix on the reaction graph.
This reaction graph can be pruned with a list of side compounds and a list of reactions to exclude.Louison FresnaisLouison Fresnaishttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/30Flat SBML (no compartments)2023-06-26T15:11:31+02:00Clement FrainayFlat SBML (no compartments)Create an app that merge compartments and create a 'flat' version of a SBML.
This is similar to what exists in the graph module, but extended to bioNetworks.Create an app that merge compartments and create a 'flat' version of a SBML.
This is similar to what exists in the graph module, but extended to bioNetworks.Clement FrainayClement Frainayhttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/28Pathway network creation2023-02-14T14:55:44+01:00Clement FrainayPathway network creation# Create app to build networks of pathways.
Two main strategies : **"pure" overlap of compounds** or **input/output (only sources and sinks, create directed network)**
## Context
Genome-scale metabolic networks are often partitioned int...# Create app to build networks of pathways.
Two main strategies : **"pure" overlap of compounds** or **input/output (only sources and sinks, create directed network)**
## Context
Genome-scale metabolic networks are often partitioned into metabolic pathways. Pathways are frequently considered independently despite frequent coupling in their activity due to shared metabolites. In order to decipher the interconnections linking overlapping pathways, this app proposes the creation of \"Pathway Network\", where two pathways are linked if they share compounds.Clement FrainayClement Frainayhttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/25Feature/bipartite distance matrix app22023-01-12T16:48:28+01:00Louison FresnaisFeature/bipartite distance matrix app2Add bipartite distance matrix app
TODO: unit testAdd bipartite distance matrix app
TODO: unit testLouison FresnaisLouison Fresnaishttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/26Fix handling of weighted metabolic graph as undirected2023-01-06T17:35:38+01:00Clement FrainayFix handling of weighted metabolic graph as undirectedThe "AsUndirected" processing of BioGraph simply add reverse edges for all existing edges. However, in the case of weighted graphs, edges' weight wasn't passed to the newly created ones. This raised other concerns, such as the use of nod...The "AsUndirected" processing of BioGraph simply add reverse edges for all existing edges. However, in the case of weighted graphs, edges' weight wasn't passed to the newly created ones. This raised other concerns, such as the use of node weighting transferred to edges (such as degree weighting used in distance matrices), where reversed and original edges sharing the same weight might not be suited despite ensuring the symmetry property of the metric space.
There is also special cases that might be of interest for some apps, such as avoiding doubling of reversible reaction edges in compound graphs.
This merge request aims at ensuring appropriate behaviour of "undirecting" BioGraphs and expand test casesClement FrainayClement Frainayhttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/18Feature/get distance manyto many2022-12-07T12:16:05+01:00Louison FresnaisFeature/get distance manyto manyAdd getDistances method to the shortestPath class and use it in the DistanceMatrix app.Add getDistances method to the shortestPath class and use it in the DistanceMatrix app.Louison FresnaisLouison Fresnaishttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/24Expand SBML Mapping2022-12-02T11:57:47+01:00Clement FrainayExpand SBML MappingExpand mapping of chemical data onto metabolic networks (i.e. retrieving chemical entities within a metabolic network)
As datasets sometimes provides only chemical names, provides fuzzy matching to get entries with most similar namesExpand mapping of chemical data onto metabolic networks (i.e. retrieving chemical entities within a metabolic network)
As datasets sometimes provides only chemical names, provides fuzzy matching to get entries with most similar namesClement FrainayClement Frainayhttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/23reaction balance2022-12-02T11:43:47+01:00Ludovic Cottretreaction balanceIn the metabolic network reconstruction process, an important step is to check the balance of the reation. This MR proposes to add an APP to check the balance of the reactions and to show which metabolites are unbalanced.In the metabolic network reconstruction process, an important step is to check the balance of the reation. This MR proposes to add an APP to check the balance of the reactions and to show which metabolites are unbalanced.Ludovic CottretLudovic Cottrethttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/22Feature/set ids from file2022-11-15T14:05:28+01:00Ludovic CottretFeature/set ids from fileThe goal is to develop an app to translate ids of metabolic entities.The goal is to develop an app to translate ids of metabolic entities.Ludovic CottretLudovic Cottrethttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/20Feature/get seeds2022-10-21T18:59:18+02:00Clement FrainayFeature/get seedsIdentify sources and/or targets in whole model or in external/exchange compartment. This could helps analyzing medium requirement and production capacity, as well as metabolic cooperationIdentify sources and/or targets in whole model or in external/exchange compartment. This could helps analyzing medium requirement and production capacity, as well as metabolic cooperationClement FrainayClement Frainayhttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/19create apps to export degree and chemical similarity weights for compound graphs2022-09-22T15:55:13+02:00Clement Frainaycreate apps to export degree and chemical similarity weights for compound graphsApps that export tabulated files with edge list and weight. Can be directly imported in Cytoscape.Apps that export tabulated files with edge list and weight. Can be directly imported in Cytoscape.Clement FrainayClement Frainayhttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/16Features/reaction side cpds2022-09-16T14:30:17+02:00Louison FresnaisFeatures/reaction side cpdsAdd the computation of reaction-wise side compounds.
The remaining tasks are:
- Add tests
- Test that the results are biologically relevant
- Update the graph construction to integrate reaction-wise side compounds
- Discuss the archit...Add the computation of reaction-wise side compounds.
The remaining tasks are:
- Add tests
- Test that the results are biologically relevant
- Update the graph construction to integrate reaction-wise side compounds
- Discuss the architecture of this new featureLouison FresnaisLouison Fresnaishttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/17Feature/app sbml extract2022-07-29T10:57:53+02:00Clement FrainayFeature/app sbml extractImprove Met4J usability for Galaxy Workflow by adding utilities apps that exploit bioNetworks functions
- [x] decomposeSBML to get bioentities in sbml as list of ids
- [x] Reaction2Reactants to get list of metabolites from sbml + list of...Improve Met4J usability for Galaxy Workflow by adding utilities apps that exploit bioNetworks functions
- [x] decomposeSBML to get bioentities in sbml as list of ids
- [x] Reaction2Reactants to get list of metabolites from sbml + list of reactions
- [x] Reaction2Gene to get list of genes from sbml + list of reactions
- [ ] ...https://forgemia.inra.fr/metexplore/met4j/-/merge_requests/15Draft: parallelize several GetShortestPath loops2022-06-01T10:40:18+02:00Louison FresnaisDraft: parallelize several GetShortestPath loopsDecreasing shortest path running time by implementing parallelstream loops in :
- getShortestPathsUnionList
- getMetricClosureGraph
- getAllShortestPathsDecreasing shortest path running time by implementing parallelstream loops in :
- getShortestPathsUnionList
- getMetricClosureGraph
- getAllShortestPathsLouison FresnaisLouison Fresnaishttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/11[toolbox] Galaxy wrappers and json description2022-05-23T15:12:55+02:00Ludovic Cottret[toolbox] Galaxy wrappers and json descriptionThe first goal is to generate automatically wrapper xml files for Galaxy.
The goal is to generate a JSON file from the parameters of the apps. This will facilitate connection with other high-level tools.The first goal is to generate automatically wrapper xml files for Galaxy.
The goal is to generate a JSON file from the parameters of the apps. This will facilitate connection with other high-level tools.Ludovic CottretLudovic Cottrethttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/13Docker2022-04-25T14:17:07+02:00Ludovic CottretDockerThe goal of this MR is to build a doccker container in the CI/CD.The goal of this MR is to build a doccker container in the CI/CD.Ludovic CottretLudovic Cottrethttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/12Singularity2022-04-22T16:44:49+02:00Ludovic CottretSingularityThe goal of this MR is to produce singularity container from CI/CD and make it available by a link.The goal of this MR is to produce singularity container from CI/CD and make it available by a link.Ludovic CottretLudovic Cottrethttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/10[ToolBox] Advanced compound graph2022-04-19T17:03:37+02:00Clement Frainay[ToolBox] Advanced compound graphMetabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes.
While Carbon Skeleton...Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes.
While Carbon Skeleton Graph offer a relevant alternative topology for graph-based analysis, it requires compounds' structure information, usually not provided in model, and difficult to retrieve for model with sparse cross-reference annotations.
In contrary to the SBML2Graph app that performs a raw conversion of the SBML content, the present app propose a fine-tuned creation of compound graph from predefined list of side compounds and degreeĀ² weighting to get relevant structure without structural data.This app also enable Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.Clement FrainayClement Frainay