Examples with Membrane cbit.vcell.model.Membrane used on opensource projects

Example 71 with Membrane

use of cbit.vcell.model.Membrane in project vcell by virtualcell.

the class ITextWriter method writeStructure.

protected void writeStructure(Model model, Structure struct, Table structTable) throws DocumentException {
    // If this structure has any reactions in it, add its name as a hyperlink to the reactions' list.
    if (hasReactions(model, struct)) {
        Paragraph linkParagraph = new Paragraph();
        Font linkFont;
        try {
            BaseFont fontBaseFont = BaseFont.createFont(BaseFont.HELVETICA, BaseFont.CP1252, BaseFont.NOT_EMBEDDED);
            linkFont = new Font(fontBaseFont, DEF_FONT_SIZE, Font.NORMAL, new java.awt.Color(0, 0, 255));
        } catch (Exception e) {
            linkFont = getFont();
            e.printStackTrace();
        }
        linkParagraph.add(new Chunk(struct.getName(), linkFont).setLocalGoto(struct.getName()));
        Cell structLinkCell = new Cell(linkParagraph);
        structLinkCell.setBorderWidth(1);
        structLinkCell.setHorizontalAlignment(Element.ALIGN_LEFT);
        structTable.addCell(structLinkCell);
    } else {
        structTable.addCell(createCell(struct.getName(), getFont()));
    }
    StructureTopology structTopology = model.getStructureTopology();
    if (struct instanceof Membrane) {
        structTable.addCell(createCell("Membrane", getFont()));
        Feature outsideFeature = structTopology.getOutsideFeature((Membrane) struct);
        Feature insideFeature = structTopology.getInsideFeature((Membrane) struct);
        structTable.addCell(createCell((insideFeature != null ? insideFeature.getName() : "N/A"), getFont()));
        structTable.addCell(createCell((outsideFeature != null ? outsideFeature.getName() : "N/A"), getFont()));
    } else {
        structTable.addCell(createCell("Feature", getFont()));
        String outsideStr = "N/A", insideStr = "N/A";
        Membrane enclosingMem = (Membrane) structTopology.getParentStructure(struct);
        if (enclosingMem != null) {
            outsideStr = enclosingMem.getName();
        }
        // To do:  retrieve the 'child' membrane here...
        structTable.addCell(createCell(insideStr, getFont()));
        structTable.addCell(createCell(outsideStr, getFont()));
    }
}

Example 72 with Membrane

use of cbit.vcell.model.Membrane in project vcell by virtualcell.

the class StructureSizeSolver method updateUnitStructureSizes.

/**
 * Insert the method's description here.
 * Creation date: (5/17/2006 10:33:38 AM)
 * @return double[]
 * @param structName java.lang.String
 * @param structSize double
 */
public static void updateUnitStructureSizes(SimulationContext simContext, GeometryClass geometryClass) {
    if (simContext.getGeometryContext().getGeometry().getDimension() == 0) {
        return;
    }
    StructureMapping[] myStructMappings = simContext.getGeometryContext().getStructureMappings(geometryClass);
    if (myStructMappings != null && myStructMappings.length == 1) {
        // if the unitSizeParameter is dimensionless, then features are mapped to SubVolumes or Membranes are mapped to surfaces (should sum to 1)
        boolean bDimensionless = myStructMappings[0].getUnitSizeParameter().getUnitDefinition().isEquivalent(simContext.getModel().getUnitSystem().getInstance_DIMENSIONLESS());
        if (bDimensionless) {
            try {
                myStructMappings[0].getUnitSizeParameter().setExpression(new Expression(1.0));
                return;
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException(e.getMessage());
            }
        }
    }
    if (myStructMappings != null && myStructMappings.length == 0) {
        // nothing to solve, there are no mappings for this geometryClass
        return;
    }
    StructureMapping[] structMappings = simContext.getGeometryContext().getStructureMappings();
    try {
        ConstraintContainerImpl ccImpl = new ConstraintContainerImpl();
        Structure struct = null;
        Expression totalVolExpr = new Expression(0.0);
        StructureTopology structureTopology = simContext.getModel().getStructureTopology();
        for (int i = 0; i < structMappings.length; i++) {
            if (structMappings[i].getGeometryClass() != geometryClass) {
                continue;
            }
            // new model with unit sizes already
            if (structMappings[i].getUnitSizeParameter() != null && structMappings[i].getUnitSizeParameter().getExpression() != null) {
                return;
            }
            if (struct == null) {
                struct = structMappings[i].getStructure();
            }
            if (structMappings[i] instanceof MembraneMapping) {
                MembraneMapping membraneMapping = (MembraneMapping) structMappings[i];
                Membrane membrane = membraneMapping.getMembrane();
                String membraneSizeName = TokenMangler.mangleToSName(membrane.getName() + "_size");
                ccImpl.addSimpleBound(new SimpleBounds(membraneSizeName, new RealInterval(0, 100000), AbstractConstraint.PHYSICAL_LIMIT, "definition"));
                Feature insideFeature = structureTopology.getInsideFeature(membrane);
                String volFractName = TokenMangler.mangleToSName(insideFeature.getName() + "_volFract");
                String svRatioName = TokenMangler.mangleToSName(insideFeature.getName() + "_svRatio");
                StructureMapping.StructureMappingParameter volFractParameter = membraneMapping.getVolumeFractionParameter();
                double volFractValue = volFractParameter.getExpression().evaluateConstant();
                ccImpl.addSimpleBound(new SimpleBounds(volFractName, new RealInterval(volFractValue, volFractValue), AbstractConstraint.MODELING_ASSUMPTION, "from model"));
                StructureMapping.StructureMappingParameter surfToVolParameter = membraneMapping.getSurfaceToVolumeParameter();
                double svRatioValue = surfToVolParameter.getExpression().evaluateConstant();
                ccImpl.addSimpleBound(new SimpleBounds(svRatioName, new RealInterval(svRatioValue, svRatioValue), AbstractConstraint.MODELING_ASSUMPTION, "from model"));
                // membrane mapped to volume
                if (geometryClass instanceof SubVolume) {
                    // 
                    // EC eclosing cyt, which contains er and golgi
                    // "(cyt_size+ er_size + golgi_size) * cyt_svRatio - PM_size == 0"
                    // 
                    Expression sumOfInsideVolumeExp = new Expression(0.0);
                    for (int j = 0; j < structMappings.length; j++) {
                        if (structMappings[j] instanceof FeatureMapping && structureTopology.enclosedBy(structMappings[j].getStructure(), insideFeature)) {
                            Feature childFeatureOfInside = ((FeatureMapping) structMappings[j]).getFeature();
                            if (simContext.getGeometryContext().getStructureMapping(childFeatureOfInside).getGeometryClass() == geometryClass) {
                                sumOfInsideVolumeExp = Expression.add(sumOfInsideVolumeExp, new Expression(TokenMangler.mangleToSName(childFeatureOfInside.getName() + "_size")));
                            }
                        }
                    }
                    Expression tempExpr = Expression.mult(sumOfInsideVolumeExp, new Expression(svRatioName));
                    tempExpr = Expression.add(tempExpr, new Expression("-" + membraneSizeName));
                    ccImpl.addGeneralConstraint(new GeneralConstraint(new Expression(tempExpr.infix() + "==0"), AbstractConstraint.MODELING_ASSUMPTION, "svRatio definition"));
                    // 
                    // EC eclosing cyt, which contains er and golgi
                    // (EC_size + cyt_size + er_size + golgi_size) * cyt_vfRatio - (cyt_size + er_size + golgi_size) == 0
                    // 
                    Feature outsideFeature = structureTopology.getOutsideFeature(membrane);
                    Expression sumOfParentVolumeExp = new Expression(0.0);
                    for (int j = 0; j < structMappings.length; j++) {
                        if (structMappings[j] instanceof FeatureMapping && structureTopology.enclosedBy(structMappings[j].getStructure(), outsideFeature)) {
                            Feature childFeatureOfParent = ((FeatureMapping) structMappings[j]).getFeature();
                            if (simContext.getGeometryContext().getStructureMapping(childFeatureOfParent).getGeometryClass() == geometryClass) {
                                sumOfParentVolumeExp = Expression.add(sumOfParentVolumeExp, new Expression(TokenMangler.mangleToSName(childFeatureOfParent.getName() + "_size")));
                            }
                        }
                    }
                    Expression exp = Expression.mult(sumOfParentVolumeExp, new Expression(volFractName));
                    exp = Expression.add(exp, Expression.negate(sumOfInsideVolumeExp));
                    ccImpl.addGeneralConstraint(new GeneralConstraint(new Expression(exp.infix() + "==0.0"), AbstractConstraint.MODELING_ASSUMPTION, "volFract definition"));
                }
            } else if (structMappings[i] instanceof FeatureMapping) {
                FeatureMapping featureMapping = (FeatureMapping) structMappings[i];
                String featureSizeName = TokenMangler.mangleToSName(featureMapping.getFeature().getName() + "_size");
                totalVolExpr = Expression.add(totalVolExpr, new Expression(featureSizeName));
                ccImpl.addSimpleBound(new SimpleBounds(featureSizeName, new RealInterval(0, 1), AbstractConstraint.PHYSICAL_LIMIT, "definition"));
            }
        }
        if (geometryClass instanceof SubVolume) {
            ccImpl.addGeneralConstraint(new GeneralConstraint(new Expression(totalVolExpr.infix() + "==1.0"), AbstractConstraint.MODELING_ASSUMPTION, "total volume"));
        }
        // ccImpl.show();
        ConstraintSolver constraintSolver = new ConstraintSolver(ccImpl);
        constraintSolver.resetIntervals();
        int numTimesNarrowed = 0;
        RealInterval[] lastSolution = null;
        boolean bChanged = true;
        while (constraintSolver.narrow() && bChanged && numTimesNarrowed < 125) {
            numTimesNarrowed++;
            bChanged = false;
            RealInterval[] thisSolution = constraintSolver.getIntervals();
            if (lastSolution != null) {
                for (int i = 0; i < thisSolution.length; i++) {
                    if (!thisSolution[i].equals(lastSolution[i])) {
                        bChanged = true;
                    }
                }
            } else {
                bChanged = true;
            }
            lastSolution = thisSolution;
        }
        System.out.println("num of times narrowed = " + numTimesNarrowed);
        if (numTimesNarrowed > 0) {
            String[] symbols = constraintSolver.getSymbols();
            net.sourceforge.interval.ia_math.RealInterval[] solution = constraintSolver.getIntervals();
            double totalArea = 0;
            double totalVolume = 0;
            for (int i = 0; i < symbols.length; i++) {
                System.out.println("solution[" + i + "] \"" + symbols[i] + "\" = " + solution[i]);
                for (int j = 0; j < structMappings.length; j++) {
                    if (symbols[i].equals(TokenMangler.mangleToSName(structMappings[j].getStructure().getName() + "_size"))) {
                        if (!Double.isInfinite(solution[i].lo()) && !Double.isInfinite(solution[i].hi())) {
                            double value = (solution[i].lo() + solution[i].hi()) / 2;
                            Expression exp = new Expression(value);
                            if (structMappings[j] instanceof FeatureMapping) {
                                FeatureMapping fm = (FeatureMapping) structMappings[j];
                                totalVolume += value;
                                if (geometryClass instanceof SubVolume) {
                                    fm.getVolumePerUnitVolumeParameter().setExpression(exp);
                                } else if (geometryClass instanceof SurfaceClass) {
                                    fm.getVolumePerUnitAreaParameter().setExpression(exp);
                                }
                            } else if (structMappings[j] instanceof MembraneMapping) {
                                MembraneMapping mm = (MembraneMapping) structMappings[j];
                                totalArea += value;
                                if (geometryClass instanceof SubVolume) {
                                    mm.getAreaPerUnitVolumeParameter().setExpression(exp);
                                } else if (geometryClass instanceof SurfaceClass) {
                                    mm.getAreaPerUnitAreaParameter().setExpression(exp);
                                }
                            }
                        }
                    }
                }
            }
            // 
            // normalize all so that total volume is 1.0 for subVolumes or
            // total area is 1.0 for surfaceClasses
            // 
            double scaleFactor = 1;
            if (geometryClass instanceof SubVolume) {
                scaleFactor = totalVolume;
            } else if (geometryClass instanceof SurfaceClass) {
                scaleFactor = totalArea;
            } else {
                throw new RuntimeException("unexpected GeometryClass");
            }
            for (int j = 0; j < structMappings.length; j++) {
                if (structMappings[j].getGeometryClass() == geometryClass) {
                    if (structMappings[j] instanceof FeatureMapping) {
                        FeatureMapping fm = (FeatureMapping) structMappings[j];
                        if (geometryClass instanceof SubVolume) {
                            fm.getVolumePerUnitVolumeParameter().setExpression(new Expression(fm.getVolumePerUnitVolumeParameter().getExpression().evaluateConstant() / scaleFactor));
                        } else if (geometryClass instanceof SurfaceClass) {
                            fm.getVolumePerUnitAreaParameter().setExpression(new Expression(fm.getVolumePerUnitAreaParameter().getExpression().evaluateConstant() / scaleFactor));
                        }
                    } else if (structMappings[j] instanceof MembraneMapping) {
                        MembraneMapping mm = (MembraneMapping) structMappings[j];
                        if (geometryClass instanceof SubVolume) {
                            mm.getAreaPerUnitVolumeParameter().setExpression(new Expression(mm.getAreaPerUnitVolumeParameter().getExpression().evaluateConstant() / scaleFactor));
                        } else if (geometryClass instanceof SurfaceClass) {
                            mm.getAreaPerUnitAreaParameter().setExpression(new Expression(mm.getAreaPerUnitAreaParameter().getExpression().evaluateConstant() / scaleFactor));
                        }
                    }
                }
            }
        } else {
            throw new RuntimeException("cannot solve for size");
        }
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException(e.getMessage());
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException(e.getMessage());
    }
}

Example 73 with Membrane

use of cbit.vcell.model.Membrane in project vcell by virtualcell.

the class StructTable method getStructure.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.ReactionParticipant
 * @param rset java.sql.ResultSet
 */
public Structure getStructure(java.sql.ResultSet rset, KeyValue structKey) throws java.sql.SQLException, DataAccessException {
    // KeyValue key = new KeyValue(rset.getBigDecimal(StructTable.id.toString(),0));
    String name = TokenMangler.getSQLRestoredString(rset.getString(StructTable.table.strName.toString()));
    String structType = rset.getString(StructTable.table.structType.toString());
    String membraneVoltageNameString = rset.getString(StructTable.table.memVoltName.toString());
    if (rset.wasNull()) {
        membraneVoltageNameString = null;
    }
    Structure structure = null;
    if (structType.equals(StructTable.STRUCTTYPE_FEATURE)) {
        try {
            structure = new Feature(structKey, name);
        } catch (java.beans.PropertyVetoException e) {
        }
    } else if (structType.equals(StructTable.STRUCTTYPE_MEMBRANE)) {
        try {
            structure = new Membrane(structKey, name);
            if (membraneVoltageNameString != null) {
                ((Membrane) structure).getMembraneVoltage().setName(membraneVoltageNameString);
            }
        } catch (java.beans.PropertyVetoException e) {
        }
    }
    return structure;
}

Example 74 with Membrane

use of cbit.vcell.model.Membrane in project vcell by virtualcell.

the class RunRefSimulationFastOp method createRefSimBioModel.

private BioModel createRefSimBioModel(KeyValue simKey, User owner, Origin origin, Extent extent, ROI cellROI_2D, double timeStepVal, TimeBounds timeBounds, String varName, Expression initialConcentration, FieldFunctionArguments psfFFA, Expression chirpedDiffusionRate) throws Exception {
    int numX = cellROI_2D.getRoiImages()[0].getNumX();
    int numY = cellROI_2D.getRoiImages()[0].getNumY();
    int numZ = cellROI_2D.getRoiImages().length;
    short[] shortPixels = cellROI_2D.getRoiImages()[0].getPixels();
    byte[] bytePixels = new byte[numX * numY * numZ];
    final byte EXTRACELLULAR_PIXVAL = 0;
    final byte CYTOSOL_PIXVAL = 1;
    for (int i = 0; i < bytePixels.length; i++) {
        if (shortPixels[i] != 0) {
            bytePixels[i] = CYTOSOL_PIXVAL;
        }
    }
    VCImage maskImage;
    try {
        maskImage = new VCImageUncompressed(null, bytePixels, extent, numX, numY, numZ);
    } catch (ImageException e) {
        e.printStackTrace();
        throw new RuntimeException("failed to create mask image for geometry");
    }
    Geometry geometry = new Geometry("geometry", maskImage);
    geometry.getGeometrySpec().setOrigin(origin);
    if (geometry.getGeometrySpec().getNumSubVolumes() != 2) {
        throw new Exception("Cell ROI has no ExtraCellular.");
    }
    String EXTRACELLULAR_NAME = "ec";
    String CYTOSOL_NAME = "cyt";
    String PLASMAMEMBRANE_NAME = "pm";
    ImageSubVolume subVolume0 = (ImageSubVolume) geometry.getGeometrySpec().getSubVolume(0);
    ImageSubVolume subVolume1 = (ImageSubVolume) geometry.getGeometrySpec().getSubVolume(1);
    if (subVolume0.getPixelValue() == EXTRACELLULAR_PIXVAL) {
        subVolume0.setName(EXTRACELLULAR_NAME);
        subVolume1.setName(CYTOSOL_NAME);
    } else {
        subVolume0.setName(CYTOSOL_NAME);
        subVolume1.setName(EXTRACELLULAR_NAME);
    }
    geometry.getGeometrySurfaceDescription().updateAll();
    BioModel bioModel = new BioModel(null);
    bioModel.setName("unnamed");
    Model model = new Model("model");
    bioModel.setModel(model);
    Feature extracellular = model.addFeature(EXTRACELLULAR_NAME);
    Feature cytosol = model.addFeature(CYTOSOL_NAME);
    Membrane plasmaMembrane = model.addMembrane(PLASMAMEMBRANE_NAME);
    SimulationContext simContext = new SimulationContext(bioModel.getModel(), geometry);
    bioModel.addSimulationContext(simContext);
    FeatureMapping cytosolFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(cytosol);
    FeatureMapping extracellularFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(extracellular);
    MembraneMapping plasmaMembraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(plasmaMembrane);
    SubVolume cytSubVolume = geometry.getGeometrySpec().getSubVolume(CYTOSOL_NAME);
    SubVolume exSubVolume = geometry.getGeometrySpec().getSubVolume(EXTRACELLULAR_NAME);
    SurfaceClass pmSurfaceClass = geometry.getGeometrySurfaceDescription().getSurfaceClass(exSubVolume, cytSubVolume);
    cytosolFeatureMapping.setGeometryClass(cytSubVolume);
    extracellularFeatureMapping.setGeometryClass(exSubVolume);
    plasmaMembraneMapping.setGeometryClass(pmSurfaceClass);
    cytosolFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    extracellularFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    plasmaMembraneMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    // Mobile Species
    Species diffusingSpecies = model.addSpecies(new Species("species", "Mobile bleachable species"));
    SpeciesContext diffusingSpeciesContext = model.addSpeciesContext(diffusingSpecies, cytosol);
    diffusingSpeciesContext.setName(varName);
    SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(diffusingSpeciesContext);
    scs.getInitialConditionParameter().setExpression(initialConcentration);
    chirpedDiffusionRate.bindExpression(scs);
    scs.getDiffusionParameter().setExpression(chirpedDiffusionRate);
    // simContext.getMicroscopeMeasurement().addFluorescentSpecies(speciesContexts[0]);
    // simContext.getMicroscopeMeasurement().setConvolutionKernel(new MicroscopeMeasurement.ProjectionZKernel());
    MathDescription mathDescription = simContext.createNewMathMapping().getMathDescription();
    // maybe there is a way that works for simContext.getMicroscopeMeasurement().... but this is needed now.
    mathDescription.addVariable(new Function(Simulation.PSF_FUNCTION_NAME, new Expression(psfFFA.infix()), null));
    simContext.setMathDescription(mathDescription);
    SimulationVersion simVersion = new SimulationVersion(simKey, "sim1", owner, new GroupAccessNone(), new KeyValue("0"), new BigDecimal(0), new Date(), VersionFlag.Current, "", null);
    Simulation newSimulation = new Simulation(simVersion, simContext.getMathDescription());
    newSimulation.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
    simContext.addSimulation(newSimulation);
    newSimulation.getSolverTaskDescription().setTimeBounds(timeBounds);
    newSimulation.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec(timeStepVal));
    newSimulation.getMeshSpecification().setSamplingSize(cellROI_2D.getISize());
    newSimulation.getSolverTaskDescription().setTimeStep(new TimeStep(timeStepVal, timeStepVal, timeStepVal));
    return bioModel;
}

Example 75 with Membrane

use of cbit.vcell.model.Membrane in project vcell by virtualcell.

the class RunRefSimulationOp method createRefSimBioModel.

private static BioModel createRefSimBioModel(KeyValue simKey, User owner, Origin origin, Extent extent, ROI cellROI_2D, double timeStepVal, TimeBounds timeBounds, String varName, Expression initialConcentration, double baseDiffusionRate) throws Exception {
    int numX = cellROI_2D.getRoiImages()[0].getNumX();
    int numY = cellROI_2D.getRoiImages()[0].getNumY();
    int numZ = cellROI_2D.getRoiImages().length;
    short[] shortPixels = cellROI_2D.getRoiImages()[0].getPixels();
    byte[] bytePixels = new byte[numX * numY * numZ];
    final byte EXTRACELLULAR_PIXVAL = 0;
    final byte CYTOSOL_PIXVAL = 1;
    for (int i = 0; i < bytePixels.length; i++) {
        if (shortPixels[i] != 0) {
            bytePixels[i] = CYTOSOL_PIXVAL;
        }
    }
    VCImage maskImage;
    try {
        maskImage = new VCImageUncompressed(null, bytePixels, extent, numX, numY, numZ);
    } catch (ImageException e) {
        e.printStackTrace();
        throw new RuntimeException("failed to create mask image for geometry");
    }
    Geometry geometry = new Geometry("geometry", maskImage);
    geometry.getGeometrySpec().setOrigin(origin);
    if (geometry.getGeometrySpec().getNumSubVolumes() != 2) {
        throw new Exception("Cell ROI has no ExtraCellular.");
    }
    String EXTRACELLULAR_NAME = "ec";
    String CYTOSOL_NAME = "cyt";
    String PLASMAMEMBRANE_NAME = "pm";
    ImageSubVolume subVolume0 = (ImageSubVolume) geometry.getGeometrySpec().getSubVolume(0);
    ImageSubVolume subVolume1 = (ImageSubVolume) geometry.getGeometrySpec().getSubVolume(1);
    if (subVolume0.getPixelValue() == EXTRACELLULAR_PIXVAL) {
        subVolume0.setName(EXTRACELLULAR_NAME);
        subVolume1.setName(CYTOSOL_NAME);
    } else {
        subVolume0.setName(CYTOSOL_NAME);
        subVolume1.setName(EXTRACELLULAR_NAME);
    }
    geometry.getGeometrySurfaceDescription().updateAll();
    BioModel bioModel = new BioModel(null);
    bioModel.setName("unnamed");
    Model model = new Model("model");
    bioModel.setModel(model);
    Feature extracellular = model.addFeature(EXTRACELLULAR_NAME);
    Feature cytosol = model.addFeature(CYTOSOL_NAME);
    Membrane plasmaMembrane = model.addMembrane(PLASMAMEMBRANE_NAME);
    SimulationContext simContext = new SimulationContext(bioModel.getModel(), geometry);
    bioModel.addSimulationContext(simContext);
    FeatureMapping cytosolFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(cytosol);
    FeatureMapping extracellularFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(extracellular);
    MembraneMapping plasmaMembraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(plasmaMembrane);
    SubVolume cytSubVolume = geometry.getGeometrySpec().getSubVolume(CYTOSOL_NAME);
    SubVolume exSubVolume = geometry.getGeometrySpec().getSubVolume(EXTRACELLULAR_NAME);
    SurfaceClass pmSurfaceClass = geometry.getGeometrySurfaceDescription().getSurfaceClass(exSubVolume, cytSubVolume);
    cytosolFeatureMapping.setGeometryClass(cytSubVolume);
    extracellularFeatureMapping.setGeometryClass(exSubVolume);
    plasmaMembraneMapping.setGeometryClass(pmSurfaceClass);
    cytosolFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    extracellularFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    plasmaMembraneMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    // Mobile Species
    Species diffusingSpecies = model.addSpecies(new Species("species", "Mobile bleachable species"));
    SpeciesContext diffusingSpeciesContext = model.addSpeciesContext(diffusingSpecies, cytosol);
    diffusingSpeciesContext.setName(varName);
    SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(diffusingSpeciesContext);
    scs.getInitialConditionParameter().setExpression(initialConcentration);
    scs.getDiffusionParameter().setExpression(new Expression(baseDiffusionRate));
    // simContext.getMicroscopeMeasurement().addFluorescentSpecies(speciesContexts[0]);
    // simContext.getMicroscopeMeasurement().setConvolutionKernel(new MicroscopeMeasurement.ProjectionZKernel());
    simContext.setMathDescription(simContext.createNewMathMapping().getMathDescription());
    SimulationVersion simVersion = new SimulationVersion(simKey, "sim1", owner, new GroupAccessNone(), new KeyValue("0"), new BigDecimal(0), new Date(), VersionFlag.Current, "", null);
    Simulation newSimulation = new Simulation(simVersion, simContext.getMathDescription());
    newSimulation.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
    simContext.addSimulation(newSimulation);
    newSimulation.getSolverTaskDescription().setTimeBounds(timeBounds);
    newSimulation.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec(timeStepVal));
    newSimulation.getMeshSpecification().setSamplingSize(cellROI_2D.getISize());
    newSimulation.getSolverTaskDescription().setTimeStep(new TimeStep(timeStepVal, timeStepVal, timeStepVal));
    return bioModel;
}