biosimulators · CodeByDrescher · Feb 17, 2024 · Feb 17, 2024
diff --git a/examples/smoldyn/Andrews-Min1-PUBLICATION.omex b/examples/smoldyn/Andrews-Min1-PUBLICATION.omex
diff --git a/examples/smoldyn/Andrews-Min1-PUBLICATION/manifest.xml b/examples/smoldyn/Andrews-Min1-PUBLICATION/manifest.xml
@@ -0,0 +1,6 @@
+<?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>
diff --git a/examples/smoldyn/Andrews-Min1-PUBLICATION/metadata.rdf b/examples/smoldyn/Andrews-Min1-PUBLICATION/metadata.rdf
@@ -0,0 +1,57 @@
+<?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.
+
+ 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>
+
diff --git a/examples/smoldyn/Andrews-Min1-PUBLICATION/model.txt b/examples/smoldyn/Andrews-Min1-PUBLICATION/model.txt
@@ -0,0 +1,115 @@
+# 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
+
+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)
+
+define UNBINDRAD	0.01	# MinD separation on surface (um)
+
+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
+
+define NUMBER_MIND	4000	# number of MinD in cell
+define NUMBER_MINE	1400	# number of MinE in cell
+
+define TIME_STOP	10	# stopping time
+
+#define KICK_START	1	# start with MinD_ATP at an end
+
+random_seed 1
+
+#graphics opengl
+#graphic_iter 100
+
+#tiff_name movie/MinMovie
+#tiff_iter 200
+#tiff_min 1
+#tiff_max 200
+
+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
+
+accuracy 5
+molperbox 4
+
+species MinD_ATP
+species MinD_ADP
+species MinE
+species MinDMinE
+
+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
+
+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
+
+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
+
+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
+
+start_compartment cell
+surface membrane
+point 0 0 0
+end_compartment
+
+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
+
+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
+
+
+output_files modelout.txt
+cmd i 0 TIME_STOP 2 executiontime modelout.txt
+cmd i 0 TIME_STOP 2 listmols modelout.txt
+
+end_file
+
diff --git a/examples/smoldyn/Andrews-Min1-PUBLICATION/simulation.sedml b/examples/smoldyn/Andrews-Min1-PUBLICATION/simulation.sedml
@@ -0,0 +1,147 @@
+<?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 &quot;MinD_ADP&quot;">
+      <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 &quot;MinD_ADP&quot;" target="molcount MinD_ADP" taskReference="task"/>
+      </listOfVariables>
+    </dataGenerator>
+    <dataGenerator id="data_generator_count_species_MinD_ADP_compartment_cell" name="Count of species &quot;MinD_ADP&quot; in compartment &quot;cell&quot;">
+      <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 &quot;MinD_ADP&quot; in compartment &quot;cell&quot;" target="molcountincmpt MinD_ADP cell" taskReference="task"/>
+      </listOfVariables>
+    </dataGenerator>
+    <dataGenerator id="data_generator_count_species_MinD_ADP_surface_membrane" name="Count of species &quot;MinD_ADP&quot; in surface &quot;membrane&quot;">
+      <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 &quot;MinD_ADP&quot; in surface &quot;membrane&quot;" target="molcountonsurf MinD_ADP membrane" taskReference="task"/>
+      </listOfVariables>
+    </dataGenerator>
+    <dataGenerator id="data_generator_count_species_MinD_ATP" name="Count of species &quot;MinD_ATP&quot;">
+      <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 &quot;MinD_ATP&quot;" target="molcount MinD_ATP" taskReference="task"/>
+      </listOfVariables>
+    </dataGenerator>
+    <dataGenerator id="data_generator_count_species_MinD_ATP_compartment_cell" name="Count of species &quot;MinD_ATP&quot; in compartment &quot;cell&quot;">
+      <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 &quot;MinD_ATP&quot; in compartment &quot;cell&quot;" target="molcountincmpt MinD_ATP cell" taskReference="task"/>
+      </listOfVariables>
+    </dataGenerator>
+    <dataGenerator id="data_generator_count_species_MinD_ATP_surface_membrane" name="Count of species &quot;MinD_ATP&quot; in surface &quot;membrane&quot;">
+      <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 &quot;MinD_ATP&quot; in surface &quot;membrane&quot;" target="molcountonsurf MinD_ATP membrane" taskReference="task"/>
+      </listOfVariables>
+    </dataGenerator>
+    <dataGenerator id="data_generator_count_species_MinDMinE" name="Count of species &quot;MinDMinE&quot;">
+      <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 &quot;MinDMinE&quot;" target="molcount MinDMinE" taskReference="task"/>
+      </listOfVariables>
+    </dataGenerator>
+    <dataGenerator id="data_generator_count_species_MinDMinE_compartment_cell" name="Count of species &quot;MinDMinE&quot; in compartment &quot;cell&quot;">
+      <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 &quot;MinDMinE&quot; in compartment &quot;cell&quot;" target="molcountincmpt MinDMinE cell" taskReference="task"/>
+      </listOfVariables>
+    </dataGenerator>
+    <dataGenerator id="data_generator_count_species_MinDMinE_surface_membrane" name="Count of species &quot;MinDMinE&quot; in surface &quot;membrane&quot;">
+      <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 &quot;MinDMinE&quot; in surface &quot;membrane&quot;" target="molcountonsurf MinDMinE membrane" taskReference="task"/>
+      </listOfVariables>
+    </dataGenerator>
+    <dataGenerator id="data_generator_count_species_MinE" name="Count of species &quot;MinE&quot;">
+      <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 &quot;MinE&quot;" target="molcount MinE" taskReference="task"/>
+      </listOfVariables>
+    </dataGenerator>
+    <dataGenerator id="data_generator_count_species_MinE_compartment_cell" name="Count of species &quot;MinE&quot; in compartment &quot;cell&quot;">
+      <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 &quot;MinE&quot; in compartment &quot;cell&quot;" target="molcountincmpt MinE cell" taskReference="task"/>
+      </listOfVariables>
+    </dataGenerator>
+    <dataGenerator id="data_generator_count_species_MinE_surface_membrane" name="Count of species &quot;MinE&quot; in surface &quot;membrane&quot;">
+      <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 &quot;MinE&quot; in surface &quot;membrane&quot;" 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 &quot;MinD_ADP&quot;" label="Count of species &quot;MinD_ADP&quot;" dataReference="data_generator_count_species_MinD_ADP"/>
+        <dataSet id="count_species_MinD_ADP_compartment_cell" name="Count of species &quot;MinD_ADP&quot; in compartment &quot;cell&quot;" label="Count of species &quot;MinD_ADP&quot; in compartment &quot;cell&quot;" dataReference="data_generator_count_species_MinD_ADP_compartment_cell"/>
+        <dataSet id="count_species_MinD_ADP_surface_membrane" name="Count of species &quot;MinD_ADP&quot; in surface &quot;membrane&quot;" label="Count of species &quot;MinD_ADP&quot; in surface &quot;membrane&quot;" dataReference="data_generator_count_species_MinD_ADP_surface_membrane"/>
+        <dataSet id="count_species_MinD_ATP" name="Count of species &quot;MinD_ATP&quot;" label="Count of species &quot;MinD_ATP&quot;" dataReference="data_generator_count_species_MinD_ATP"/>
+        <dataSet id="count_species_MinD_ATP_compartment_cell" name="Count of species &quot;MinD_ATP&quot; in compartment &quot;cell&quot;" label="Count of species &quot;MinD_ATP&quot; in compartment &quot;cell&quot;" dataReference="data_generator_count_species_MinD_ATP_compartment_cell"/>
+        <dataSet id="count_species_MinD_ATP_surface_membrane" name="Count of species &quot;MinD_ATP&quot; in surface &quot;membrane&quot;" label="Count of species &quot;MinD_ATP&quot; in surface &quot;membrane&quot;" dataReference="data_generator_count_species_MinD_ATP_surface_membrane"/>
+        <dataSet id="count_species_MinDMinE" name="Count of species &quot;MinDMinE&quot;" label="Count of species &quot;MinDMinE&quot;" dataReference="data_generator_count_species_MinDMinE"/>
+        <dataSet id="count_species_MinDMinE_compartment_cell" name="Count of species &quot;MinDMinE&quot; in compartment &quot;cell&quot;" label="Count of species &quot;MinDMinE&quot; in compartment &quot;cell&quot;" dataReference="data_generator_count_species_MinDMinE_compartment_cell"/>
+        <dataSet id="count_species_MinDMinE_surface_membrane" name="Count of species &quot;MinDMinE&quot; in surface &quot;membrane&quot;" label="Count of species &quot;MinDMinE&quot; in surface &quot;membrane&quot;" dataReference="data_generator_count_species_MinDMinE_surface_membrane"/>
+        <dataSet id="count_species_MinE" name="Count of species &quot;MinE&quot;" label="Count of species &quot;MinE&quot;" dataReference="data_generator_count_species_MinE"/>
+        <dataSet id="count_species_MinE_compartment_cell" name="Count of species &quot;MinE&quot; in compartment &quot;cell&quot;" label="Count of species &quot;MinE&quot; in compartment &quot;cell&quot;" dataReference="data_generator_count_species_MinE_compartment_cell"/>
+        <dataSet id="count_species_MinE_surface_membrane" name="Count of species &quot;MinE&quot; in surface &quot;membrane&quot;" label="Count of species &quot;MinE&quot; in surface &quot;membrane&quot;" 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>