met4j merge requestshttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests2021-12-16T12:14:40+01:00https://forgemia.inra.fr/metexplore/met4j/-/merge_requests/5skip coverage deploy2021-12-16T12:14:40+01:00Ludovic Cottretskip coverage deployLudovic 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/6Remove equals overriding of BioEntity and protects creation of BioParticipant2022-01-25T16:27:58+01:00Ludovic CottretRemove equals overriding of BioEntity and protects creation of BioParticipant- Two bioentity were equals if they had the same id. Now, the two objects must be equal.
- Constructors of BioEnzymeParticipant and BioReactant are now "protected". This avoids to create redundant participants. A BioCollection for each o...- Two bioentity were equals if they had the same id. Now, the two objects must be equal.
- Constructors of BioEnzymeParticipant and BioReactant are now "protected". This avoids to create redundant participants. A BioCollection for each one has been created in the BioNetwork
- The constant parameter is not saved anymore when loading a SBML file. It's not used in Met4j applications. If we want to save reactant attributes, we have to do at the reaction level now.Ludovic CottretLudovic Cottrethttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/4remove coverage from the cache in ci2021-12-16T11:37:41+01:00Ludovic Cottretremove coverage from the cache in ciLudovic CottretLudovic Cottrethttps://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/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/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/8handling mutliple compartments in side compound scan2022-04-01T17:43:22+02:00Clement Frainayhandling mutliple compartments in side compound scanThis is aimed at improving side compound detection when using models with compartments. The traditional filter by degree often removes H2O and other cofactors from cytosol, but those compounds usually remains in compartments with fewer ...This is aimed at improving side compound detection when using models with compartments. The traditional filter by degree often removes H2O and other cofactors from cytosol, but those compounds usually remains in compartments with fewer biochemical activities, thus with lower overall degree for their constituentsClement FrainayClement Frainayhttps://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/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/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/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/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/7Feature/extract sub reaction net2022-02-22T17:01:30+01:00Clement FrainayFeature/extract sub reaction netExtract reaction graph subnetwork (union of shortest paths or steiner tree) from lists of sources reactions and target reactions, analog to existing subgraph extraction on the compound graph. This version do not have default weighting sc...Extract reaction graph subnetwork (union of shortest paths or steiner tree) from lists of sources reactions and target reactions, analog to existing subgraph extraction on the compound graph. This version do not have default weighting scheme, thus requires a file of side compoundsLudovic CottretLudovic Cottrethttps://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/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/9Expand Toolbox with SBML scrapping app2022-04-19T15:09:49+02:00Clement FrainayExpand Toolbox with SBML scrapping appAllows user to extract and format data encapsulated in SBML filesAllows user to extract and format data encapsulated in SBML filesClement FrainayClement Frainayhttps://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 Frainay