update changelog and readme

CHANGELOG.md

@@ -4,46 +4,64 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## Next Release
+## 1.4.0
 
-[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-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  
 
 ## 1.3.1
 
 [met4j-io] Fix Kegg import
+
 [met4j-graph] Fix Steiner tree approximation
+
 [ci] Fix docker & singularity image generation
 
 ## 1.3.0
 
 ### Features
+
 [met4j-toolbox] New app for pathway-networks creation (compound overlap or source/sink intersection)
+
 [met4j-graph] Added undirected graph simplification method for export
 
 ### Fix
+
 [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
 
 ## 1.2.2
 
 ### Fix
+
 [met4j-io] Fix Kegg2BioNetwork: change http to https 
 
 ## 1.2.1
 
 ### Features
+
 [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
 
 ### Fix
+
 [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
 
 

README.md

@@ -30,7 +30,7 @@ Install all modules :
 <dependency>
 <groupId>fr.inrae.toulouse.metexplore</groupId>
 <artifactId>met4j-toolbox</artifactId>
-<version>0.12.0</version>
+<version>1.4.0</version>
 </dependency>
 ```
 
@@ -39,7 +39,7 @@ or a specific module (example : met4j-core ):
 <dependency>
 <groupId>fr.inrae.toulouse.metexplore</groupId>
 <artifactId>met4j-core</artifactId>
-<version>0.12.0</version>
+<version>1.4.0</version>
 </dependency>
 ```
 

met4j-toolbox/README.md

@@ -678,7 +678,7 @@ Wrappers launch the met4j singularity container, so the server where your Galaxy
  -o VAL          : output results file
  -s (--side) VAL : an optional file containing list of side compounds to ignore
 </code></pre></details></td></tr>
-<tr><td>MetaboRank</td><td>Compute the MetaboRank, a custom personalized PageRank for metabolic network.<details><summary><small>more</small></summary>Compute the MetaboRank, a custom personalized PageRank for metabolic network.<br/>The MetaboRank takes a metabolic network and a list of compounds of interest, and provide a score of relevance for all of the other compounds in the network.<br/>The MetaboRank can, from metabolomics results, be used to fuel a recommender system highlighting interesting compounds to investigate, retrieve missing identification and drive literature mining.<br/>It is a two dimensional centrality computed from personalized PageRank and CheiRank, with special transition probability and normalization to handle the specificities of metabolic networks.<br/>See publication for more information: Frainay et al. MetaboRank: network-based recommendation system to interpret and enrich metabolomics results, Bioinformatics (35-2), https://doi.org/10.1093/bioinformatics/bty577<br/><br/><pre><code> -d N    : damping factor (default: 0.85)
+<tr><td>MetaboRank</td><td>Compute the MetaboRank, a custom personalized PageRank for metabolic network.<details><summary><small>more</small></summary>Compute the MetaboRank, a custom personalized PageRank for metabolic network.<br/>The MetaboRank takes a metabolic network and a list of compounds of interest, and provide a score of relevance for all of the other compounds in the network.<br/>The MetaboRank can, from metabolomics results, be used to fuel a recommender system highlighting interesting compounds to investigate, retrieve missing identification and drive literature mining.<br/>It is a two dimensional centrality computed from personalized PageRank and CheiRank, with special transition probability and normalization to handle the specificities of metabolic networks.<br/>For convenience, a one dimensional centrality rank is also computed from the highest rank from PageRank or CheiRank, and using lowest rank as tie-breaker.<br/>See publication for more information: Frainay et al. MetaboRank: network-based recommendation system to interpret and enrich metabolomics results, Bioinformatics (35-2), https://doi.org/10.1093/bioinformatics/bty577<br/><br/><pre><code> -d N    : damping factor (default: 0.85)
  -h      : prints the help (default: false)
  -i VAL  : input SBML file: path to network used for computing centrality, in
            sbml format.