Mercurial > repos > metexplore > met4j_extractsubnetwork

comparison ExtractSubNetwork.xml @ 4:27497451ecb8 draft default tip

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planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit c3527564d230b36ac1a196606c60c97a5b8ad9cf
author metexplore
date Mon, 02 Feb 2026 08:48:22 +0000
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59 The subnetwork corresponds to the part of the network that connects compounds from the first list to compounds from the second list. 59 The subnetwork corresponds to the part of the network that connects compounds from the first list to compounds from the second list.
60 Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. The relevance of considered path can be increased by weighting the edges using degree squared, chemical similarity (require InChI or SMILES annotations) or any provided weighting. 60 Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. The relevance of considered path can be increased by weighting the edges using degree squared, chemical similarity (require InChI or SMILES annotations) or any provided weighting.
61 See previous works on subnetwork extraction for parameters recommendations. 61 See previous works on subnetwork extraction for parameters recommendations.
62 @ATTRIBUTION@]]></help> 62 @ATTRIBUTION@]]></help>
63 <citations> 63 <citations>
64 <citation type="doi">10.1093/nar/gki437</citation>
65 <citation type="doi">10.1093/bioinformatics/btu760</citation> 64 <citation type="doi">10.1093/bioinformatics/btu760</citation>
66 <citation type="doi">10.1093/bib/bbv115</citation> 65 <citation type="doi">10.1093/bib/bbv115</citation>
66 <citation type="doi">10.1093/bioinformatics/bti116</citation>
67 <citation type="doi">10.1093/nar/gki437</citation>
68 <citation type="doi">10.1093/bioinformatics/btg217</citation>
69 <citation type="doi">10.1016/j.jmb.2005.09.079</citation>
67 <citation type="doi">10.1016/j.biosystems.2011.05.004</citation> 70 <citation type="doi">10.1016/j.biosystems.2011.05.004</citation>
68 <citation type="doi">10.1016/j.biosystems.2011.05.004</citation>
69 <citation type="doi">10.1093/nar/gki437</citation>
70 <citation type="doi">10.1016/j.jmb.2005.09.079</citation>
71 <citation type="doi">10.1093/bioinformatics/btg217</citation>
72 <citation type="doi">10.1093/bib/bbv115</citation>
73 <citation type="doi">10.1093/bioinformatics/bti116</citation>
74 <citation type="doi">10.1093/bioinformatics/btu760</citation>
75 </citations> 71 </citations>
76 </tool> 72 </tool>