met4j merge requestshttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests2021-11-26T13:50:19+01:00https://forgemia.inra.fr/metexplore/met4j/-/merge_requests/2[io] handle indentifiers.org urls with https2021-11-26T13:50:19+01:00Clement Frainay[io] handle indentifiers.org urls with httpsXref parsing from sbml only accept valid identifiers.org uri.
Since they changed from http to https, the validity check has been modified accordingly, accepting both http and https uri.
The default base uri has been switched to https in ...Xref parsing from sbml only accept valid identifiers.org uri.
Since they changed from http to https, the validity check has been modified accordingly, accepting both http and https uri.
The default base uri has been switched to https in met4J too, so change has been made to the unit tests.
However, please note that a sbml with http://identifiers.org uris will have them converted to https after exportLudovic CottretLudovic Cottrethttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/3Add coverage module2021-12-06T15:56:14+01:00Ludovic CottretAdd coverage moduleFrom https://cylab.be/blog/97/compute-code-coverage-for-a-multi-module-maven-project-with-jacocoFrom https://cylab.be/blog/97/compute-code-coverage-for-a-multi-module-maven-project-with-jacocoLudovic 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/5skip coverage deploy2021-12-16T12:14:40+01:00Ludovic Cottretskip coverage deployLudovic 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/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/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/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/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 Frainayhttps://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/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/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/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/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/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/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/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/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/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/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