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feat: added Min1 publication to test suite examples
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <omexManifest xmlns="http://identifiers.org/combine.specifications/omex-manifest"> | ||
| <content location="model.txt" format="http://purl.org/NET/mediatypes/text/smoldyn+plain" master="false"/> | ||
| <content location="simulation.sedml" format="http://identifiers.org/combine.specifications/sed-ml" master="true"/> | ||
| <content location="metadata.rdf" format="http://identifiers.org/combine.specifications/omex-metadata" master="false"/> | ||
| </omexManifest> |
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| <?xml version="1.1" encoding="utf-8"?> | ||
| <rdf:RDF xmlns:OMEXlib="http://omex-library.org/" | ||
| xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" | ||
| xmlns:bqmodel="http://biomodels.net/model-qualifiers/" | ||
| xmlns:dc="http://purl.org/dc/terms/" | ||
| xmlns:foaf="http://xmlns.com/foaf/0.1/" | ||
| xmlns:local="http://omex-library.org/NewOmex.omex/NewModel.rdf#" | ||
| xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> | ||
| <rdf:Description rdf:about="http://omex-library.org/Min1.omex"> | ||
| <bqmodel:is rdf:resource="local:00003"/> | ||
| <bqmodel:isDescribedBy rdf:resource="local:00004"/> | ||
| <ns1:abstract xmlns:ns1="http://purl.org/dc/elements/1.1/"> | ||
| E. coli Min system, based on Huang, Meir, Wingreen (HMW) with surface diffusion. | ||
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| Motivation: Smoldyn is a spatial and stochastic biochemical simulator. | ||
| It treats each molecule of interest as an individual particle in continuous space, | ||
| simulating molecular diffusion, molecule-membrane interactions and chemical reactions, | ||
| all with good accuracy. | ||
| </ns1:abstract> | ||
| <ns2:contributor xmlns:ns2="http://purl.org/dc/elements/1.1/" | ||
| rdf:resource="local:00002"/> | ||
| <ns3:created xmlns:ns3="http://purl.org/dc/elements/1.1/">2024-01-15</ns3:created> | ||
| <ns4:creator xmlns:ns4="http://purl.org/dc/elements/1.1/" | ||
| rdf:resource="local:00001"/> | ||
| <ns5:license xmlns:ns5="http://purl.org/dc/elements/1.1/" | ||
| rdf:resource="local:00005"/> | ||
| <ns6:modified xmlns:ns6="http://purl.org/dc/elements/1.1/">2024-02-05</ns6:modified> | ||
| <ns7:title xmlns:ns7="http://purl.org/dc/elements/1.1/">E. coli Min system based on Huang, Meir, Wingreen (Andrews, 2009)</ns7:title> | ||
| </rdf:Description> | ||
| <rdf:Description rdf:about="local:00001"> | ||
| <ns8:label xmlns:ns8="http://www.w3.org/2000/01/rdf-schema#">Steven Andrews</ns8:label> | ||
| <foaf:name>Steven Andrews</foaf:name> | ||
| </rdf:Description> | ||
| <rdf:Description rdf:about="local:00002"> | ||
| <ns9:identifier xmlns:ns9="http://purl.org/dc/elements/1.1/" | ||
| rdf:resource="http://identifiers.org/orcid:0009-0002-6886-2291"/> | ||
| <ns10:label xmlns:ns10="http://www.w3.org/2000/01/rdf-schema#">Alex Patrie</ns10:label> | ||
| <foaf:accountName rdf:resource="https://orcid.org/0009-0002-6886-2291"/> | ||
| <foaf:name>Alex Patrie</foaf:name> | ||
| </rdf:Description> | ||
| <rdf:Description rdf:about="local:00003"> | ||
| <ns11:identifier xmlns:ns11="http://purl.org/dc/elements/1.1/" | ||
| rdf:resource="https://github.com/ssandrews/Smoldyn/blob/master/examples/S99_more/Min/Min1.txt"/> | ||
| <ns12:label xmlns:ns12="http://www.w3.org/2000/01/rdf-schema#">smoldyn:S99_more/Min/Min1.txt</ns12:label> | ||
| </rdf:Description> | ||
| <rdf:Description rdf:about="local:00004"> | ||
| <ns13:identifier xmlns:ns13="http://purl.org/dc/elements/1.1/" | ||
| rdf:resource="http://identifiers.org/doi:10.1093/bioinformatics/btw700"/> | ||
| <ns14:label xmlns:ns14="http://www.w3.org/2000/01/rdf-schema#">Steven S Andrews. Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface. Bioinformatics 33, 5 (2017).</ns14:label> | ||
| </rdf:Description> | ||
| <rdf:Description rdf:about="local:00005"> | ||
| <ns15:identifier xmlns:ns15="http://purl.org/dc/elements/1.1/" | ||
| rdf:resource="http://identifiers.org/spdx:GPL-3.0-only"/> | ||
| <ns16:label xmlns:ns16="http://www.w3.org/2000/01/rdf-schema#">GPL-3.0-only</ns16:label> | ||
| </rdf:Description> | ||
| </rdf:RDF> | ||
|
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| # File Min1.txt, by Steve Andrews, 11/2009. | ||
| # E. coli Min system, based on Huang, Meir, Wingreen (HMW) | ||
| # This file is HMW system exactly, plus surface diffusion | ||
| # units are micron, second | ||
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| define D_D 2.5 # MinD diffusion coefficient (um^2/s) | ||
| define D_E 2.5 # MinE diffusion coefficient (um^2/s) | ||
| define D_d 0.01 # MinD_ATP(front) diff. coeff. (um^2/s) | ||
| define D_de 0.01 # MinDMinE(front) diff. coeff. (um^2/s) | ||
| define SIGMA_D_D2T 1 # MinD phosphorylation rate (s^-1) | ||
| define SIGMA_D 0.025 # MinD_ATP adsorption coeff. (um/s) | ||
| define SIGMA_dD 0.0015 # cooperative adsorption coeff. (um^3/s) | ||
| define SIGMA_de 0.7 # desorption rate of MinDMinE (s^-1) | ||
| define SIGMA_E 0.093 # MinE binding to surface-bound MinD (um^3/s) | ||
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| define UNBINDRAD 0.01 # MinD separation on surface (um) | ||
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| define R 0.5 # cell radius | ||
| define L_PARAM 2 # half of cell length | ||
| define L_PARAM2 1.5 # half of cell length minus radius | ||
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| define NUMBER_MIND 4000 # number of MinD in cell | ||
| define NUMBER_MINE 1400 # number of MinE in cell | ||
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| define TIME_STOP 10 # stopping time | ||
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| #define KICK_START 1 # start with MinD_ATP at an end | ||
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| random_seed 1 | ||
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| #graphics opengl | ||
| #graphic_iter 100 | ||
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| #tiff_name movie/MinMovie | ||
| #tiff_iter 200 | ||
| #tiff_min 1 | ||
| #tiff_max 200 | ||
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| dim 3 | ||
| boundaries 0 -L_PARAM L_PARAM | ||
| boundaries 1 -R R | ||
| boundaries 2 -R R | ||
| frame_thickness 0 | ||
| time_start 0 | ||
| time_stop TIME_STOP | ||
| time_step 0.002 # 2 millisecond time step | ||
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| accuracy 5 | ||
| molperbox 4 | ||
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| species MinD_ATP | ||
| species MinD_ADP | ||
| species MinE | ||
| species MinDMinE | ||
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| molecule_lists list1 list2 list3 list4 list5 | ||
| mol_list MinD_ATP(soln) list1 | ||
| mol_list MinD_ATP(front) list2 | ||
| mol_list MinD_ADP(all) list3 | ||
| mol_list MinE(all) list4 | ||
| mol_list MinDMinE(all) list5 | ||
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| difc MinD_ATP(solution) D_D | ||
| difc MinD_ATP(front) D_d | ||
| difc MinD_ADP(solution) D_D | ||
| difc MinE(solution) D_E | ||
| difc MinDMinE(front) D_de | ||
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| color MinD_ATP(soln) 0 0 0.6 # MinD_ATP(solution) is dark blue | ||
| color MinD_ATP(front) 0 0.6 0 # MinD_ATP(front) is dark green | ||
| color MinD_ADP(soln) 0.4 0.6 1 # MinD_ADP is light blue | ||
| color MinE(soln) 1 0 0 # MinE is red | ||
| color MinDMinE(front) 0.2 1 0.2 # MinDMinE is bright green | ||
| display_size all(solution) 2 | ||
| display_size all(front) 4 | ||
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| start_surface membrane | ||
| action both all reflect | ||
| rate MinD_ATP fsoln front SIGMA_D # reaction 1a | ||
| polygon both edge | ||
| panel cylinder -L_PARAM2 0 0 L_PARAM2 0 0 -R 20 10 cyl0 | ||
| panel hemi -L_PARAM2 0 0 -R 1 0 0 20 5 hemi0 | ||
| panel hemi L_PARAM2 0 0 -R -1 0 0 20 5 hemi1 | ||
| neighbors cyl0 hemi0 hemi1 | ||
| neighbors hemi0 cyl0 | ||
| neighbors hemi1 cyl0 | ||
| end_surface | ||
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| start_compartment cell | ||
| surface membrane | ||
| point 0 0 0 | ||
| end_compartment | ||
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| reaction rxn1b MinD_ATP(fsoln) + MinD_ATP(front) -> MinD_ATP(front) + MinD_ATP(front) SIGMA_dD | ||
| product_placement rxn1b unbindrad UNBINDRAD | ||
| reaction rxn1c MinD_ATP(fsoln) + MinDMinE(front) -> MinD_ATP(front) + MinDMinE(front) SIGMA_dD | ||
| product_placement rxn1c unbindrad UNBINDRAD | ||
| reaction rxn2 MinE(fsoln) + MinD_ATP(front) -> MinDMinE(front) SIGMA_E | ||
| reaction rxn3 MinDMinE(front) -> MinD_ADP(fsoln) + MinE(fsoln) SIGMA_de | ||
| reaction rxn4 MinD_ADP -> MinD_ATP SIGMA_D_D2T | ||
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| ifundefine KICK_START | ||
| surface_mol NUMBER_MIND MinD_ATP(front) membrane all all | ||
| else | ||
| surface_mol NUMBER_MIND MinD_ATP(front) membrane hemi hemi1 | ||
| endif | ||
| compartment_mol NUMBER_MINE MinE cell | ||
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| output_files modelout.txt | ||
| cmd i 0 TIME_STOP 2 executiontime modelout.txt | ||
| cmd i 0 TIME_STOP 2 listmols modelout.txt | ||
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| end_file | ||
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examples/smoldyn/Andrews-Min1-PUBLICATION/simulation.sedml
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <sedML xmlns="http://sed-ml.org/sed-ml/level1/version3" level="1" version="3"> | ||
| <listOfModels> | ||
| <model id="model" language="urn:sedml:language:smoldyn" source="model.txt"/> | ||
| </listOfModels> | ||
| <listOfSimulations> | ||
| <uniformTimeCourse id="simulation" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfPoints="5000"> | ||
| <algorithm kisaoID="KISAO:0000057"/> | ||
| </uniformTimeCourse> | ||
| </listOfSimulations> | ||
| <listOfTasks> | ||
| <task id="task" modelReference="model" simulationReference="simulation"/> | ||
| </listOfTasks> | ||
| <listOfDataGenerators> | ||
| <dataGenerator id="data_generator_time" name="Time"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> variable_time </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="variable_time" name="Time" symbol="urn:sedml:symbol:time" taskReference="task"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| <dataGenerator id="data_generator_count_species_MinD_ADP" name="Count of species "MinD_ADP""> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> variable_count_species_MinD_ADP </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="variable_count_species_MinD_ADP" name="Count of species "MinD_ADP"" target="molcount MinD_ADP" taskReference="task"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| <dataGenerator id="data_generator_count_species_MinD_ADP_compartment_cell" name="Count of species "MinD_ADP" in compartment "cell""> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> variable_count_species_MinD_ADP_compartment_cell </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="variable_count_species_MinD_ADP_compartment_cell" name="Count of species "MinD_ADP" in compartment "cell"" target="molcountincmpt MinD_ADP cell" taskReference="task"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| <dataGenerator id="data_generator_count_species_MinD_ADP_surface_membrane" name="Count of species "MinD_ADP" in surface "membrane""> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> variable_count_species_MinD_ADP_surface_membrane </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="variable_count_species_MinD_ADP_surface_membrane" name="Count of species "MinD_ADP" in surface "membrane"" target="molcountonsurf MinD_ADP membrane" taskReference="task"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| <dataGenerator id="data_generator_count_species_MinD_ATP" name="Count of species "MinD_ATP""> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> variable_count_species_MinD_ATP </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="variable_count_species_MinD_ATP" name="Count of species "MinD_ATP"" target="molcount MinD_ATP" taskReference="task"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| <dataGenerator id="data_generator_count_species_MinD_ATP_compartment_cell" name="Count of species "MinD_ATP" in compartment "cell""> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> variable_count_species_MinD_ATP_compartment_cell </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="variable_count_species_MinD_ATP_compartment_cell" name="Count of species "MinD_ATP" in compartment "cell"" target="molcountincmpt MinD_ATP cell" taskReference="task"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| <dataGenerator id="data_generator_count_species_MinD_ATP_surface_membrane" name="Count of species "MinD_ATP" in surface "membrane""> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> variable_count_species_MinD_ATP_surface_membrane </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="variable_count_species_MinD_ATP_surface_membrane" name="Count of species "MinD_ATP" in surface "membrane"" target="molcountonsurf MinD_ATP membrane" taskReference="task"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| <dataGenerator id="data_generator_count_species_MinDMinE" name="Count of species "MinDMinE""> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> variable_count_species_MinDMinE </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="variable_count_species_MinDMinE" name="Count of species "MinDMinE"" target="molcount MinDMinE" taskReference="task"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| <dataGenerator id="data_generator_count_species_MinDMinE_compartment_cell" name="Count of species "MinDMinE" in compartment "cell""> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> variable_count_species_MinDMinE_compartment_cell </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="variable_count_species_MinDMinE_compartment_cell" name="Count of species "MinDMinE" in compartment "cell"" target="molcountincmpt MinDMinE cell" taskReference="task"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| <dataGenerator id="data_generator_count_species_MinDMinE_surface_membrane" name="Count of species "MinDMinE" in surface "membrane""> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> variable_count_species_MinDMinE_surface_membrane </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="variable_count_species_MinDMinE_surface_membrane" name="Count of species "MinDMinE" in surface "membrane"" target="molcountonsurf MinDMinE membrane" taskReference="task"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| <dataGenerator id="data_generator_count_species_MinE" name="Count of species "MinE""> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> variable_count_species_MinE </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="variable_count_species_MinE" name="Count of species "MinE"" target="molcount MinE" taskReference="task"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| <dataGenerator id="data_generator_count_species_MinE_compartment_cell" name="Count of species "MinE" in compartment "cell""> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> variable_count_species_MinE_compartment_cell </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="variable_count_species_MinE_compartment_cell" name="Count of species "MinE" in compartment "cell"" target="molcountincmpt MinE cell" taskReference="task"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| <dataGenerator id="data_generator_count_species_MinE_surface_membrane" name="Count of species "MinE" in surface "membrane""> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> variable_count_species_MinE_surface_membrane </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="variable_count_species_MinE_surface_membrane" name="Count of species "MinE" in surface "membrane"" target="molcountonsurf MinE membrane" taskReference="task"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| </listOfDataGenerators> | ||
| <listOfOutputs> | ||
| <report id="report"> | ||
| <listOfDataSets> | ||
| <dataSet id="time" name="Time" label="Time" dataReference="data_generator_time"/> | ||
| <dataSet id="count_species_MinD_ADP" name="Count of species "MinD_ADP"" label="Count of species "MinD_ADP"" dataReference="data_generator_count_species_MinD_ADP"/> | ||
| <dataSet id="count_species_MinD_ADP_compartment_cell" name="Count of species "MinD_ADP" in compartment "cell"" label="Count of species "MinD_ADP" in compartment "cell"" dataReference="data_generator_count_species_MinD_ADP_compartment_cell"/> | ||
| <dataSet id="count_species_MinD_ADP_surface_membrane" name="Count of species "MinD_ADP" in surface "membrane"" label="Count of species "MinD_ADP" in surface "membrane"" dataReference="data_generator_count_species_MinD_ADP_surface_membrane"/> | ||
| <dataSet id="count_species_MinD_ATP" name="Count of species "MinD_ATP"" label="Count of species "MinD_ATP"" dataReference="data_generator_count_species_MinD_ATP"/> | ||
| <dataSet id="count_species_MinD_ATP_compartment_cell" name="Count of species "MinD_ATP" in compartment "cell"" label="Count of species "MinD_ATP" in compartment "cell"" dataReference="data_generator_count_species_MinD_ATP_compartment_cell"/> | ||
| <dataSet id="count_species_MinD_ATP_surface_membrane" name="Count of species "MinD_ATP" in surface "membrane"" label="Count of species "MinD_ATP" in surface "membrane"" dataReference="data_generator_count_species_MinD_ATP_surface_membrane"/> | ||
| <dataSet id="count_species_MinDMinE" name="Count of species "MinDMinE"" label="Count of species "MinDMinE"" dataReference="data_generator_count_species_MinDMinE"/> | ||
| <dataSet id="count_species_MinDMinE_compartment_cell" name="Count of species "MinDMinE" in compartment "cell"" label="Count of species "MinDMinE" in compartment "cell"" dataReference="data_generator_count_species_MinDMinE_compartment_cell"/> | ||
| <dataSet id="count_species_MinDMinE_surface_membrane" name="Count of species "MinDMinE" in surface "membrane"" label="Count of species "MinDMinE" in surface "membrane"" dataReference="data_generator_count_species_MinDMinE_surface_membrane"/> | ||
| <dataSet id="count_species_MinE" name="Count of species "MinE"" label="Count of species "MinE"" dataReference="data_generator_count_species_MinE"/> | ||
| <dataSet id="count_species_MinE_compartment_cell" name="Count of species "MinE" in compartment "cell"" label="Count of species "MinE" in compartment "cell"" dataReference="data_generator_count_species_MinE_compartment_cell"/> | ||
| <dataSet id="count_species_MinE_surface_membrane" name="Count of species "MinE" in surface "membrane"" label="Count of species "MinE" in surface "membrane"" dataReference="data_generator_count_species_MinE_surface_membrane"/> | ||
| </listOfDataSets> | ||
| </report> | ||
| <plot2D id="Figure" name="Figure"> | ||
| <listOfCurves> | ||
| <curve id="curve_MinD_ADP" name="MinD_ADP" xDataReference="data_generator_time" yDataReference="data_generator_count_species_MinD_ADP"/> | ||
| <curve id="curve_MinE" name="MinE" xDataReference="data_generator_time" yDataReference="data_generator_count_species_MinE"/> | ||
| <curve id="curve_MinD_ATP" name="MinD_ATP" xDataReference="data_generator_time" yDataReference="data_generator_count_species_MinD_ATP"/> | ||
| <curve id="curve_MinDMinE" name="MinDMinE" xDataReference="data_generator_time" yDataReference="data_generator_count_species_MinDMinE"/> | ||
| </listOfCurves> | ||
| </plot2D> | ||
| </listOfOutputs> | ||
| </sedML> |