public static void Main(String[] args) { if (args.Length == 0) { Console.WriteLine("Need one argument, copasi file"); Environment.Exit(1); } CCopasiDataModel dataModel = CCopasiRootContainer.addDatamodel(); if (!dataModel.loadModel(args[0])) { Console.WriteLine("Could not open file"); Console.WriteLine(CCopasiMessage.getAllMessageText()); Environment.Exit(1); } CModel model = dataModel.getModel(); ModelParameterSetVectorN sets = model.getModelParameterSets(); // if we don't have one, create one if (sets.size() == 0) { CModelParameterSet newSet = new CModelParameterSet("Current State", model); newSet.createFromModel(); printParameterSet(newSet); sets.add(newSet); } // interrogate the exiting parameter sets printExistingParametersets(model.getModelParameterSets()); }
/// <summary> /// Frees the COPASI Datamodel /// </summary> public void Dispose() { CCopasiRootContainer.removeDatamodel(dataModel); copasiMetabBySpecies.Clear(); copasiReactionByReactionType.Clear(); copasiReactionFluxValueByReaction.Clear(); }
public static void Main(String[] args) { // create a new datamodel CCopasiDataModel dataModel = CCopasiRootContainer.addDatamodel(); if (args.Length != 1) { Console.WriteLine("Need one argument: SBML | CPS filename."); Environment.Exit(1); } String filename = args[0]; try { String ext = System.IO.Path.GetExtension(filename); if (ext.Trim().ToLowerInvariant().EndsWith("xml")) { // load the model without progress report dataModel.importSBML(filename); } else { // load the model without progress report dataModel.loadModel(filename); } } catch { Console.WriteLine("Error while loading the model from file named \"" + filename + "\"."); Environment.Exit(1); } try { CModel model = dataModel.getModel(); int numAnnotations = model.getNumUnsupportedAnnotations(); Console.WriteLine("The model has: " + numAnnotations + " unsupported annotations."); if (numAnnotations == 0) { Console.WriteLine("adding custom annotation"); // we don't have an annotation, so lets add one if (!model.addUnsupportedAnnotation("http://myannotation.org", "<test xmlns='http://myannotation.org' value='blaaaahaaa'/>")) { Console.WriteLine("couldn't set annotation: "); Console.WriteLine(CCopasiMessage.getAllMessageText()); } } Console.WriteLine("The name of the first is: " + model.getUnsupportedAnnotationName(0)); Console.WriteLine("The raw xml of the first is: " + model.getUnsupportedAnnotation(0)); } catch (Exception ex) { Console.WriteLine("Error: " + ex.Message); } }
public static void Main(String[] args) { // create a new datamodel CCopasiDataModel dataModel = CCopasiRootContainer.addDatamodel(); if (args.Length != 2) { Console.WriteLine("Need two arguments: filename and filter."); Environment.Exit(1); } String filename = args[0]; try { String ext = System.IO.Path.GetExtension(filename); if (ext.Trim().ToLowerInvariant() == "xml") { // load the model without progress report dataModel.importSBML(filename); } else { // load the model without progress report dataModel.loadModel(filename); } } catch { Console.WriteLine("Error while loading the model from file named \"" + filename + "\"."); Environment.Exit(1); } try { // clear warnings / error messages CCopasiMessage.clearDeque(); // convert String translation = dataModel.exportMathModelToString(args[1]); // if conversion failed print message if (string.IsNullOrEmpty(translation)) { Console.WriteLine("Translation failed: "); Console.WriteLine(CCopasiMessage.getAllMessageText()); } // print translation Console.WriteLine(translation); } catch { Console.WriteLine("Error. Exporting the model to math failed."); } }
private static void InitCopasi() { if (!initCopasiCalled) { // TODO: error handling CCopasiRootContainer.init(); System.Diagnostics.Debug.Assert(CCopasiRootContainer.getRoot() != null); initCopasiCalled = true; } }
public Copasi() { InitCopasi(); // create a new datamodel dataModel = CCopasiRootContainer.addDatamodel(); // get the model from the datamodel model = dataModel.getModel(); // set the units for the model // we want seconds as the time unit // nanoliter as the volume units // and nanomole as the substance units model.setTimeUnit(CUnit.s); model.setVolumeUnit(CUnit.nl); model.setQuantityUnit(CUnit.nMol); // create a compartment with the name cell compartment = model.createCompartment("cell"); changedObjects = new ObjectStdVector(); }
static void Main() { Debug.Assert(CCopasiRootContainer.getRoot() != null); // create a new datamodel CCopasiDataModel dataModel = CCopasiRootContainer.addDatamodel(); Debug.Assert(CCopasiRootContainer.getDatamodelList().size() == 1); // get the model from the datamodel CModel model = dataModel.getModel(); Debug.Assert(model != null); model.setVolumeUnit(CUnit.fl); model.setTimeUnit(CUnit.s); model.setQuantityUnit(CUnit.fMol); CModelValue fixedModelValue = model.createModelValue("F"); Debug.Assert(fixedModelValue != null); fixedModelValue.setStatus(CModelEntity.FIXED); fixedModelValue.setInitialValue(3.0); CModelValue variableModelValue = model.createModelValue("V"); Debug.Assert(variableModelValue != null); variableModelValue.setStatus(CModelEntity.ASSIGNMENT); // we create a very simple assignment that is easy on the optimization // a parabole with the minimum at x=6 should do just fine string s = fixedModelValue.getValueReference().getCN().getString(); s = "(<" + s + "> - 6.0)^2"; variableModelValue.setExpression(s); // now we compile the model and tell COPASI which values have changed so // that COPASI can update the values that depend on those model.compileIfNecessary(); ObjectStdVector changedObjects = new ObjectStdVector(); changedObjects.Add(fixedModelValue.getInitialValueReference()); changedObjects.Add(variableModelValue.getInitialValueReference()); model.updateInitialValues(changedObjects); // now we set up the optimization // we want to do an optimization for the time course // so we have to set up the time course task first CTrajectoryTask timeCourseTask = (CTrajectoryTask)dataModel.getTask("Time-Course"); Debug.Assert(timeCourseTask != null); // since for this example it really doesn't matter how long we run the time course // we run for 1 second and calculate 10 steps // run a deterministic time course timeCourseTask.setMethodType(CTaskEnum.deterministic); // pass a pointer of the model to the problem timeCourseTask.getProblem().setModel(dataModel.getModel()); // get the problem for the task to set some parameters CTrajectoryProblem problem = (CTrajectoryProblem)timeCourseTask.getProblem(); Debug.Assert(problem != null); // simulate 10 steps problem.setStepNumber(10); // start at time 0 dataModel.getModel().setInitialTime(0.0); // simulate a duration of 1 time units problem.setDuration(1); // tell the problem to actually generate time series data problem.setTimeSeriesRequested(true); // get the optimization task COptTask optTask = (COptTask)dataModel.getTask("Optimization"); Debug.Assert(optTask != null); // we want to use Levenberg-Marquardt as the optimization method optTask.setMethodType(CTaskEnum.LevenbergMarquardt); // next we need to set subtask type on the problem COptProblem optProblem = (COptProblem)optTask.getProblem(); Debug.Assert(optProblem != null); optProblem.setSubtaskType(CTaskEnum.timeCourse); // we create the objective function // we want to minimize the value of the variable model value at the end of // the simulation // the objective function is normally minimized string objectiveFunction = variableModelValue.getObject(new CCopasiObjectName("Reference=Value")).getCN().getString(); // we need to put the angled brackets around the common name of the object objectiveFunction = "<" + objectiveFunction + ">"; // now we set the objective function in the problem optProblem.setObjectiveFunction(objectiveFunction); // now we create the optimization items // i.e. the model elements that have to be changed during the optimization // in order to get to the optimal solution COptItem optItem = optProblem.addOptItem(new CCopasiObjectName(fixedModelValue.getObject(new CCopasiObjectName("Reference=InitialValue")).getCN())); // we want to change the fixed model value from -100 to +100 with a start // value of 50 optItem.setStartValue(50.0); optItem.setLowerBound(new CCopasiObjectName("-100")); optItem.setUpperBound(new CCopasiObjectName("100")); // now we set some parameters on the method // these parameters are specific to the method type we set above // (in this case Levenberg-Marquardt) COptMethod optMethod = (COptMethod)optTask.getMethod(); Debug.Assert(optMethod != null); // now we set some method parameters for the optimization method // iteration limit CCopasiParameter parameter = optMethod.getParameter("Iteration Limit"); Debug.Assert(parameter != null); parameter.setIntValue(2000); // tolerance parameter = optMethod.getParameter("Tolerance"); Debug.Assert(parameter != null); parameter.setDblValue(1.0e-5); // create a report with the correct filename and all the species against // time. CReportDefinitionVector reports = dataModel.getReportDefinitionList(); // create a new report definition object CReportDefinition report = reports.createReportDefinition("Report", "Output for optimization"); // set the task type for the report definition to timecourse report.setTaskType(CTaskEnum.optimization); // we don't want a table report.setIsTable(false); // the entries in the output should be seperated by a ", " report.setSeparator(new CCopasiReportSeparator(", ")); // we need a handle to the header and the body // the header will display the ids of the metabolites and "time" for // the first column // the body will contain the actual timecourse data ReportItemVector header = report.getHeaderAddr(); ReportItemVector body = report.getBodyAddr(); // in the report header we write two strings and a separator header.Add(new CRegisteredObjectName(new CCopasiStaticString("best value of objective function").getCN().getString())); header.Add(new CRegisteredObjectName(report.getSeparator().getCN().getString())); header.Add(new CRegisteredObjectName(new CCopasiStaticString("initial value of F").getCN().getString())); // in the report body we write the best value of the objective function and // the initial value of the fixed parameter separated by a komma body.Add(new CRegisteredObjectName(optProblem.getObject(new CCopasiObjectName("Reference=Best Value")).getCN().getString())); body.Add(new CRegisteredObjectName(report.getSeparator().getCN().getString())); body.Add(new CRegisteredObjectName(fixedModelValue.getObject(new CCopasiObjectName("Reference=InitialValue")).getCN().getString())); // set the report for the task optTask.getReport().setReportDefinition(report); // set the output filename optTask.getReport().setTarget("example5.txt"); // don't append output if the file exists, but overwrite the file optTask.getReport().setAppend(false); bool result = false; try { result = optTask.processWithOutputFlags(true, (int)CCopasiTask.ONLY_TIME_SERIES); } catch (System.ApplicationException e) { System.Console.Error.WriteLine("ERROR: " + e.Message); String lastErrors = optTask.getProcessError(); // check if there are additional error messages if (!string.IsNullOrEmpty(lastErrors)) { // print the messages in chronological order System.Console.Error.WriteLine(lastErrors); } System.Environment.Exit(1); } if (!result) { System.Console.Error.WriteLine("Running the optimization failed."); String lastErrors = optTask.getProcessError(); // check if there are additional error messages if (!string.IsNullOrEmpty(lastErrors)) { // print the messages in chronological order System.Console.Error.WriteLine(lastErrors); } System.Environment.Exit(1); } // now we check if the optimization actually got the correct result // the best value it should have is 0 and the best parameter value for // that result should be 6 for the initial value of the fixed parameter double bestValue = optProblem.getSolutionValue(); Debug.Assert(System.Math.Abs(bestValue) < 1e-3); // we should only have one solution variable since we only have one // optimization item Debug.Assert(optProblem.getSolutionVariables().size() == 1); double solution = optProblem.getSolutionVariables().get(0); Debug.Assert(System.Math.Abs((solution - 6.0) / 6.0) < 1e-3); }
static void Main(string[] args) { Debug.Assert(CCopasiRootContainer.getRoot() != null); // create a new datamodel CCopasiDataModel dataModel = CCopasiRootContainer.addDatamodel(); Debug.Assert(CCopasiRootContainer.getDatamodelList().size() == 1); // the only argument to the main routine should be the name of a CPS file if (args.Length == 1) { string filename = args[0]; try { // load the model without progress report dataModel.loadModel(filename); } catch { System.Console.Error.WriteLine("Error while loading the model from file named \"" + filename + "\"."); System.Environment.Exit(1); } CModel model = dataModel.getModel(); Debug.Assert(model != null); System.Console.WriteLine("Model statistics for model \"" + model.getObjectName() + "\"."); // output number and names of all compartments uint i, iMax = (uint)model.getCompartments().size(); System.Console.WriteLine("Number of Compartments: " + System.Convert.ToString(iMax)); System.Console.WriteLine("Compartments: "); for (i = 0; i < iMax; ++i) { CCompartment compartment = model.getCompartment(i); Debug.Assert(compartment != null); System.Console.WriteLine("\t" + compartment.getObjectName()); } // output number and names of all metabolites iMax = (uint)model.getMetabolites().size(); System.Console.WriteLine("Number of Metabolites: " + System.Convert.ToString(iMax)); System.Console.WriteLine("Metabolites: "); for (i = 0; i < iMax; ++i) { CMetab metab = model.getMetabolite(i); Debug.Assert(metab != null); System.Console.WriteLine("\t" + metab.getObjectName()); } // output number and names of all reactions iMax = (uint)model.getReactions().size(); System.Console.WriteLine("Number of Reactions: " + System.Convert.ToString(iMax)); System.Console.WriteLine("Reactions: "); for (i = 0; i < iMax; ++i) { CReaction reaction = model.getReaction(i); Debug.Assert(reaction != null); System.Console.WriteLine("\t" + reaction.getObjectName()); } } else { System.Console.Error.WriteLine("Usage: example2 CPSFILE"); System.Environment.Exit(1); } }
static void Main() { Debug.Assert((CCopasiRootContainer.getRoot() != null)); // create a new datamodel CCopasiDataModel dataModel = CCopasiRootContainer.addDatamodel(); Debug.Assert((dataModel != null)); Debug.Assert((CCopasiRootContainer.getDatamodelList().size() == 1)); // next we import a simple SBML model from a string // clear the message queue so that we only have error messages from the import in the queue CCopasiMessage.clearDeque(); bool result = true; try { result = dataModel.importSBMLFromString(MODEL_STRING); } catch { System.Console.Error.WriteLine("Import of model failed miserably."); System.Environment.Exit(1); } // check if the import was successful int mostSevere = CCopasiMessage.getHighestSeverity(); // if it was a filtered error, we convert it to an unfiltered type // the filtered error messages have the same value as the unfiltered, but they // have the 7th bit set which basically adds 128 to the value mostSevere = mostSevere & 127; // we assume that the import succeeded if the return value is true and // the most severe error message is not an error or an exception if (result != true && mostSevere < CCopasiMessage.ERROR) { System.Console.Error.WriteLine("Sorry. Model could not be imported."); System.Environment.Exit(1); } // // now we tell the model object to calculate the jacobian // CModel model = dataModel.getModel(); Debug.Assert((model != null)); if (model != null) { // running a task, e.g. a trajectory will automatically make sure that // the initial values are transferred to the current state before the calculation begins. // If we use low level calculation methods like the one to calculate the jacobian, we // have to make sure the the initial values are applied to the state model.applyInitialValues(); // we need an array that stores the result // the size of the matrix does not really matter because // the calculateJacobian autoamtically resizes it to the correct // size FloatMatrix jacobian = new FloatMatrix(); // the first parameter to the calculation function is a reference to // the matrix where the result is to be stored // the second parameter is the derivationFactor for the calculation // it basically represents a relative delta value for the calculation of the derivatives // the third parameter is a boolean indicating whether the jacobian should // be calculated from the reduced (true) or full (false) system model.getMathContainer().calculateJacobian(jacobian, 1e-12, false); // now we print the result // the jacobian stores the values in the order they are // given in the user order in the state template so it is not really straight // forward to find out which column/row corresponds to which species CStateTemplate stateTemplate = model.getStateTemplate(); // and we need the user order SizeTVector userOrder = stateTemplate.getUserOrder(); // from those two, we can construct an new vector that contains // the names of the entities in the jacobian in the order in which they appear in // the jacobian System.Collections.Generic.List <string> nameVector = new System.Collections.Generic.List <string>(); CModelEntity entity = null; int status; for (uint i = 0; i < userOrder.size(); ++i) { entity = stateTemplate.getEntity(userOrder.get(i)); Debug.Assert((entity != null)); // now we need to check if the entity is actually // determined by an ODE or a reaction status = entity.getStatus(); if (status == CModelEntity.ODE || (status == CModelEntity.REACTIONS && entity.isUsed())) { nameVector.Add(entity.getObjectName()); } } Debug.Assert((nameVector.Count == jacobian.numRows())); // now we print the matrix, for this we assume that no // entity name is longer then 5 character which is a save bet since // we know the model System.Console.Out.NewLine = ""; System.Console.WriteLine(System.String.Format("Jacobian Matrix:{0}", System.Environment.NewLine)); System.Console.WriteLine(System.String.Format("size:{0}x{1}{2}", jacobian.numRows(), jacobian.numCols(), System.Environment.NewLine)); System.Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine)); System.Console.Out.WriteLine(System.String.Format("{0,7}", " ")); for (int i = 0; i < nameVector.Count; ++i) { System.Console.Out.WriteLine(System.String.Format("{0,7}", nameVector[i])); } System.Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine)); for (uint i = 0; i < nameVector.Count; ++i) { System.Console.Out.WriteLine(System.String.Format("{0,7}", nameVector[(int)i])); for (uint j = 0; j < nameVector.Count; ++j) { System.Console.Out.WriteLine(System.String.Format("{0,7:0.###}", jacobian.get(i, j))); } System.Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine)); } // we can also calculate the jacobian of the reduced system // in a similar way model.getMathContainer().calculateJacobian(jacobian, 1e-12, true); // this time generating the output is actually simpler because the rows // and columns are ordered in the same way as the independent variables of the state temple System.Console.WriteLine(System.String.Format("{0}{0}", System.Environment.NewLine)); System.Console.WriteLine(System.String.Format("Reduced Jacobian Matrix:{0}{0}", System.Environment.NewLine)); System.Console.Out.WriteLine(System.String.Format("{0:6}", " ")); uint iMax = stateTemplate.getNumIndependent(); for (uint i = 0; i < iMax; ++i) { System.Console.Out.WriteLine(System.String.Format("\t{0:7}", stateTemplate.getIndependent(i).getObjectName())); } System.Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine)); for (uint i = 0; i < iMax; ++i) { System.Console.Out.WriteLine(System.String.Format("{0:7}", stateTemplate.getIndependent(i).getObjectName())); for (uint j = 0; j < iMax; ++j) { System.Console.Out.WriteLine(System.String.Format("{0,7:0.###}", jacobian.get(i, j))); } System.Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine)); } } }
static void Main(string[] args) { Debug.Assert(CCopasiRootContainer.getRoot() != null); // create a new datamodel CCopasiDataModel dataModel = CCopasiRootContainer.addDatamodel(); Debug.Assert(CCopasiRootContainer.getDatamodelList().size() == 1); // first we load a simple model try { // load the model dataModel.importSBMLFromString(MODEL_STRING); } catch { System.Console.Error.WriteLine("Error while importing the model."); System.Environment.Exit(1); } // now we need to run some time course simulation to get data to fit // against // get the trajectory task object CTrajectoryTask trajectoryTask = (CTrajectoryTask)dataModel.getTask("Time-Course"); // run a deterministic time course trajectoryTask.setMethodType(CTaskEnum.deterministic); // pass a pointer of the model to the problem trajectoryTask.getProblem().setModel(dataModel.getModel()); // activate the task so that it will be run when the model is saved // and passed to CopasiSE trajectoryTask.setScheduled(true); // get the problem for the task to set some parameters CTrajectoryProblem problem = (CTrajectoryProblem)trajectoryTask.getProblem(); // simulate 4000 steps problem.setStepNumber(4000); // start at time 0 dataModel.getModel().setInitialTime(0.0); // simulate a duration of 400 time units problem.setDuration(400); // tell the problem to actually generate time series data problem.setTimeSeriesRequested(true); // set some parameters for the LSODA method through the method // Currently we don't use the method to set anything //CTrajectoryMethod method = (CTrajectoryMethod)trajectoryTask.getMethod(); bool result = true; try { // now we run the actual trajectory result = trajectoryTask.processWithOutputFlags(true, (int)CCopasiTask.ONLY_TIME_SERIES); } catch { System.Console.Error.WriteLine("Error. Running the time course simulation failed."); String lastErrors = trajectoryTask.getProcessError(); // check if there are additional error messages if (!string.IsNullOrEmpty(lastErrors)) { // print the messages in chronological order System.Console.Error.WriteLine(lastErrors); } System.Environment.Exit(1); } if (result == false) { System.Console.Error.WriteLine("An error occured while running the time course simulation."); String lastErrors = trajectoryTask.getProcessError(); // check if there are additional error messages if (!string.IsNullOrEmpty(lastErrors)) { // print the messages in chronological order System.Console.Error.WriteLine(lastErrors); } System.Environment.Exit(1); } // we write the data to a file and add some noise to it // This is necessary since COPASI can only read experimental data from // file. CTimeSeries timeSeries = trajectoryTask.getTimeSeries(); // we simulated 100 steps, including the initial state, this should be // 101 step in the timeseries Debug.Assert(timeSeries.getRecordedSteps() == 4001); uint i; uint iMax = (uint)timeSeries.getNumVariables(); // there should be four variables, the three metabolites and time Debug.Assert(iMax == 5); uint lastIndex = (uint)timeSeries.getRecordedSteps() - 1; // open the file // we need to remember in which order the variables are written to file // since we need to specify this later in the parameter fitting task List <uint> indexSet = new List <uint>(); List <CMetab> metabVector = new List <CMetab>(); // write the header // the first variable in a time series is a always time, for the rest // of the variables, we use the SBML id in the header double random = 0.0; System.Random rand_gen = new System.Random(); try { System.IO.StreamWriter os = new System.IO.StreamWriter("fakedata_example6.txt"); os.Write("# time "); CKeyFactory keyFactory = CCopasiRootContainer.getKeyFactory(); Debug.Assert(keyFactory != null); for (i = 1; i < iMax; ++i) { string key = timeSeries.getKey(i); CCopasiObject obj = keyFactory.get(key); Debug.Assert(obj != null); // only write header data or metabolites System.Type type = obj.GetType(); if (type.FullName.Equals("org.COPASI.CMetab")) { os.Write(", "); os.Write(timeSeries.getSBMLId(i, dataModel)); CMetab m = (CMetab)obj; indexSet.Add(i); metabVector.Add(m); } } os.Write("\n"); double data = 0.0; for (i = 0; i < lastIndex; ++i) { uint j; string s = ""; for (j = 0; j < iMax; ++j) { // we only want to write the data for metabolites // the compartment does not interest us here if (j == 0 || indexSet.Contains(j)) { // write the data with some noise (+-5% max) random = rand_gen.NextDouble(); data = timeSeries.getConcentrationData(i, j); // don't add noise to the time if (j != 0) { data += data * (random * 0.1 - 0.05); } s = s + (System.Convert.ToString(data)); s = s + ", "; } } // remove the last two characters again os.Write(s.Substring(0, s.Length - 2)); os.Write("\n"); } os.Close(); } catch (System.ApplicationException e) { System.Console.Error.WriteLine("Error. Could not write time course data to file."); System.Console.WriteLine(e.Message); System.Environment.Exit(1); } // now we change the parameter values to see if the parameter fitting // can really find the original values random = rand_gen.NextDouble() * 10; CReaction reaction = dataModel.getModel().getReaction(0); // we know that it is an irreversible mass action, so there is one // parameter Debug.Assert(reaction.getParameters().size() == 1); Debug.Assert(reaction.isLocalParameter(0)); // the parameter of a irreversible mass action is called k1 reaction.setParameterValue("k1", random); reaction = dataModel.getModel().getReaction(1); // we know that it is an irreversible mass action, so there is one // parameter Debug.Assert(reaction.getParameters().size() == 1); Debug.Assert(reaction.isLocalParameter(0)); reaction.setParameterValue("k1", random); CFitTask fitTask = (CFitTask)dataModel.addTask(CTaskEnum.parameterFitting); Debug.Assert(fitTask != null); // the method in a fit task is an instance of COptMethod or a subclass of // it. COptMethod fitMethod = (COptMethod)fitTask.getMethod(); Debug.Assert(fitMethod != null); // the object must be an instance of COptMethod or a subclass thereof // (CFitMethod) CFitProblem fitProblem = (CFitProblem)fitTask.getProblem(); Debug.Assert(fitProblem != null); CExperimentSet experimentSet = (CExperimentSet)fitProblem.getParameter("Experiment Set"); Debug.Assert(experimentSet != null); // first experiment (we only have one here) CExperiment experiment = new CExperiment(dataModel); Debug.Assert(experiment != null); // tell COPASI where to find the data // reading data from string is not possible with the current C++ API experiment.setFileName("fakedata_example6.txt"); // we have to tell COPASI that the data for the experiment is a komma // separated list (the default is TAB separated) experiment.setSeparator(","); // the data start in row 1 and goes to row 4001 experiment.setFirstRow(1); Debug.Assert(experiment.getFirstRow() == 1); experiment.setLastRow(4001); Debug.Assert(experiment.getLastRow() == 4001); experiment.setHeaderRow(1); Debug.Assert(experiment.getHeaderRow() == 1); experiment.setExperimentType(CTaskEnum.timeCourse); Debug.Assert(experiment.getExperimentType() == CTaskEnum.timeCourse); experiment.setNumColumns(4); Debug.Assert(experiment.getNumColumns() == 4); CExperimentObjectMap objectMap = experiment.getObjectMap(); Debug.Assert(objectMap != null); result = objectMap.setNumCols(4); Debug.Assert(result == true); result = objectMap.setRole(0, CExperiment.time); Debug.Assert(result == true); Debug.Assert(objectMap.getRole(0) == CExperiment.time); CModel model = dataModel.getModel(); Debug.Assert(model != null); CCopasiObject timeReference = model.getValueReference(); Debug.Assert(timeReference != null); objectMap.setObjectCN(0, timeReference.getCN().getString()); // now we tell COPASI which column contain the concentrations of // metabolites and belong to dependent variables objectMap.setRole(1, CExperiment.dependent); CMetab metab = metabVector[0]; Debug.Assert(metab != null); CCopasiObject particleReference = metab.getConcentrationReference(); Debug.Assert(particleReference != null); objectMap.setObjectCN(1, particleReference.getCN().getString()); objectMap.setRole(2, CExperiment.dependent); metab = metabVector[1]; Debug.Assert(metab != null); particleReference = metab.getConcentrationReference(); Debug.Assert(particleReference != null); objectMap.setObjectCN(2, particleReference.getCN().getString()); objectMap.setRole(3, CExperiment.dependent); metab = metabVector[2]; Debug.Assert(metab != null); particleReference = metab.getConcentrationReference(); Debug.Assert(particleReference != null); objectMap.setObjectCN(3, particleReference.getCN().getString()); experimentSet.addExperiment(experiment); Debug.Assert(experimentSet.getExperimentCount() == 1); // addExperiment makes a copy, so we need to get the added experiment // again experiment = experimentSet.getExperiment(0); Debug.Assert(experiment != null); // now we have to define the two fit items for the two local parameters // of the two reactions reaction = model.getReaction(0); Debug.Assert(reaction != null); Debug.Assert(reaction.isLocalParameter(0) == true); CCopasiParameter parameter = reaction.getParameters().getParameter(0); Debug.Assert(parameter != null); // define a CFitItem CCopasiObject parameterReference = parameter.getValueReference(); Debug.Assert(parameterReference != null); CFitItem fitItem1 = new CFitItem(dataModel); Debug.Assert(fitItem1 != null); fitItem1.setObjectCN(parameterReference.getCN()); fitItem1.setStartValue(4.0); fitItem1.setLowerBound(new CCopasiObjectName("0.00001")); fitItem1.setUpperBound(new CCopasiObjectName("10")); // add the fit item to the correct parameter group CCopasiParameterGroup optimizationItemGroup = (CCopasiParameterGroup)fitProblem.getParameter("OptimizationItemList"); Debug.Assert(optimizationItemGroup != null); optimizationItemGroup.addParameter(fitItem1); reaction = model.getReaction(1); Debug.Assert(reaction != null); Debug.Assert(reaction.isLocalParameter(0) == true); parameter = reaction.getParameters().getParameter(0); Debug.Assert(parameter != null); // define a CFitItem parameterReference = parameter.getValueReference(); Debug.Assert(parameterReference != null); CFitItem fitItem2 = new CFitItem(dataModel); Debug.Assert(fitItem2 != null); fitItem2.setObjectCN(parameterReference.getCN()); fitItem2.setStartValue(4.0); fitItem2.setLowerBound(new CCopasiObjectName("0.00001")); fitItem2.setUpperBound(new CCopasiObjectName("10")); // add the fit item to the correct parameter group optimizationItemGroup.addParameter(fitItem2); result = true; try { // running the task for this example will probably take some time System.Console.WriteLine("This can take some time..."); result = fitTask.processWithOutputFlags(true, (int)CCopasiTask.ONLY_TIME_SERIES); } catch { System.Console.Error.WriteLine("Error. Parameter fitting failed."); String lastErrors = fitTask.getProcessError(); // check if there are additional error messages if (!string.IsNullOrEmpty(lastErrors)) { // print the messages in chronological order System.Console.Error.WriteLine(lastErrors); } System.Environment.Exit(1); } Debug.Assert(result == true); // assert that there are two optimization items Debug.Assert(fitProblem.getOptItemList().Count == 2); // the order should be the order in whih we added the items above COptItem optItem1 = fitProblem.getOptItemList()[0]; COptItem optItem2 = fitProblem.getOptItemList()[1]; // the actual results are stored in the fit problem Debug.Assert(fitProblem.getSolutionVariables().size() == 2); System.Console.WriteLine("value for " + optItem1.getObject().getCN().getString() + ": " + fitProblem.getSolutionVariables().get(0)); System.Console.WriteLine("value for " + optItem2.getObject().getCN().getString() + ": " + fitProblem.getSolutionVariables().get(1)); // depending on the noise, the fit can be quite bad, so we are a litle // relaxed here (we should be within 3% of the original values) Debug.Assert((System.Math.Abs(fitProblem.getSolutionVariables().get(0) - 0.03) / 0.03) < 3e-2); Debug.Assert((System.Math.Abs(fitProblem.getSolutionVariables().get(1) - 0.004) / 0.004) < 3e-2); }
static void Main() { Debug.Assert(CCopasiRootContainer.getRoot() != null); // create a new datamodel CCopasiDataModel dataModel = CCopasiRootContainer.addDatamodel(); Debug.Assert(CCopasiRootContainer.getDatamodelList().size() == 1); // get the model from the datamodel CModel model = dataModel.getModel(); Debug.Assert(model != null); // set the units for the model // we want seconds as the time unit // microliter as the volume units // and nanomole as the substance units model.setTimeUnit(CUnit.s); model.setVolumeUnit(CUnit.microl); model.setQuantityUnit(CUnit.nMol); // we have to keep a set of all the initial values that are changed during // the model building process // They are needed after the model has been built to make sure all initial // values are set to the correct initial value ObjectStdVector changedObjects = new ObjectStdVector(); // create a compartment with the name cell and an initial volume of 5.0 // microliter CCompartment compartment = model.createCompartment("cell", 5.0); CCopasiObject obj = compartment.getInitialValueReference(); Debug.Assert(obj != null); changedObjects.Add(obj); Debug.Assert(compartment != null); Debug.Assert(model.getCompartments().size() == 1); // create a new metabolite with the name glucose and an inital // concentration of 10 nanomol // the metabolite belongs to the compartment we created and is is to be // fixed CMetab glucose = model.createMetabolite("glucose", compartment.getObjectName(), 10.0, CMetab.FIXED); obj = glucose.getInitialValueReference(); Debug.Assert(obj != null); changedObjects.Add(obj); Debug.Assert(glucose != null); Debug.Assert(model.getMetabolites().size() == 1); // create a second metabolite called glucose-6-phosphate with an initial // concentration of 0. This metabolite is to be changed by reactions CMetab g6p = model.createMetabolite("glucose-6-phosphate", compartment.getObjectName(), 0.0, CMetab.REACTIONS); Debug.Assert(g6p != null); obj = g6p.getInitialValueReference(); Debug.Assert(obj != null); changedObjects.Add(obj); Debug.Assert(model.getMetabolites().size() == 2); // another metabolite for ATP, also fixed CMetab atp = model.createMetabolite("ATP", compartment.getObjectName(), 10.0, CMetab.FIXED); Debug.Assert(atp != null); obj = atp.getInitialValueReference(); Debug.Assert(obj != null); changedObjects.Add(obj); Debug.Assert(model.getMetabolites().size() == 3); // and one for ADP CMetab adp = model.createMetabolite("ADP", compartment.getObjectName(), 0.0, CMetab.REACTIONS); Debug.Assert(adp != null); obj = adp.getInitialValueReference(); Debug.Assert(obj != null); changedObjects.Add(obj); Debug.Assert(model.getMetabolites().size() == 4); // now we create a reaction CReaction reaction = model.createReaction("hexokinase"); Debug.Assert(reaction != null); Debug.Assert(model.getReactions().size() == 1); // hexokinase converts glucose and ATP to glucose-6-phosphate and ADP // we can set these on the chemical equation of the reaction CChemEq chemEq = reaction.getChemEq(); // glucose is a substrate with stoichiometry 1 chemEq.addMetabolite(glucose.getKey(), 1.0, CChemEq.SUBSTRATE); // ATP is a substrate with stoichiometry 1 chemEq.addMetabolite(atp.getKey(), 1.0, CChemEq.SUBSTRATE); // glucose-6-phosphate is a product with stoichiometry 1 chemEq.addMetabolite(g6p.getKey(), 1.0, CChemEq.PRODUCT); // ADP is a product with stoichiometry 1 chemEq.addMetabolite(adp.getKey(), 1.0, CChemEq.PRODUCT); Debug.Assert(chemEq.getSubstrates().size() == 2); Debug.Assert(chemEq.getProducts().size() == 2); // this reaction is to be irreversible reaction.setReversible(false); Debug.Assert(reaction.isReversible() == false); // now we ned to set a kinetic law on the reaction // maybe constant flux would be OK // we need to get the function from the function database CFunctionDB funDB = CCopasiRootContainer.getFunctionList(); Debug.Assert(funDB != null); // it should be in the list of suitable functions // lets get all suitable functions for an irreversible reaction with 2 substrates // and 2 products CFunctionStdVector suitableFunctions = funDB.suitableFunctions(2, 2, COPASI.TriFalse); Debug.Assert((suitableFunctions.Count > 0)); int i, iMax = (int)suitableFunctions.Count; for (i = 0; i < iMax; ++i) { // we just assume that the only suitable function with Constant in // it's name is the one we want if (suitableFunctions[i].getObjectName().IndexOf("Constant") != -1) { break; } } if (i != iMax) { // we set the function // the method should be smart enough to associate the reaction entities // with the correct function parameters reaction.setFunction(suitableFunctions[i]); Debug.Assert(reaction.getFunction() != null); // constant flux has only one function parameter Debug.Assert(reaction.getFunctionParameters().size() == 1); // so there should be only one entry in the parameter mapping as well Debug.Assert(reaction.getParameterMappings().Count == 1); CCopasiParameterGroup parameterGroup = reaction.getParameters(); Debug.Assert(parameterGroup.size() == 1); CCopasiParameter parameter = parameterGroup.getParameter(0); // make sure the parameter is a local parameter Debug.Assert(reaction.isLocalParameter(parameter.getObjectName())); // now we set the value of the parameter to 0.5 Debug.Assert(parameter.getType() == CCopasiParameter.DOUBLE); parameter.setDblValue(0.5); obj = parameter.getValueReference(); Debug.Assert(obj != null); changedObjects.Add(obj); } else { System.Console.Error.WriteLine("Error. Could not find a kinetic law that conatins the term \"Constant\"."); System.Environment.Exit(1); } // now we also create a separate reaction for the backwards reaction and // set the kinetic law to irreversible mass action // now we create a reaction reaction = model.createReaction("hexokinase-backwards"); Debug.Assert(reaction != null); Debug.Assert(model.getReactions().size() == 2); chemEq = reaction.getChemEq(); // glucose is a product with stoichiometry 1 chemEq.addMetabolite(glucose.getKey(), 1.0, CChemEq.PRODUCT); // ATP is a product with stoichiometry 1 chemEq.addMetabolite(atp.getKey(), 1.0, CChemEq.PRODUCT); // glucose-6-phosphate is a substrate with stoichiometry 1 chemEq.addMetabolite(g6p.getKey(), 1.0, CChemEq.SUBSTRATE); // ADP is a substrate with stoichiometry 1 chemEq.addMetabolite(adp.getKey(), 1.0, CChemEq.SUBSTRATE); Debug.Assert(chemEq.getSubstrates().size() == 2); Debug.Assert(chemEq.getProducts().size() == 2); // this reaction is to be irreversible reaction.setReversible(false); Debug.Assert(reaction.isReversible() == false); // now we ned to set a kinetic law on the reaction CFunction massAction = (CFunction)funDB.findFunction("Mass action (irreversible)"); Debug.Assert(massAction != null); // we set the function // the method should be smart enough to associate the reaction entities // with the correct function parameters reaction.setFunction(massAction); Debug.Assert(reaction.getFunction() != null); Debug.Assert(reaction.getFunctionParameters().size() == 2); // so there should be two entries in the parameter mapping as well Debug.Assert(reaction.getParameterMappings().Count == 2); // mass action is a special case since the parameter mappings for the // substrates (and products) are in a vector // Let us create a global parameter that is determined by an assignment // and that is used as the rate constant of the mass action kinetics // it gets the name rateConstant and an initial value of 1.56 CModelValue modelValue = model.createModelValue("rateConstant", 1.56); Debug.Assert(modelValue != null); obj = modelValue.getInitialValueReference(); Debug.Assert(obj != null); changedObjects.Add(obj); Debug.Assert(model.getModelValues().size() == 1); // set the status to assignment modelValue.setStatus(CModelValue.ASSIGNMENT); // the assignment does not have to make sense modelValue.setExpression("1.0 / 4.0 + 2.0"); // now we have to adjust the parameter mapping in the reaction so // that the kinetic law uses the global parameter we just created instead // of the local one that is created by default // The first parameter is the one for the rate constant, so we point it to // the key of out model value reaction.setParameterMapping(0, modelValue.getKey()); // now we have to set the parameter mapping for the substrates reaction.addParameterMapping("substrate", g6p.getKey()); reaction.addParameterMapping("substrate", adp.getKey()); // finally compile the model // compile needs to be done before updating all initial values for // the model with the refresh sequence model.compileIfNecessary(); // now that we are done building the model, we have to make sure all // initial values are updated according to their dependencies model.updateInitialValues(changedObjects); // save the model to a COPASI file // we save to a file named example1.cps // and we want to overwrite any existing file with the same name // Default tasks are automatically generated and will always appear in cps // file unless they are explicitley deleted before saving. dataModel.saveModel("example1.cps", true); // export the model to an SBML file // we save to a file named example1.xml, we want to overwrite any // existing file with the same name and we want SBML L2V3 try { dataModel.exportSBML("example1.xml", true, 2, 3); } catch { System.Console.Error.WriteLine("Error. Exporting the model to SBML failed."); } }
static void Main() { // initialize the backend library // since we are not interested in the arguments // that are passed to main, we pass 0 and NULL to // init Debug.Assert(CCopasiRootContainer.getRoot() != null); // create a new datamodel CCopasiDataModel dataModel = CCopasiRootContainer.addDatamodel(); Debug.Assert((dataModel != null)); Debug.Assert((CCopasiRootContainer.getDatamodelList().size() == 1)); // next we import a simple SBML model from a string // clear the message queue so that we only have error messages from the import in the queue CCopasiMessage.clearDeque(); bool result = true; try { result = dataModel.importSBMLFromString(MODEL_STRING); } catch { System.Console.Error.WriteLine("An exception has occured during the import of the SBML model"); System.Environment.Exit(1); } // check if the import was successful int mostSevere = CCopasiMessage.getHighestSeverity(); // if it was a filtered error, we convert it to an unfiltered type // the filtered error messages have the same value as the unfiltered, but they // have the 7th bit set which basically adds 128 to the value mostSevere = mostSevere & 127; // we assume that the import succeeded if the return value is true and // the most severe error message is not an error or an exception if (result != true && mostSevere < CCopasiMessage.ERROR) { System.Console.Error.WriteLine("Sorry. Model could not be imported."); System.Environment.Exit(1); } // get the trajectory task object CSteadyStateTask task = (CSteadyStateTask)dataModel.getTask("Steady-State"); CCopasiMessage.clearDeque(); try { // now we run the actual trajectory task.processWithOutputFlags(true, (int)CCopasiTask.ONLY_TIME_SERIES); } catch { System.Console.Error.WriteLine("Error. Running the scan failed."); String lastErrors = task.getProcessError(); // check if there are additional error messages if (!string.IsNullOrEmpty(lastErrors)) { // print the messages in chronological order System.Console.Error.WriteLine(lastErrors); } System.Environment.Exit(1); } // now we can get the result of the steady state calculation, e.g. the jacobian // matrix of the model at the steady state // here we can either get the jacobian as we did in example 8 as a matrix with // getJacobian, or we can use getJacobianAnnotated to get an annotated matrix // Corresponding methods for the reduced jacobian are getJacobianX and getJacobianXAnnotated CArrayAnnotation aj = task.getJacobianAnnotated(); Debug.Assert((aj != null)); if (aj != null) { // we do the output, but as in contrast to the jacobian in example 8, // we now have all the information for the output in one place // first the array annotation can tell us how many dimensions it has. // Since the matrix is a 2D array, it should have 2 dimensions Debug.Assert((aj.dimensionality() == 2)); // since the matrix has a dimensionality of 2, the inde for the underlaying abstract array // object is a vector with two unsigned int elements // First element is the index for the outer dimension and the second element is the index // for the inner dimension SizeTStdVector index = new SizeTStdVector(); // The constructor does not seem to interpret an integer argument // as the size // I though that in C# we might be able to achieve this using the Capacity property // but that didn't work. Maybe I was using it incorrectly since I don't really know C# // So for now, we just add two elements to the vector which seems to do the trick. index.Add(0); index.Add(0); // since the rows and columns have the same annotation for the jacobian, it doesn't matter // for which dimension we get the annotations StringStdVector annotations = aj.getAnnotationsString(1); System.Console.Out.NewLine = ""; System.Console.WriteLine(System.String.Format("Jacobian Matrix:{0}{0}", System.Environment.NewLine)); System.Console.Out.WriteLine(System.String.Format("{0,7}", " ")); for (int i = 0; i < annotations.Count; ++i) { Console.Out.WriteLine(System.String.Format("{0,7}", annotations[i])); } Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine)); for (int i = 0; i < annotations.Count; ++i) { System.Console.Out.WriteLine(System.String.Format("{0,7} ", annotations[i])); index[0] = (uint)i; for (int j = 0; j < annotations.Count; ++j) { index[1] = (uint)j; System.Console.Out.WriteLine(System.String.Format("{0,7:G2} ", aj.array().get(index))); } System.Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine)); } } System.Environment.Exit(0); }
/// <summary> /// Updates a reaction. /// </summary> /// <param name="reaction">COPASI Reaction.</param> /// <param name="reagents">Reagents.</param> /// <param name="products">Products.</param> /// <param name="rate">Rate.</param> public void UpdateReaction(CReaction reaction, MoleculeSpecies[] reagents, MoleculeSpecies[] products, double rate) { // we can set these on the chemical equation of the reaction CChemEq chemEq = reaction.getChemEq(); // remove all existing metabolites chemEq.getSubstrates().clear(); chemEq.getProducts().clear(); // add substrates CMetab[] substrates = GetMetabs(reagents); foreach (CMetab item in substrates) { // add substrate with stoichiometry 1 chemEq.addMetabolite(item.getKey(), 1.0, CChemEq.SUBSTRATE); } // add products CMetab[] metabProducts = GetMetabs(products); foreach (CMetab item in metabProducts) { // add product with stoichiometry 1 chemEq.addMetabolite(item.getKey(), 1.0, CChemEq.PRODUCT); } // this reaction is to be irreversible reaction.setReversible(false); // now we ned to set a kinetic law on the reaction // maybe constant flux would be OK // we need to get the function from the function database CFunctionDB funDB = CCopasiRootContainer.getFunctionList(); // it should be in the list of suitable functions // lets get all suitable functions for an irreversible reaction with x substrates // and y products CFunctionStdVector suitableFunctions = funDB.suitableFunctions((uint)substrates.Length, (uint)products.Length, COPASI.TriFalse); CFunction function = null; for (int i = 0; i < suitableFunctions.Count; i++) { // we just assume that the only suitable function with mass action in // it's name is the one we want if (suitableFunctions[i].getObjectName().ToLower().Contains("mass action")) { function = suitableFunctions[i]; break; } } if (function != null) { reaction.setFunction(function); CCopasiParameterGroup parameterGroup = reaction.getParameters(); CCopasiParameter parameter = parameterGroup.getParameter(0); // make sure the parameter is a local parameter System.Diagnostics.Debug.Assert(reaction.isLocalParameter(parameter.getObjectName())); // now we set the value of the parameter to 0.5 System.Diagnostics.Debug.Assert(parameter.getType() == CCopasiParameter.DOUBLE); parameter.setDblValue(rate); CCopasiObject obj = parameter.getValueReference(); changedObjects.Add(obj); //reaction.getParameterMappings().Clear(); foreach (var substrate in substrates) { reaction.addParameterMapping("substrate", substrate.getKey()); } } else { throw new System.Exception("Error. Could not find a kinetic law that conatins the term \"mass action\"."); } }
static void Main() { Debug.Assert(CCopasiRootContainer.getRoot() != null); // create a new datamodel CCopasiDataModel dataModel = CCopasiRootContainer.addDatamodel(); Debug.Assert(CCopasiRootContainer.getDatamodelList().size() == 1); // get the model from the datamodel CModel model = dataModel.getModel(); Debug.Assert(model != null); // set the units for the model // we want seconds as the time unit // microliter as the volume units // and nanomole as the substance units model.setTimeUnit(CUnit.s); model.setVolumeUnit(CUnit.microl); model.setQuantityUnit(CUnit.nMol); // we have to keep a set of all the initial values that are changed during // the model building process // They are needed after the model has been built to make sure all initial // values are set to the correct initial value ObjectStdVector changedObjects = new ObjectStdVector(); // create a compartment with the name cell and an initial volume of 5.0 // microliter CCompartment compartment = model.createCompartment("cell", 5.0); CCopasiObject obj = compartment.getValueReference(); Debug.Assert(obj != null); changedObjects.Add(obj); Debug.Assert(compartment != null); Debug.Assert(model.getCompartments().size() == 1); // create a new metabolite with the name S and an inital // concentration of 10 nanomol // the metabolite belongs to the compartment we created and is is to be // fixed CMetab S = model.createMetabolite("S", compartment.getObjectName(), 10.0, CMetab.FIXED); obj = S.getInitialConcentrationReference(); Debug.Assert((obj != null)); changedObjects.Add(obj); Debug.Assert((compartment != null)); Debug.Assert(S != null); Debug.Assert(model.getMetabolites().size() == 1); // create a second metabolite called P with an initial // concentration of 0. This metabolite is to be changed by reactions CMetab P = model.createMetabolite("P", compartment.getObjectName(), 0.0, CMetab.REACTIONS); Debug.Assert(P != null); obj = P.getInitialConcentrationReference(); Debug.Assert(obj != null); changedObjects.Add(obj); Debug.Assert(model.getMetabolites().size() == 2); // now we create a reaction CReaction reaction = model.createReaction("reaction"); Debug.Assert(reaction != null); Debug.Assert(model.getReactions().size() == 1); // reaction converts S to P // we can set these on the chemical equation of the reaction CChemEq chemEq = reaction.getChemEq(); // S is a substrate with stoichiometry 1 chemEq.addMetabolite(S.getKey(), 1.0, CChemEq.SUBSTRATE); // P is a product with stoichiometry 1 chemEq.addMetabolite(P.getKey(), 1.0, CChemEq.PRODUCT); Debug.Assert(chemEq.getSubstrates().size() == 1); Debug.Assert(chemEq.getProducts().size() == 1); // this reaction is to be irreversible reaction.setReversible(false); Debug.Assert(reaction.isReversible() == false); CModelValue MV = model.createModelValue("K", 42.0); // set the status to FIXED MV.setStatus(CModelValue.FIXED); Debug.Assert(MV != null); obj = MV.getInitialValueReference(); Debug.Assert(obj != null); changedObjects.Add(obj); Debug.Assert(model.getModelValues().size() == 1); // now we ned to set a kinetic law on the reaction // for this we create a user defined function CFunctionDB funDB = CCopasiRootContainer.getFunctionList(); Debug.Assert(funDB != null); CFunction function = (CFunction)funDB.createFunction("My Rate Law", CEvaluationTree.UserDefined); CFunction rateLaw = (CFunction)funDB.findFunction("My Rate Law"); Debug.Assert(rateLaw != null); // now we create the formula for the function and set it on the function string formula = "(1-0.4/(EXPONENTIALE^(temp-37)))*0.00001448471257*1.4^(temp-37)*substrate"; bool result = function.setInfix(formula); Debug.Assert(result == true); // make the function irreversible function.setReversible(COPASI.TriFalse); // the formula string should have been parsed now // and COPASI should have determined that the formula string contained 2 parameters (temp and substrate) CFunctionParameters variables = function.getVariables(); // per default the usage of those parameters will be set to VARIABLE uint index = function.getVariableIndex("temp"); CFunctionParameter param = variables.getParameter(index); Debug.Assert(param.getUsage() == CFunctionParameter.VARIABLE); // This is correct for temp, but substrate should get the usage SUBSTRATE in order // for us to use the function with the reaction created above // So we need to set the usage for "substrate" manually index = function.getVariableIndex("substrate"); param = variables.getParameter(index); param.setUsage(CFunctionParameter.SUBSTRATE); // set the rate law for the reaction reaction.setFunction(function); Debug.Assert(reaction.getFunction() != null); // COPASI also needs to know what object it has to assocuiate with the individual function parameters // In our case we need to tell COPASI that substrate is to be replaced by the substrate of the reaction // and temp is to be replaced by the global parameter K reaction.setParameterMapping("substrate", S.getKey()); reaction.setParameterMapping("temp", MV.getKey()); // finally compile the model // compile needs to be done before updating all initial values for // the model with the refresh sequence model.compileIfNecessary(); // now that we are done building the model, we have to make sure all // initial values are updated according to their dependencies model.updateInitialValues(changedObjects); // save the model to a COPASI file // we save to a file named example1.cps // and we want to overwrite any existing file with the same name // Default tasks are automatically generated and will always appear in cps // file unless they are explicitley deleted before saving. dataModel.saveModel("example7.cps", true); // export the model to an SBML file // we save to a file named example1.xml, we want to overwrite any // existing file with the same name and we want SBML L2V3 try { dataModel.exportSBML("example7.xml", true, 2, 3); } catch { System.Console.Error.WriteLine("Error. Exporting the model to SBML failed."); } }
static void Main(string[] args) { Debug.Assert(CCopasiRootContainer.getRoot() != null); // create a new datamodel CCopasiDataModel dataModel = CCopasiRootContainer.addDatamodel(); Debug.Assert(CCopasiRootContainer.getDatamodelList().size() == 1); // the only argument to the main routine should be the name of an SBML file if (args.Length == 1) { string filename = args[0]; try { // load the model dataModel.importSBML(filename); } catch { System.Console.Error.WriteLine("Error while importing the model from file named \"" + filename + "\"."); System.Environment.Exit(1); } CModel model = dataModel.getModel(); Debug.Assert(model != null); // create a report with the correct filename and all the species against // time. CReportDefinitionVector reports = dataModel.getReportDefinitionList(); // create a new report definition object CReportDefinition report = reports.createReportDefinition("Report", "Output for timecourse"); // set the task type for the report definition to timecourse report.setTaskType(CTaskEnum.timeCourse); // we don't want a table report.setIsTable(false); // the entries in the output should be seperated by a ", " report.setSeparator(new CCopasiReportSeparator(", ")); // we need a handle to the header and the body // the header will display the ids of the metabolites and "time" for // the first column // the body will contain the actual timecourse data ReportItemVector header = report.getHeaderAddr(); ReportItemVector body = report.getBodyAddr(); body.Add(new CRegisteredObjectName(model.getObject(new CCopasiObjectName("Reference=Time")).getCN().getString())); body.Add(new CRegisteredObjectName(report.getSeparator().getCN().getString())); header.Add(new CRegisteredObjectName(new CCopasiStaticString("time").getCN().getString())); header.Add(new CRegisteredObjectName(report.getSeparator().getCN().getString())); uint i, iMax = (uint)model.getMetabolites().size(); for (i = 0; i < iMax; ++i) { CMetab metab = model.getMetabolite(i); Debug.Assert(metab != null); // we don't want output for FIXED metabolites right now if (metab.getStatus() != CModelEntity.FIXED) { // we want the concentration oin the output // alternatively, we could use "Reference=Amount" to get the // particle number body.Add(new CRegisteredObjectName(metab.getObject(new CCopasiObjectName("Reference=Concentration")).getCN().getString())); // add the corresponding id to the header header.Add(new CRegisteredObjectName(new CCopasiStaticString(metab.getSBMLId()).getCN().getString())); // after each entry, we need a seperator if (i != iMax - 1) { body.Add(new CRegisteredObjectName(report.getSeparator().getCN().getString())); header.Add(new CRegisteredObjectName(report.getSeparator().getCN().getString())); } } } // get the trajectory task object CTrajectoryTask trajectoryTask = (CTrajectoryTask)dataModel.getTask("Time-Course"); // run a deterministic time course trajectoryTask.setMethodType(CTaskEnum.deterministic); // pass a pointer of the model to the problem trajectoryTask.getProblem().setModel(dataModel.getModel()); // actiavate the task so that it will be run when the model is saved // and passed to CopasiSE trajectoryTask.setScheduled(true); // set the report for the task trajectoryTask.getReport().setReportDefinition(report); // set the output filename trajectoryTask.getReport().setTarget("example3.txt"); // don't append output if the file exists, but overwrite the file trajectoryTask.getReport().setAppend(false); // get the problem for the task to set some parameters CTrajectoryProblem problem = (CTrajectoryProblem)trajectoryTask.getProblem(); // simulate 100 steps problem.setStepNumber(100); // start at time 0 dataModel.getModel().setInitialTime(0.0); // simulate a duration of 10 time units problem.setDuration(10); // tell the problem to actually generate time series data problem.setTimeSeriesRequested(true); // set some parameters for the LSODA method through the method CTrajectoryMethod method = (CTrajectoryMethod)trajectoryTask.getMethod(); CCopasiParameter parameter = method.getParameter("Absolute Tolerance"); Debug.Assert(parameter != null); Debug.Assert(parameter.getType() == CCopasiParameter.DOUBLE); parameter.setDblValue(1.0e-12); bool result = true; try { // now we run the actual trajectory result = trajectoryTask.processWithOutputFlags(true, (int)CCopasiTask.ONLY_TIME_SERIES); } catch { System.Console.Error.WriteLine("Error. Running the time course simulation failed."); String lastErrors = trajectoryTask.getProcessError(); // check if there are additional error messages if (!string.IsNullOrEmpty(lastErrors)) { // print the messages in chronological order System.Console.Error.WriteLine(lastErrors); } System.Environment.Exit(1); } if (result == false) { System.Console.Error.WriteLine("An error occured while running the time course simulation."); String lastErrors = trajectoryTask.getProcessError(); // check if there are additional error messages if (!string.IsNullOrEmpty(lastErrors)) { // print the messages in chronological order System.Console.Error.WriteLine(lastErrors); } System.Environment.Exit(1); } // look at the timeseries CTimeSeries timeSeries = trajectoryTask.getTimeSeries(); // we simulated 100 steps, including the initial state, this should be // 101 step in the timeseries Debug.Assert(timeSeries.getRecordedSteps() == 101); System.Console.WriteLine("The time series consists of " + System.Convert.ToString(timeSeries.getRecordedSteps()) + "."); System.Console.WriteLine("Each step contains " + System.Convert.ToString(timeSeries.getNumVariables()) + " variables."); System.Console.WriteLine("The final state is: "); iMax = (uint)timeSeries.getNumVariables(); uint lastIndex = (uint)timeSeries.getRecordedSteps() - 1; for (i = 0; i < iMax; ++i) { // here we get the particle number (at least for the species) // the unit of the other variables may not be particle numbers // the concentration data can be acquired with getConcentrationData System.Console.WriteLine(timeSeries.getTitle(i) + ": " + System.Convert.ToString(timeSeries.getData(lastIndex, i))); } } else { System.Console.Error.WriteLine("Usage: example3 SBMLFILE"); System.Environment.Exit(1); } }
static void Main() { Debug.Assert(CCopasiRootContainer.getRoot() != null); // create a new datamodel CCopasiDataModel dataModel = CCopasiRootContainer.addDatamodel(); Debug.Assert(CCopasiRootContainer.getDatamodelList().size() == 1); // the only argument to the main routine should be the name of an SBML file try { // load the model dataModel.importSBMLFromString(MODEL_STRING); } catch { System.Console.Error.WriteLine("Error while importing the model from the given String."); System.Environment.Exit(1); } CModel model = dataModel.getModel(); Debug.Assert(model != null); // create a report with the correct filename and all the species against // time. CReportDefinitionVector reports = dataModel.getReportDefinitionList(); // create a new report definition object CReportDefinition report = reports.createReportDefinition("Report", "Output for timecourse"); // set the task type for the report definition to timecourse report.setTaskType(CTaskEnum.timeCourse); // we don't want a table report.setIsTable(false); // the entries in the output should be seperated by a ", " report.setSeparator(new CCopasiReportSeparator(", ")); // we need a handle to the header and the body // the header will display the ids of the metabolites and "time" for // the first column // the body will contain the actual timecourse data ReportItemVector header = report.getHeaderAddr(); ReportItemVector body = report.getBodyAddr(); body.Add(new CRegisteredObjectName(new CCopasiObjectName(dataModel.getModel().getCN().getString() + ",Reference=Time").getString())); body.Add(new CRegisteredObjectName(report.getSeparator().getCN().getString())); header.Add(new CRegisteredObjectName(new CCopasiStaticString("time").getCN().getString())); header.Add(new CRegisteredObjectName(report.getSeparator().getCN().getString())); uint i, iMax = (uint)model.getMetabolites().size(); for (i = 0; i < iMax; ++i) { CMetab metab = model.getMetabolite(i); Debug.Assert(metab != null); // we don't want output for FIXED metabolites right now if (metab.getStatus() != CModelEntity.FIXED) { // we want the concentration oin the output // alternatively, we could use "Reference=Amount" to get the // particle number body.Add(new CRegisteredObjectName(metab.getObject(new CCopasiObjectName("Reference=Concentration")).getCN().getString())); // add the corresponding id to the header header.Add(new CRegisteredObjectName(new CCopasiStaticString(metab.getSBMLId()).getCN().getString())); if (i != iMax - 1) { // after each entry, we need a seperator body.Add(new CRegisteredObjectName(report.getSeparator().getCN().getString())); // and a seperator header.Add(new CRegisteredObjectName(report.getSeparator().getCN().getString())); } } } // get the trajectory task object CTrajectoryTask trajectoryTask = (CTrajectoryTask)dataModel.getTask("Time-Course"); // run a stochastic time course trajectoryTask.setMethodType(CTaskEnum.stochastic); // pass a pointer of the model to the problem trajectoryTask.getProblem().setModel(dataModel.getModel()); // we don't want the trajectory task to run by itself, but we want to // run it from a scan, so we deactivate the standalone trajectory task trajectoryTask.setScheduled(false); // get the problem for the task to set some parameters CTrajectoryProblem problem = (CTrajectoryProblem)trajectoryTask.getProblem(); // simulate 100 steps problem.setStepNumber(100); // start at time 0 dataModel.getModel().setInitialTime(0.0); // simulate a duration of 10 time units problem.setDuration(10); // tell the problem to actually generate time series data problem.setTimeSeriesRequested(true); // now we set up the scan CScanTask scanTask = (CScanTask)dataModel.getTask("Scan"); // get the problem CScanProblem scanProblem = (CScanProblem)scanTask.getProblem(); Debug.Assert(scanProblem != null); // set the model for the problem scanProblem.setModel(dataModel.getModel()); // activate the task so that is is run // if the model is saved and passed to CopasiSE scanTask.setScheduled(true); // set the report for the task scanTask.getReport().setReportDefinition(report); // set the output file for the report scanTask.getReport().setTarget("example4.txt"); // don't append to an existing file, but overwrite scanTask.getReport().setAppend(false); // tell the scan that we want to make a scan over a trajectory task scanProblem.setSubtask(CTaskEnum.timeCourse); // we just want to run the timecourse task a number of times, so we // create a repeat item with 100 repeats scanProblem.addScanItem(CScanProblem.SCAN_REPEAT, 100); // we want the output from the trajectory task scanProblem.setOutputInSubtask(true); // we don't want to set the initial conditions of the model to the end // state of the last run scanProblem.setContinueFromCurrentState(false); try { // now we run the actual trajectory scanTask.processWithOutputFlags(true, (int)CCopasiTask.ONLY_TIME_SERIES); } catch { System.Console.Error.WriteLine("Error. Running the scan failed."); String lastErrors = scanTask.getProcessError(); // check if there are additional error messages if (!string.IsNullOrEmpty(lastErrors)) { // print the messages in chronological order System.Console.Error.WriteLine(lastErrors); } System.Environment.Exit(1); } }