Tags:
metabolism, bioinformatics, modeling
Owner:
david.sherman@inria.fr
Mimoza combines the model generalization method with the zooming user interface (ZUI) paradigm and allows a human expert to explore metabolic network models in a semantically zoomable manner.
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Mimoza is a a Python library for metabolic model visualization and navigation that allows you to explore your metabolic models in a semantically zoomable manner.
Mimoza combines the model generalization method with the zooming user interface (ZUI) paradigm and allows a human expert to explore metabolic network models in a semantically zoomable manner.
Mimoza takes a metabolic model in SBML format, generalizes it to detect similar metabolites and similar reactions, and automatically creates a 3-level zoomable map:
Mimoza highlights the general model structure and the divergences from it, such as alternative paths or missing reactions, and allows a user to analyse it in a top-down manner.
The network map can be browsed online or downloaded as a COMBINE archive, containing:
Zhukova, A., Sherman, D. J. (2015) Mimoza: Web-Based Semantic Zooming and Navigation in Metabolic Networks BMC Systems Biology, 9:10 doi:10.1186/s12918-015-0151-5
Execute:
bash
python3 ./mimoza.py --model path_to_your_model.xml --verbose
This will produce a COMBINE archive, containing:
In input :
<?xml version="1.0" encoding="UTF-8"?> <sbml xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" level="3" version="1"> <model metaid="meta_ymn" id="ymn" substanceUnits="dimensionless" timeUnits="dimensionless" volumeUnits="dimensionless"> <notes> <body xmlns="http://www.w3.org/1999/xhtml"> <p>This SBML representation of the yeast metabolic network is made available under the Creative Commons Attribution-Share Alike 3.0 Unported Licence (see www.creativecommons.org).</p> </body> </notes> <annotation> <rdf:RDF> <rdf:Description rdf:about="#meta_ymn"> <dc:creator> <rdf:Bag> <rdf:li rdf:parseType="Resource"> <vCard:N rdf:parseType="Resource"> <vCard:Family>Smallbone</vCard:Family> <vCard:Given>Kieran</vCard:Given> </vCard:N> <vCard:EMAIL>kieran.smallbone@manchester.ac.uk</vCard:EMAIL> <vCard:ORG rdf:parseType="Resource"> <vCard:Orgname>University of Manchester</vCard:Orgname> </vCard:ORG> </rdf:li> <rdf:li rdf:parseType="Resource"> <vCard:N rdf:parseType="Resource"> <vCard:Family>Heavner</vCard:Family> <vCard:Given>Ben</vCard:Given> </vCard:N> <vCard:EMAIL>bheavner@systemsbiology.org</vCard:EMAIL> <vCard:ORG rdf:parseType="Resource"> <vCard:Orgname>Institute for Systems Biology</vCard:Orgname> </vCard:ORG> </rdf:li> <rdf:li rdf:parseType="Resource"> <vCard:N rdf:parseType="Resource"> <vCard:Family>Herrgard</vCard:Family> <vCard:Given>Markus</vCard:Given> </vCard:N> <vCard:EMAIL>mherrgar@ucsd.edu</vCard:EMAIL> <vCard:ORG rdf:parseType="Resource"> <vCard:Orgname>University of California, San Diego</vCard:Orgname> </vCard:ORG> </rdf:li> <rdf:li rdf:parseType="Resource"> <vCard:N rdf:parseType="Resource"> <vCard:Family>Swainston</vCard:Family> <vCard:Given>Neil</vCard:Given> </vCard:N> <vCard:EMAIL>neil.swainston@manchester.ac.uk</vCard:EMAIL> <vCard:ORG rdf:parseType="Resource"> <vCard:Orgname>University of Manchester</vCard:Orgname> </vCard:ORG> </rdf:li> <rdf:li rdf:parseType="Resource"> <vCard:N rdf:parseType="Resource"> <vCard:Family>Aung</vCard:Family> <vCard:Given>Hnin</vCard:Given> </vCard:N> <vCard:EMAIL>hwa22@cornell.edu</vCard:EMAIL> <vCard:ORG rdf:parseType="Resource"> <vCard:Orgname>Cornell University</vCard:Orgname> </vCard:ORG> </rdf:li> </rdf:Bag> </dc:creator> <dcterms:created rdf:parseType="Resource"> <dcterms:W3CDTF>2008-02-20T10:05:10Z</dcterms:W3CDTF> </dcterms:created> <dcterms:modified rdf:parseType="Resource"> <dcterms:W3CDTF>2013-04-18T22:10:36Z</dcterms:W3CDTF> </dcterms:modified> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/taxonomy/559292"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfCompartments> <compartment metaid="meta_c_02" sboTerm="SBO:0000290" id="c_02" name="cell envelope" spatialDimensions="3" size="1" constant="true"> <annotation> <rdf:RDF> <rdf:Description rdf:about="#meta_c_02"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0030313"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="meta_c_03" sboTerm="SBO:0000290" id="c_03" name="cytoplasm" spatialDimensions="3" size="1" constant="true"> <annotation> <rdf:RDF> <rdf:Description rdf:about="#meta_c_03"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0005737"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="meta_c_04" sboTerm="SBO:0000290" id="c_04" name="endoplasmic reticulum" spatialDimensions="3" size="1" constant="true"> <annotation> <rdf:RDF> <rdf:Description rdf:about="#meta_c_04"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0005783"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="meta_c_05" sboTerm="SBO:0000290" id="c_05" name="endoplasmic reticulum membrane" spatialDimensions="3" size="1" constant="true"> <annotation> <rdf:RDF> <rdf:Description rdf:about="#meta_c_05"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0005789"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="meta_c_06" sboTerm="SBO:0000290" id="c_06" name="extracellular" spatialDimensions="3" size="1" constant="true"> <annotation> <rdf:RDF> <rdf:Description rdf:about="#meta_c_06"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0005576"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="meta_c_07" sboTerm="SBO:0000290" id="c_07" name="Golgi" spatialDimensions="3" size="1" constant="true"> <annotation> <rdf:RDF> <rdf:Description rdf:about="#meta_c_07"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0005794"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="meta_c_08" sboTerm="SBO:0000290" id="c_08" name="Golgi membrane" spatialDimensions="3" size="1" constant="true"> <annotation> <rdf:RDF> <rdf:Description rdf:about="#meta_c_08"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0000139"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="meta_c_09" sboTerm="SBO:0000290" id="c_09" name="lipid particle" spatialDimensions="3" size="1" constant="true"> <annotation> <rdf:RDF> <rdf:Description rdf:about="#meta_c_09"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0005811"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="meta_c_10" sboTerm="SBO:0000290" id="c_10" name="mitochondrial membrane" spatialDimensions="3" size="1" constant="true"> <annotation> <rdf:RDF> <rdf:Description rdf:about="#meta_c_10"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0031966"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="meta_c_11" sboTerm="SBO:0000290" id="c_11" name="mitochondrion" spatialDimensions="3" size="1" constant="true"> <annotation> <rdf:RDF> <rdf:Description rdf:about="#meta_c_11"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0005739"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="meta_c_13" sboTerm="SBO:0000290" id="c_13" name="nucleus" spatialDimensions="3" size="1" constant="true"> <annotation> <rdf:RDF> <rdf:Description rdf:about="#meta_c_13"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0005634"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="meta_c_14" sboTerm="SBO:0000290" id="c_14" name="peroxisomal membrane" spatialDimensions="3" size="1" constant="true"> <annotation> <rdf:RDF> <rdf:Description rdf:about="#meta_c_14"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0005778"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="meta_c_15" sboTerm="SBO:0000290" id="c_15" name="peroxisome" spatialDimensions="3" size="1" constant="true"> <annotation> <rdf:RDF> <rdf:Description rdf:about="#meta_c_15"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0005777"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="meta_c_16" sboTerm="SBO:0000290" id="c_16" name="vacuolar membrane" spatialDimensions="3" size="1" constant="true"> <annotation> <rdf:RDF> <rdf:Description rdf:about="#meta_c_16"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0009705"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> <compartment metaid="meta_c_17" sboTerm="SBO:0000290" id="c_17" name="vacuole" spatialDimensions="3" size="1" constant="true"> <annotation> <rdf:RDF> <rdf:Description rdf:about="#meta_c_17"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0005773"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> </listOfCompartments> <listOfSpecies> <species metaid="meta_s_0001" sboTerm="SBO:0000247" id="s_0001" name="(1->3)-beta-D-glucan [cell envelope]" compartment="c_02" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_s_0001"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:37671"/> <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00965"/> <rdf:li rdf:resource="http://identifiers.org/obo.chebi/chebi:37671"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="meta_s_0003" sboTerm="SBO:0000247" id="s_0003" name="(1->3)-beta-D-glucan [extracellular]" compartment="c_06" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_s_0003"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:37671"/> <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00965"/> <rdf:li rdf:resource="http://identifiers.org/obo.chebi/chebi:37671"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="meta_s_0004" sboTerm="SBO:0000247" id="s_0004" name="(1->6)-beta-D-glucan [cell envelope]" compartment="c_02" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_s_0004"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:27380"/> <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C02493"/> <rdf:li rdf:resource="http://identifiers.org/obo.chebi/chebi:27380"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="meta_s_0006" sboTerm="SBO:0000247" id="s_0006" name="(2-amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl trihydrogen diphosphate [mitochondrion]" compartment="c_11" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_s_0006"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:57602"/> <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C04807"/> <rdf:li rdf:resource="http://identifiers.org/obo.chebi/chebi:57602"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="meta_s_0007" sboTerm="SBO:0000247" id="s_0007" name="(2E)-3-(methoxycarbonyl)pent-2-enedioic acid [cytoplasm]" compartment="c_03" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_s_0007"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:57470"/> <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C11514"/> <rdf:li rdf:resource="http://identifiers.org/obo.chebi/chebi:57470"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="meta_s_0008" sboTerm="SBO:0000247" id="s_0008" name="(2R,3R)-2,3-dihydroxy-3-methylpentanoate [mitochondrion]" compartment="c_11" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_s_0008"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:49258"/> <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C06007"/> <rdf:li rdf:resource="http://identifiers.org/obo.chebi/chebi:49258"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="meta_s_0009" sboTerm="SBO:0000247" id="s_0009" name="(2R,3S)-3-isopropylmalate [cytoplasm]" compartment="c_03" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_s_0009"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:35121"/> <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C04411"/> <rdf:li rdf:resource="http://identifiers.org/obo.chebi/chebi:35121"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="meta_s_0010" sboTerm="SBO:0000247" id="s_0010" name="(2S)-2-isopropyl-3-oxosuccinate [cytoplasm]" compartment="c_03" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_s_0010"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:17214"/> <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C04236"/> <rdf:li rdf:resource="http://identifiers.org/obo.chebi/chebi:17214"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="meta_s_0011" sboTerm="SBO:0000247" id="s_0011" name="(2S)-2-isopropyl-3-oxosuccinate [mitochondrion]" compartment="c_11" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_s_0011"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:17214"/> <rdf:li 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