met4j tagshttps://forgemia.inra.fr/metexplore/met4j/-/tags2023-07-26T15:56:03+02:00https://forgemia.inra.fr/metexplore/met4j/-/tags/1.5.01.5.0release 1.5.0 1.5.0<h3 data-sourcepos="1:1-1:16" dir="auto">
<a id="user-content-new-features" class="anchor" href="#new-features" aria-hidden="true"></a>New Features</h3>
<ul data-sourcepos="3:1-9:79" dir="auto">
<li data-sourcepos="3:1-4:0">
<p data-sourcepos="3:3-3:94">[met4j-graph] Overload getReactionGraph to be able to provide a list of reactions to exclude</p>
</li>
<li data-sourcepos="5:1-6:0">
<p data-sourcepos="5:3-5:71">[met4j-toolbox] New app to compute the reaction graph distance matrix</p>
</li>
<li data-sourcepos="7:1-8:0">
<p data-sourcepos="7:3-7:68">[met4j-toolbox] New app to perform topology-based pathway analysis</p>
</li>
<li data-sourcepos="9:1-9:79">
<p data-sourcepos="9:3-9:79">[met4j-toolbox] New app to perform over-representation based pathway analysis</p>
</li>
</ul>2023-07-26T15:56:03+02:00cfrainayclement.frainay@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/1.4.01.4.01.4.0<h2 data-sourcepos="1:1-1:8" dir="auto">
<a id="user-content-anchor-140" class="anchor" href="#anchor-140" aria-hidden="true"></a>1.4.0</h2>
<h3 data-sourcepos="3:1-3:16" dir="auto">
<a id="user-content-new-features" class="anchor" href="#new-features" aria-hidden="true"></a>New features</h3>
<ul data-sourcepos="4:1-10:0" dir="auto">
<li data-sourcepos="4:1-4:211">[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</li>
<li data-sourcepos="5:1-5:104">[met4j-toolbox] New app for pathway-networks creation (compound overlap or source/sink intersection)</li>
<li data-sourcepos="6:1-6:156">[met4j-core] Added a class to create, from a network with multiple compartments, a new network with a single compartment, avoiding duplicated compounds.</li>
<li data-sourcepos="7:1-7:66">[met4j-core] Added utility method to remove duplicated reactions</li>
<li data-sourcepos="8:1-10:0">[met4j-graph] Added undirected graph simplification method for export</li>
</ul>
<h3 data-sourcepos="11:1-11:13" dir="auto">
<a id="user-content-new-fixes" class="anchor" href="#new-fixes" aria-hidden="true"></a>New fixes</h3>
<ul data-sourcepos="13:1-18:28" dir="auto">
<li data-sourcepos="13:1-13:48">[ci] Fix docker & singularity image generation</li>
<li data-sourcepos="14:1-14:80">[met4j-graph] Fix Steiner tree approximation, add pruning step to avoid cycles</li>
<li data-sourcepos="15:1-15:56">[met4j-graph] expand handled attributes for gml export</li>
<li data-sourcepos="16:1-16:58">[met4j-io] Fix Tab2Sbml : allows empty side in reactions</li>
<li data-sourcepos="17:1-17:55">[met4j-io] Fix Kegg2BioNetwork: change http to https</li>
<li data-sourcepos="18:1-18:28">[met4j-io] Fix Kegg import</li>
</ul>2023-06-30T10:39:37+02:00cfrainayclement.frainay@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/1.2.11.2.11.2.1<h2 data-sourcepos="1:1-1:8" dir="auto">
<a id="user-content-anchor-121" class="anchor" href="#anchor-121" aria-hidden="true"></a>1.2.1</h2>
<h3 data-sourcepos="3:1-3:16" dir="auto">
<a id="user-content-new-features" class="anchor" href="#new-features" aria-hidden="true"></a>New features</h3>
<ul data-sourcepos="4:1-8:0" dir="auto">
<li data-sourcepos="4:1-4:93">[met4j-toolbox] Add App to perform chemical names fuzzy mapping between datasets and models</li>
<li data-sourcepos="5:1-5:66">[met4j-mapping] Add classes for edit-distance based fuzzy search</li>
<li data-sourcepos="6:1-6:63">[met4j-graph] Add utilities to get distance matrix from paths</li>
<li data-sourcepos="7:1-8:0">[met4j-graph] More flexible weighting policy definition using lambdas</li>
</ul>
<h3 data-sourcepos="9:1-9:13" dir="auto">
<a id="user-content-new-fixes" class="anchor" href="#new-fixes" aria-hidden="true"></a>New fixes</h3>
<ul data-sourcepos="10:1-12:88" dir="auto">
<li data-sourcepos="10:1-10:65">[met4j-graph] Improve Shortest Paths union computing efficiency</li>
<li data-sourcepos="11:1-11:109">[met4j-graph] Fix use of weighted graphs as undirected. Reversed edges now bear same weight as their origin</li>
<li data-sourcepos="12:1-12:88">[met4j-io] Fix SetIdsFromFile : do not throw an exception when a new id is found twice</li>
</ul>2023-01-11T16:15:40+01:00cfrainayclement.frainay@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/1.2.01.2.0Finish 1.2.0lcottretludovic.cottret@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/1.1.11.1.1Finish 1.1.1lcottretludovic.cottret@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/1.1.01.1.0Finish 1.1.0lcottretludovic.cottret@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/1.0.11.0.1Finish 1.0.1lcottretludovic.cottret@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/1.01.0Finish 1.0lcottretludovic.cottret@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/0.12.00.12.0Finish 0.12.0lcottretludovic.cottret@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/0.110.11Finish 0.11lcottretludovic.cottret@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/0.100.10Finish tag 0.10lcottretludovic.cottret@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/0.9.10.9.1Finish 0.9.1lcottretludovic.cottret@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/0.90.9Finish 0.9lcottretludovic.cottret@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/0.8.30.8.3Finish hotfix 0.8.3lcottretludovic.cottret@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/0.8.20.8.2Finish 0.8.2lcottretludovic.cottret@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/0.8.10.8.1Finish hotfix 0.8.1 : jsbml 1.6.1lcottretludovic.cottret@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/0.8.00.8.0Finish release 0.8.0
App Kegg2Sbmllcottretludovic.cottret@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/0.7.110.7.11Finish hotfix 0.7.11 : new jsbml versionlcottretludovic.cottret@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/0.7.100.7.10Finish hotfix 0.7.10
Debug kegg import.lcottretludovic.cottret@inrae.frhttps://forgemia.inra.fr/metexplore/met4j/-/tags/0.7.90.7.90.7.9 Update CDK, fix log4Shellcfrainayclement.frainay@inrae.fr