All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
[met4j-graph] Overload getReactionGraph to be able to provide a list of reactions to exclude
[met4j-toolbox] New app to compute the reaction graph distance matrix
[met4j-toolbox] New app to perform topology-based pathway analysis
[met4j-toolbox] New app to perform over-representation based pathway analysis
[met4j-toolbox] New app for general SBML model processing including compound removal (such as side compounds or isolated compounds), reaction removal (ex. blocked or exchange reaction), and compartment merging
[met4j-core] Added a class to create, from a network with multiple compartments, a new network with a single compartment, avoiding duplicated compounds.
[met4j-core] Added utility method to remove duplicated reactions
[met4j-io] Fix Kegg import
[met4j-graph] Fix Steiner tree approximation
[ci] Fix docker & singularity image generation
[met4j-toolbox] New app for pathway-networks creation (compound overlap or source/sink intersection)
[met4j-graph] Added undirected graph simplification method for export
[met4j-graph] expand handled attributes for gml export
[met4j-graph] fix steiner Tree aproximation, add pruning step to avoid cycles
[met4j-io] Fix Tab2Sbml : allows empty side in reactions
[met4j-io] Fix Kegg2BioNetwork: change http to https
[met4j-toolbox] Add App to perform chemical names fuzzy mapping between datasets and models
[met4j-mapping] Add classes for edit-distance based fuzzy search
[met4j-graph] Add utilities to get distance matrix from paths
[met4j-graph] More flexible weighting policy definition using lambdas
[met4j-toolbox] Add app to calculate the distance matrix on bipartite graphs
[met4j-graph] Improve Shortest Paths union computing efficiency
[met4j-graph] Fix use of weighted graphs as undirected. Reversed edges now bear same weight as their origin
[met4j-io] Fix SetIdsFromFile : do not throw an exception when a new id is found twice
[met4j-toolbox] Add Apps to compute compound graph's classical weights (degree/chemical similarity)
[met4j-toolbox] Add App to identify model seeds and targets
[met4j-toolbox] Add App to set new ids to metabolic entities in a SBML file
[met4j-graph] Add method to create RPAIRs-like tags on compound graph's edges
[met4j-io] Fix Met4JSbmlReaderException. Error messages will be more explicit.
[met4j-toolbox] Improve Met4J usability for Galaxy Workflow by adding utilities apps that exploit bioNetworks functions
- decomposeSBML to get bioentities in sbml as list of ids
- GetReactantsFromReactions to get list of metabolites from sbml + list of reactions
- GetGenesFromReactions to get list of genes from sbml + list of reactions
[met4j-toolbox] Better error handling
[met4j-toolbox][SbmlSetPathways] Format pathway id to avoid redundancies
[met4j-graph] DefaultWeightPolicy class renamed UnweightedPolicy. Use weights option removed from shortest paths computation, now handled directly from graph to avoid conflict
[met4j-toolbox] Executable jar in the met4j gitlab registry
[met4j-core] Improve documentation in README.md
[met4j-toolbox] Subnetwork Extraction Improvement :
- bipartite graph compatibility
- export as table
- allows undirected case for paths and steiner tree computation
[met4j-graph] shortest paths union and steiner tree optimization
[met4j-graph] fix error in gml export causing import in igraph and cytoscape to fail
[met4j-mathUtils] fix sub-matrix creation not retaining rows&columns labels
[met4j-toolbox] Improvements of GenerateGalaxyFiles and GenerateJson
[met4j-toolbox] New app : GenerateGalaxyFiles to generate automatically wrappers for Galaxy
[met4j-toolbox] New app : GenerateJson to generate a json describing the apps
[devops] Automatic generation of the singularity and docker images for the develop & master versions.
[met4j-toolbox] New app: networkAnalysis.CompoundNet: Advanced compound graph building
[met4j-toolbox] New app: attributes.ExtractPathways: SBML sub network creation from a list of pathways
[met4j-toolbox] New app: attributes.ExtractSbmlAnnot: Extract sbml annotations
[met4j-toolbox] App improvements: networkAnalysis.SideCompoundsScan: Handle multiple compartments
[met4j-io] Great speed improvements to read gene reaction associations
[met4j-toolbox] ExtractSubReactionNetwork app
[met4j-io] Debug Tab2BioNetwork
[met4j-io] Deals better when a reactant has a stoichiometry equals to 0. Before, there was an Exception, now the reactant is simply not taken into account.
[met4j-io] New stable version of JSBML (1.6.1 that corrects log4j vulnerabilities)
App Kegg2Sbml
[met4j-io] Accepts stoichiometric coefficient equals to 0
[met4j-core] debug remove(gene)
[met4j-io] replace negative coefficients by positive coefficients
[maven]: Change rule of deploy
[met4j-io]: Check that pathways are not created before note parsing
- [met4j-io] Removes the exception when no unit definition is set
- [met4j-io] If no unit definition is set in the SBML header, there is no exception anymore when the FBC parser is used : a new unit definition is created when it is specified in the parameters
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[met4j-core] Reaction.getMetabolitesView method allows to get all left and right metabolites in the same collection.
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[met4j-core] If the id of a new BioEntity is not valid, a new random one is created
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[met4j-io] ReactionAttributes.getSideCompounds now returns a BioCollection of BioMetabolite instead of a Set of String
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[met4j-core] Fix issues in BioNetwork.removeOnCascade
- [met4j-io] MetExploreXml support : classes and apps
- [met4j-graph] Graph Analysis Apps: chokepoints, distance matrix, subnetwork extraction, loadpoint, metaborank, scopecompounds and other utilities
- [met4j-graph] Improve graph export to gml: attributes can be exported too
- FlexFlux
- [met4j-graph] Reaction graph creation was very slow, now fixed
- [met4j-graph] Fixed FloydWarshall undirected with multi-graphs