Cellerator™ Command Reference

Copyright © 2005 California Institute of Technology. All Rights Reserved. U.S. Government sponsorship acknowledged.

This listing was generated by createCelleratorReference January 13, 2005 14:40:12 using Cellerator Version 1.5.0 (03-Jan-2005) in Mathematica 5.1 for Mac OS X (October 25, 2004)

addLeaf

addLeaf[tree, options] adds a leaf at the selected address in a tree. The selected address i ... leaf on the right.\ndata-> the data to be added to the new leaf. Default is an empty list {}

addLink

addLink[g,n1,n2] returns a graph with a new directed link between node n1 and n2 (integers); ... node 2 exerts a force on node 1 and not vice-versa. See also addLinkBothways, addLinksBothWays.

addLinkBothWays

addLinkbothWays[g,n1,n2] adds two links: one from n1 to n2, and a second from n2 to n1. Both links are identical. See also addLink, addLinksBothways.

addLinks

addLinks[g,{{n1,n2},{n1,n2},...}}] returns a new graph with the specified links added. If any links that are requested already exist, those links are ignored. The spring force is NOT updated.

addLinksBothWays

addLinksBothWays[g, {{n1,m1},{n2,m2},{n3,m3},...}] adds two-way links between each of the sp ... addLinks (addLinks is the preferred method because it is more efficient thatn addLinksbothWays).

addNode

addNode[g,n] returns a graph with the node g added to it\naddNode[g,n,parent->k] modifies the lineage of the graph to indicate the specified parent.

addSpecies

addSpecies[x1,x2,...] adds the species x1, x2,... to the global list $reactionSpecies, which ... d during construction of SBML level 1 to save the names of the species that need to be defined.

andedString

andedString[x1,x2,...] returns the string \"(x1&&x2&&...)\"

andedStringMultisperseBefore

andedStringMultisperseBefore[{s1,s2,...,sn},{{ta1,ta2,...,tan},{tb1,tb2,...,tbn},...,{tz1,tz ... ,\"(A4)&&(B5)&&(C6)\",\"(A7)&&(B8)&&(C9)\"}

applyIndex

applyIndex[var, index] returns an indexed variable, var[index]; if var is already indexed, additional indices are added, e.g., applyIndex[x[5],{1,2}] returns x[5,1 2]

applySpringForce

applySpringForce[g,options] calculates the spring-force ODEs for every node in the graph g a ... Stem\" might be used\nfastForceTrue used fastSpringForce, otherwise use springForce

argument

argument[f[x]] returns x\nargument[f[x1,x2,...] returns {x1,x2,...}\nargument[x] returns x when x is an atom.

arrow

... {act, inh}

arrows

... 1 + 

arrowType

... rev rev b b

assignToCompartments

assignToCompartments[var1[i1], var2[i2],var3[i3],...] returns a list {{var1,{i1,i2,...}}, {v ... g each variable gives the numbers of the compartments (cells) that each variable is defined for.

autoRate

autoRate[options] returns a new rate constant of the form <prefix>nnn<suffix>, w ... ut-of-the ordinary occurs, e.g., a previously defined constant is reused or a number is skipped.

binaryTreeQ

binaryTreeQ[x] returns True if x is a binary tree, and False when x is a non-binary tree or when x is not a tree.

blocks

blocks[options] returns True if a line segment defined by two points intersects a circle. Th ... 54;1\nendPoints{{x1,y1},{x2,y2}}\nplot->False\nSee also: intersects, findIntersection

bracketedList

bracketedList[x1,x2,...] returns a string \"[x1][x2]...\"; the x's may be any heir ... ll strings will be ignored, e.g., bracketedList[a,{},c] returns the string \"[a][c]\".

breaklinks

breaklinks is an option for run[graph,...] that determines if link breakage will be allowed. ... alue of dmax in an increasing direction. If breaklinks->False, no checking will be performed.

breakPoints

breakPoints[s,options] returns a list of the (integer) offsets in the string where line-wrap ... from the default character list\nwrapAll-> False, if True, allow wrapping at all characters.

cellDivisionDomain

cellDivisionDomain[options] returns a modelDomain with two variables x and y such that x'==& ... o use on model; default is Unit (use Mathematica UnitStep); stepFuzzy (use fuzzyStep[x])

Cellerator

Cellerator™ is a Mathematica package designed to facilitate biological modeling via au ... in software. \nFor more details see the Cellerator™ web site at http://www.cellerator.info

celleratorFileName

celleratorFileName[name, type, options] returns a string of the formn\"directory/nameyy ... :\ndirectory directory name (defaults to the global varialbe $CelleratorOutputDirectory)

celleratorGraph

celleratorGraph[n] is the name of the global data structure to store a graph referenced as p ... f graphs that have been defined is given by graphCounter; to clear all graphs use ClearGraphs[].

celleratorGraphSolutionQ

celleratorGraphSolutionQ[s] returns True if s appears to be the output of run[graph,...] and False otherwise. Compare with celleratorRunSolutionQ

celleratorODE

celleratorODE[n] is the name of the global data structure to store a differential equation r ... mber of ODEs that have been defined is given by odeCounter; to clear all graphs use ClearODEs[].

celleratorRunSolutionQ

celleratorRunSolutionQ[s] returns True if s appears to be the output of a run[STN,...] and False otherwise. Compare with celleratorGraphSolutionQ

celleratorSolution

celleratorSolution[n] is the name of the global data structure to store a numerical solution ... that have been defined is given by solutionCounter; to clear all solutions use clearSolutions[].

cellerator$mass$growth$formula

cellerator$mass$growth$formula[m] is an uninstantiated function that is replaced at run time with the selected formula for mass growth.

check4Event

RowBox[{check4Event[g,solution, tstart, tend, tsplit, dmax,options] determines what event sh ... es to use in solution\ntsplit: name of split variable\ndmax: link length trigger for breaking.}]

checkDistance

checkDistance[l, tstart, tend, dmax] determines if link number l has crossed dmax in length ... the global set of interpolating functions current$solution. Not intended for end-user execution.

checkIfSplit

checkIfSplit[g, solution, tsplit, tend] determines if any variables in the graph g meet the ... to check (the indexed variable that grows linearly with time after split conditions are met). .

circularTable

flatTable[r] generates a list of coordinates for cell centers for a two-dimensional hemisphe ... e system, but all cell centers lie in the x-y plane, i.e., the third coordinate is always zero.

cloneNode

cloneNode[n, i] returns a new node copied from n but with the variable index replaced by i.\ ... , zoffset}] moves the initial conditions of the new node by a vector {xoffset, yoffset, zoffset}

combineHillReactionsByProduct

combineHillReactionsByProduct[reaction,type] is called by prepReactionsForSBML, and is not m ... r1]},\n\t{A↦C,hill[vmax{v3},nhilln3,khalfK3,basalRater3]}}

comma

comma is a global symbol used during Cellerator output translation to hold the desired text symbol used for a comma.

commaDelimitedString

commaDelimitedString[x1,x2,...] returns the string\"x1,x2,...\".

commaSeparatedString

commaSeparatedString[x1,x2,...] returns a string \"x1♭comman♭x2♭comma♭...\"; see also commaDelimitedString

Comp

... 1 + K - q[t]

compartment

compartment is an option for writeSBML that specifies the name to used for the SBML compartment that represents a Cellerator graph node.If unspecified a unique name is generated automatically.

complex

The symbols complexLeft and complexRight are used to automatically generated new symbol name ... t;s2<complexRight>\nSee also complexLeft, complexRight, compoundName, intermediateCompound

complexLeft

complexLeft (default value=) is a globally defined string that is used to generate the name of an intermediateCompound. See intermediateCompound.

complexRight

complexRight (default value=) is a globally defined string that is used to generate the name of an intermediateCompound. See intermediateCompound.

compoundName

compoundName[x,y] returns a string representing the name of an intermediate compound formed ... Name[fred,wilma] returns \"Complex$fred$wilma$\". See also intermediateCompound, dash.

connectionMatrix

connectionMatrix[g] returns a matrix of ones and zeros, where m[i,j] is one of there is a li ... urns it filtered by MatrixForm.\nconectionMatrix[g,form-> PLOT] returns it as a density plot.

consolidateDomains

consolidateDomains[listOfDomains, options] consolidates the domains in a string that contain ... ense that all symbols that represent the same domain are combined in a single domain definition.

consolidateOptions

consolidateOptions[options] returns an option list with only the first occurance of any part ... 4; 17, C 12, B 93] returns the option list {A96,B17,C12}

convertGK

convertGK generates a single differential equation by combining the terms generated by subconvert. It is not intended to be invoked directly. It is called by interpret when necessary.

countTerms

countTerms[x] counts the terms in a system of dfiferential equations produced by interpret. ... ff eqn such as A'[t]== .... At the present time it is non-function (returns an incorrect value)

cpDomain

cpDomain[d1, d2] represents the cross product between two different domains.  To instantiate, use expandDomain.

createCelleratorReference

createCelleratorReference[] generates a Mathematica-reference style description of all Celle ... e been loaded into memory will be included, even if these commands are not Cellerator commands.

createDistanceRules

createDistanceRules[g] creates rules of the form Distance[i,j]-> distance[g,{i,j}]; these ... in terms of the embedding variables. createDistanceRules is used by run when option run->True

createGardnerModel

createGardnerModel is a function called to modularize createMitoticOsillator; it is not intended to be used directly.

createGOLDBETERmodel

createGOLDBETERmodel is a function called to modularize createMitoticOsillator; it is not intended to be used directly.

createGRNvSBML

createGRNvSBML[GRN$PROTEIN, compartment, options] creates SBML for a function GRNv[celli,proteinj] which returns the value of the protein j in cell i.

createIndexedSpecieDefinitions

createIndexedSpecieDefinitions[options] returns {domain-definition-sbml, specie-definition-SBML } for all the Cellerator Indexed Species in the model

createLambdaMatrix

createLambdaMatrix[g, options] creates a set of Mathematica rules that implement the geometr ... variables. This function is not intended for end user execution. It is used by integrateGraph.

createLAMBDASBML

createLAMBDASBML[compartment,options] creates an SBML level 2 function definition for the LA ... lly by writeSBML and is not normally intended to be user-invoked. Options are:variables, indent.

createMassGrowthSBML

createMassGrowthSBML[compartment, options] creates SBML for a function that describes mass g ... on name is dmdt.\nOptions are:\nindent->\"\"\nOr any valid option for mass$formula.

createMitoticOscillator

createMitoticOscillator[options] returns a model domains for the specified oscillator. The m ... rue. ReleaseHold will be applied to $CelleratorMiticIC to define the actual initial conditions.

createNonIndexedSpecieDefinitions

createNonIndexedSpecieDefinitions[options] creates the level 2 sbml for non-indexed species, ... ..; variables like M[1,2,3][4] will be ignored!! Options are the same as createSpecieDefinitions

createNorelModel

createNorelModel is a function called to modularize createMitoticOsillator; it is not intended to be used directly.

createRef

createRef[context] creates a quick-reference manual of all functions in the given context. c ... ce. createRef[System] produces a quick-reference for all Mathematica objects with usage strings.

createSBML2forANewDomain

createSBML2forANewDomain[name, upper, lower, tabs] creates the level 2 SBML for a new domain ... t;/>\n\t\t<symbol name=\"wilma\"/>\n\t</listOfSymbols>\n</domain>

createSBML2forASparseDomain

createSBML2forASparseDomain[name, range tabs] creates the level 2 pseudo-SBML for a sparse d ... \t\t<symbol name=\"barney\"/>\n\t\t\t</listOfSymbols>\n\t\t</domain>

createSpecieDefinitions

createSpecieDefinitions[options] returns sbml for a list of indexed species.\nOptions are:\n ... itial conditions for the variables\nindent->optional string to add to the front of each line.

createTyson1991SixVariableModel

createTyson1991SixVariableModel is a function called to modularize createMitoticOsillator; it is not intended to be used directly.

createTyson1991TwoVariableModel

createTyson1991TwoVariableModel is a function called to modularize createMitoticOsillator; it is not intended to be used directly.

createUserModel

... l[1]},ic{PC[1][0]==0,PQ[1][0]==0,QR[1][0]==0,splv[1][0]==0,tspl[1][0]==0},time0]

crossProduct

crossProduct[a, b] gives the set cross product, i.e., the set of lists {ai, bj} where ai is an element of a and bj is an element of bj. Not to be confused with Cross (vector cross product).

crunchGRN

crunchGRN[options] is called by combineHillReactionsByProduct to generate a validated option list for grnExpFunction.

crunchHill

crunchHill[options] is called by combineHillReactionsByProduct to generate a validated option list for hillFunction.

crunchNHCA

crunchNHCA[options] is called by combineHillReactionsByProduct to generate a validated option list for NCHAFunction.

dash

The symbol dash contains the character used to create names of molecular complexes. The defa ... p character on some operating systems (rev. 4/1/02). See also intermediateCompound, compoundName

debugPrint

debugPrint[debug, m1, m2, m3] prints the message 'm1: m2: m3 ' if the flag debug is True

dependentVariable

dependentvariable[differentialEquation] returns the variable on the left hand side of differentialEquation .

dhmsDate

dhmsDate[] returns a string of the form \n\"Feb. 15, 2002, 10:50:59\"\nfor the current date and time; compare with Now

digest

digest[reactionList] returns a list {{specie1, list of reactions involving specie1}, {specie ... e user to ever invoke digest directly. It is invoked automatically, when required, by interpret.

directory

directory is an option for writeSBML that specifies the name of the directory that the outpu ... ed by the Mathematica Directory[] function is used is used. This directory is system dependent.

disjointUnion

disjointUnion[x1,x2,...] forms a union of all the lists x1, x2, where each element is tagged ... ample disjointUnion[Range[5], {A,B,C}] returns {{1,1},{1,2},{1,3},{1,4},{1,5},{2,A},{2,B},{2,C}}

displayRates

displayRates[] displays an annotated list of the rate constants in the global rateDB for an ... ; Y\nNon-symbolic Value = 1 (hill Thill)\t\tXSTAR ↦ Y\nvx (hill vmax)\t\tXSTAR ↦ Y\n

distance

distance[g,{n1,n2}]  or distance[g, n1,n2] gives the distance (a formula) between two nodes in a graph, even if they are not linked. See also linkDistance, linkLength,icDistance.

Distance

Distance[i,j] is an uninstantiated function that is used by Cellerator to hold a place for t ... the graph, which evaluates to Sqrt[(x[i][t]-x[j][t])^2+(y[i][t]-y[j][t])^2+(z[i][t]-z[j][t])^2]

dmax

dmax is an option for run[graph,...] is the distance at which links are broken. Links will o ... the link will remain intact. To inhibit checking for link breakage, use breaklinks-> False\n

domainDescriptionQ

domainDescriptionQ[expression] returns True if expression is a correctly formatted Cellerator for SBML domain description, which has the form {name, {value1,value2,...}}

dotHolder

dot is a global symbol used during Cellerator output translation to hold the desired text symbol used for a period.

embeddingDomain

embeddingDomain[options] represents a cell's embedding\nembeddingDomain[emb, options] where ... nitial conditions, all default to zero\ntime0: time at which to apply initial conditions

embeddingDomains

embeddingDomains[graphDomain[...]] returns a list of all the embeddings in the requested graph

embeddingIC

embeddingIC[embeddingDomain[...] retrieves the list of initial conditions for the specified ... nth node of the specified graph\nsee also: embeddingICvalue, embeddingICs, embeddingICEquations

embeddingICEquations

embeddingICEquations[graphDomain[...]] retrieves the initial conditions from every embedding in the graph as a single list of equations; see also embeddingICs, embeddingICvalue, embeddingIC

embeddingICs

embeddingICs[graphDomain[...]] retrieves the list of initial conditions  from ever ... },{x2value,y2value,z2value},...}\n. See also: embeddingIC, embeddingICvalue, embeddingICEquation

embeddingICvalue

embeddingICvalue[embeddingDomain[...]] retrives the initial conditions from the specified em ... embedding of the nth node of the graph See also: embeddingIC, embeddingICs, embeddingICEquation

embeddingODEs

embeddingODEs[embeddingDomain[...] retrieves the list of differential equations for the spec ... [...],n] retrieves the embedding differential equations from the nth node of the specified graph

embeddingPOSITION

embeddingPOSITION[embeddingDomain[...] retrieves the list of position variable names for the ... ...],n] retrieves the embedding position variable names from the nth node of the specified graph

embeddingTime

embeddingTime[embeddingDomain[...]] retrives the time from an embeddingDomain\nembeddingTime[graphDomain[...]] retrieves the time from the embedding of the first node in the graph.

EmptySet

EmptySet is a variable that is used to represent the symbol ∅ when SBML is generated.

eq2Rule

eq2Rule[expression] will convert an equation of the form a==b into a rule ab; no add ... a or b. If expression is not of the form a==b then an errorAbort will occur. See also equal2Rule

equalToRule

equalToRule[expr] converts an expression of the form \"x==y\" to an expression of ... by sprint to pre-process initial conditions into the form required by run. See also equalToRule

equationListQ

equationListQ[x] returns True if x is a list of the form {eq1, eq2, ...} where all the eqi are equations, i.e., equationQ[eqi] is true for all i.

equationQ

equationQ[x] returns True of x is an equation, i.e., an expression of the form Equal[...], such as a==b, and returns False otherwise.

errorAbort

errorAbort[]: prints 'ERROR:Further Processing Aborted' and aborts.\nerrorAbort[test, option ... 54;name of calling module (used for message)\n\tmessagemessage to print in case of abort

euclideanDistance

euclideanDistance[p1, p2] calculates the euclidean distance between two poitns. Coordinates ... the same dimenstion. Scalars are converted to vectors with the scalar value in the x-coordinate.

evaluateEmbedding

evaluateEmbedding[embeddingDomain, solution, t] returns a new embeddingDomain with updated initial conditons drawn from the interpolating function solution at time t

evaluateGraph

evaluateGraph[graphDomain, solution, t] returns a new graph with updated initial conditons drawn from the interpolating function solution at time t

evaluateModel

evaluateModel[modelDomain, solution, t] returns a new modelDomain with updated initial conditons drawn from the interpolating function solution at time t

evaluateNode

evaluateNode[nodeDomain, solution, t] returns a new nodeDomain with updated initial conditon ... s and the embedding domain in the node) drawn from the interpolating function solution at time t

evaluateVariable

evaluateVariable[variable, t, solution] returns the value of variable at time t in the interpolating function solution .

exclude

exclude is an option to run[graph,options] and writeSBML[graph,options] that specifies which ... he exclude option is ignored and only those listed in include are included in the grn equations.

excludeOption

excludeOption[string, option-list]\nexcludeOption[{string1,string2,string3,...}, option-list ... ions string1->value,string2->value,... removed from the original list (if they are there).

exclusionList

exclusionList[options] generates a list of variables to exclude from processing; used by run ...     variables->{var1, var2, ...} list of all the variables in the system.

expandAllLHSBrackets

expandAllLHSBrackets[circuit] returns a modified circuit with all brackets of the form {a,b, ... reactions with the same rate constants. circuit is any circuit that is compatible with interpret

expandGraph

expandGraph[g] expands any pointers within the graph g; g may itself be a pointer to a graph ... [s] where s is a string giving the name of a global object that contains the true data structure

expandGraphVariables

expandGraphVariables[v,s] returns a list of possible variablesfor plotting when s is a run[g ... f True, will print a message to the screen for each variable that is expanded by adding indices.

expandLHSBrackets

expandLHSBrackets[{reaction,rates}] expands reactions of the form {a+b+c... ↦ d, opts} into {{a↦d, opts}, {b↦d,opts},...}. See also expandallLHSBrackets

expandRateConstant

expandRateConstant[k] returns a (possibly annotated) list of rate constants as strings. The ... stants in an (already-interpreted) set of reactions, and is not normally called by the end user.

expandSTNRunVariables

expandSTNRunVariables[v,r] returns a list of variables that match v in the the run[STN,...] ... s.If v=All, a list of all variables will be returned. If v=None, an empty list will be returned.

expandSum

expandSum[sumOverDomain[expression]] expands the actual sum represented by expression, e.g., ... ndSum[sumOverDomain[x[j],{{j,Range[5]}}]] returns x[1]+x[2]+x[3]+x[4]+x[5]. See also expandSums.

expandSums

expandSums[expression] expands all of the sumOverDomain functions in expression, i.e., repla ... 1] y[1]+3 y[2]+2 x[2] y[2]+2 x[3] y[3]+3 y[4],2 x[1] y[1]+3 y[2]+2 x[2] y[2]+2 x[3] y[3]+3 y[4]}

expandTree

expandTree[x] expands a tree structure in terms of its basic implementation.

exportODEs

exportODEs[s,options] will export a system of differential equations to a file with the sele ... TRAN\": write equations in FORTRAN. Note: Dimension states may need to be edited manually.

extractRateConstant

extractRateConstant[dbentry] returns a symbolic rate constant from a database entry in rateD ... ates to display an (already interpreted) database, and is not typically needed by the end-user.

extractReaction

extractReaction[dbentry] returns a reaction from a database entry in rateDB. The format of a ... Rates to display an (already interpreted) database, and is not typically needed by the end-user.

fastSpringForce

fastSpringForce[g,n] calculates the total spring force on node n in graph g\nfastSpringForce ... o springForce. fastSpringForce is turned on in organism[] and meristem[] using option fastForce.

fccTable

fccTable[r] generates a hemispherical array of 3 dimensional points on a face-centered-cubic grid. The argument r is the radius of the grid in cell diameters and hence should be an integer.

field

field[function,domain] is a domain that represents the effect of a function on a domain. To ... ain[field[Sqrt,intDomain[100,250,75]]] returns {10,5 Sqrt[7],5 Sqrt[10]}. See also threadfield

file

file is an option for writeSBML that specifies the name of the output file. If the directory ... ctory/file. If file is not specified a file name is generated based on the current system clock.

findBlockedLinks

findBlockedLinks[options] returns a list of links that are blocked in the given graph. Options are: graph

findIntersection

findIntersection[{x0,y0},r, {x1,y1}, {x2,y2}] finds the points of intersection of the line f ... connecting them\nfindIntersection returns a null list {} if there are no points of intersection.

findParameterValues

findParameterValues[x1,x2,...,xn,optionlist] returns a list {value1, value2, ..., valuen}, w ... nd\nExample: findParameterValues[f,g,h,x 23,g 14,k 27] returns {0,14,0}.

findSteadyState

findSteadyState[STN, options] returns the steady steady state of a system of reactions.  ... e hill,nhill 2},{P∅,k1}}] returns {{P -> TF^2/(k1*(1 + TF^2))}}

flatTable

flatTable[r] generates a list of coordinates for cell centers for a two-dimensional hemisphe ... e system, but all cell centers lie in the x-y plane, i.e., the third coordinate is always zero.

fuzzyStep

fuzzStep[x,r] approximates a step function at x=0 with a Tanh of slope r (default 1000)

generateColorTable

generateColorTable[graph, options] returns a list of the form {{nodetype, color}, {nodetype, ... nNOTE: Not intended for end user use; this is called by showGraph, showFlatGraph, and makeMovie.

generateICList4SBML

generateICList4SBML[{x1,x2,x3,...},opt] returns a list of initial condition assignments of t ... s->{y1->val1,y2->val2,...}. If an initial condition is not specified it is set to zero.

generateMeristemLinks

generateMeristemLinks[{{x1,y1,z1},{x2,y2,z2},...}, options] generates a table of link pairs ... 2 is the second triple, etc.\nOptions are:\ngrid->fcc, hcp, flat, how are the cells arranged.

generateOutputFileName

generateOutputFileName[options] returns an output file name specification. No file is create ... \"];\nOptions are\nfile->file name\ndirectory->directory name\nfiletype->file type

generateReactionSBML

generateReactionSBML[r, options] returns a string containing a complete level-1 SBML specifi ... addition, values for rate constants may be specified as namevalue,namevalue,...

genericValidateRateConstant

genericValidateRateConstant[{expr,k},options] is called by validateRateConstants.   ... nstant to the screen.\nvalidate->True, if False, don't automatically generate rate constants.

getEnzyme

C getEnzyme[reaction] returns the catalyst in a catalytic reaction such as A⇄B

getEquationOrder

getEquationOrder[eq] returns the order of the derivative for an equation of the form lhs==rh ... oes not have Head[eq]==Equal, a value of -1 is returned. Algebraic equations have an order of 0.

getGrowthRates

getGrowthRates[n, options] checks the option list for the parameters rates or periods and returns a formatted list to 'organism'. Not intended to be user-invoked, only called by 'organism'.

getInitialValue

getInitialValue[var, {var1[t0]==val1, var2[t0]==val2,...}] searchs the list of initial condi ... ist of initial values for the variables var1, var2,... in the graph by calling getInitialValues.

getInitialValues

getInitialValues is used by getInitialValue[list,...] when the first argument is a list; the ... var, graph] returns a list of initial values for the variables var[i1],var[i2],... in the graph.

getMassGrowthRateList

getMassGrowthRateList[mu, n] returns a list of  mass growth rates of length n. The ... te masses that are placed in the steadyStateMass field of the nodeData field of each graph node.

getMassList

getMassList[mass, n] returns a list of masses of length n. mass may be one of the following: ... ultvalue. getMassList is used by organism to determine the desired initial masses for the cells.

getMassRange

getMassRange[r], where r is the output of run[graph...] (or runFixedInterval) returns a rule ... performed; so long as mass is monotonic increasing, except at cell division, this is sufficient)

getMeristemGrowthRates

getMeristemGrowthRates[nlist, meristemGrowthRates-> {CZ->r1,PZ->R2,Rib->r3,Floor ... thRates returns a list of the same length as nlist. Not intended for end-use. Used by 'meristem'

getNodeData

getNodeData[n] returns the nodeData from node n\ngetNodeData[g,n] returns the nodeData from ... .\ngetNodeData[graph] returns an ordered list of the nodeData field from all nodes in the graph.

getNodeType

getNodeType[n] returns the nodeType from node n (a nodeDomain)\ngetNodeType[g,n] returns the nodeType from the nth node of graph g. See also getNodeTypes

getNodeTypes

getNodeTypes[g] returns a list of the nodeTypes from all nodes in the graph g.See also getNodeType

getODE

getODE[g] returns a list of all the differential equations in graph g\ngetODE[g, variable ... , variable {v1, v2, ...}] returns the differential equations for the specified variables

getOption

getOption[function,optionName, optionList]\nSearchs through optionList for 'optionvalue' and returns value.

getOptionSymbols

getOptionSymbols[] returns a list of the names of all the options that defined in a Global` context via the Options function.

getPointers

getPointers[nodeDomain] retursn a list of all the Cellerator pointers reference in the nodeDomain.

getSpecies

getSpecies[n,options] is used by organism to determine what species are wanted.\n

getSpeciesIC

getSpeciesIC[n,options] retrieves and formats the species initial conditions options for organism. Only minimal error checking is performed.

getSpeciesODEs

getSpeciesODEs[n,options] retrieves and formats the speciesodes options for organism. Only minimal error checking is performed.

getSpeciesReactions

getSpeciesReactions[n,options] retrieves and formats the species reactions option for organism. Only minimal error checking is performed.

getSteadyStateMass

getSteadyStateMass[n] returns the steadyStateMass option from the nodeData field of node n\n ... teMass[graph] returns an ordered list of the steadyStateMass fields from all nodes in the graph.

getSteadyStateMassList

getSteadyStateMassList[s, n] returns a list of steady state masses of length n. s may be one ... te masses that are placed in the steadyStateMass field of the nodeData field of each graph node.

getSymbols

getSymbols[expression] returns a list of all the symbols in expression whose context is Global`

getVariableRange

getVariableRange[r], where r is the output of run[graph...] (or runFixedInterval) returns a ... easing, except at cell division, this is sufficient)\nvariable->mass, name of variable to use

globalGraphs

globalGraphs stores the most recently computed list of graphs computed by runFixedInteval.See also recoverSolution.

globalSolutions

globalSolutiosn stores the most recently computed list of solutions computed by runFixedInterval. See also recoverSolution.

globalSYSTEM

globalSystem stores the most recently generated list of differential equations. It is sometimes useful for debugging early terminations in integrateGraph.

GMWC

... ip ij ip

GMWCRateFunction

dP Si ... {{A1, A2, ...}, {I1, I2, ...}}

goldbeterMinimalSystem

goldbeterMinimalSystem[options] returns a modelDomain with a three-variable mitotic oscillat ... iology; If Slow. a set that gives a slower oscillation is used; if Stopped, all are set to zero.

graphCounter

graphCounter counts the number Cellerator graph pointers that have been allocated

graphDomain

graphDomain[nodesnodelist, links linklist, lineage lineagetree]\ngra ... eDomain[...],...}\n\tlinklist = {linkDomain[...],linkDomain[...],...}\n\tlineageTree = tree[...]

graphelator

Graphelator™ is a generic term for the parts of Cellerator™ that involve graph manipulation. There is no separate file for function called Graphelator.

Graphelator

Graphelator™ is a generic term for the parts of Cellerator™ that involve graph manipulation. There is no separate file for function called Graphelator.

graphIC

graphIC[g] returns a list of the initial conditions for all variables in the graph g.\ngraph ... xclude->{var1,var2,...}, returns the initial conditions with the specified variables excluded

graphICrules

graphICrules[g] returns a list of the initial conditions for all variables in the graph g as a rule list.

graphLinks

graphLinks[g] retursn a list of the link Domains in g.

graphNodes

graphNodes[g] returns a list of the node Domains in g.

graphODEs

graphODEs[g] returns a list of the differential equations in the graph g\nOptions:\nevaluate->True, expand pointers\nexclude->{}, list of variables to exclude from list

graphParameters

graphParameters[g] makes a list of all the symbols used in g that are not listed in graphVariables[g]

graphQ

graphQ[x] returns True if x is a graphDomain (or a pointer to a graphDomain), and false otherwise.

graphRunSolution2gridMultiPlotSolution

graphRunSolution2gridMultiPlotSolution[s] converts s, the output of run[graph...] to the format necessary for gridMultiPlot.

graphVariables

graphVariables[g] returns a list of all the variables in the graph g\ngraphVariables,g,exclude->{var1,var2,...} will return a list with the specified varialbes excluded

greek2string

greek2string[x] returns a string with all greek characters replaced by their names.

greek2StringRules

greek2StringRules are the rules {α  alpha, β  beta, γ  ... #62754; CapitalPhi, Χ  X, Ψ  CapitalPsi, Ω  CapitalOmega}

grn

grn is an option for run[grpah,options] and writeSBML[graph,options] that specifies whether or not the grn equations should be included along with the Cellerator equations.

GRN

... 1 + e

GRNEQ

GRNEQ[equations {equation1, equation2,...}, variables {variable1, variable2, ... GRN-equations. To access individual fields see equations, parameters, parameterNames, variables.

GRNequations

GRNequations[g, options] returns a GRNEQ[] data structure that encapsulates the GRN equation ... nincludeArrows False, True to include Cellerator arrow generated terms in the odes also.

GRNRatesQ

GRNRatesQ[k] returns True if k is a valid rate constant list for a GRN reaction, i.e., it is ... precisely the form GRN[options], or is an option list that contains the option typeGRN.

GRNSigmoidFunction

1 x GRNSigmoidFunction[x] returns - (1+------------); 2 2 Sqrt[1 + x ]

GRN$PROTEIN

GRN$PROTEIN is a Cellerator global generated whenever GRN equations are requested. It contai ... n GRN$PROTEIN={GRN$v[1]RAFK,GRN$v[2]Y,GRN$v[3]Z,GRN$v[4]K[3,2]}.

growthExponent

growthExponent calculates and returns the value of the exponent used to determine growth rat ... ed by the value of the global variable node$shape and can be reset by by using the option shape.

help

Cellerator help can be found in the following ways:\nTyping ?symbol will give the Mathematic ... ] is equivalent to ?x or x::usage\ncreateCelleratorReference[] will generate a reference manual.

hexTable

hexTable[r] generates a hemispherical array of 3 dimensional points on a hexagonal-close-packed grid. The argument r is the radius of the grid in cell diameters and hence should be an integer.

hill

... 1 i = 1 i i

hillFunction

n ... n n K + x

hillRatesQ

hillRatesQ[k] returns True if k is a valid rate constant list for a hill reaction, i.e., it ... recisely the form hill[options], or is an option list that contains the option typehill.

holderRules

holderRules is a list of string replacement rules that replace common symbols like dots and brackets with string place holders; to invert, use releaseRules.

htmlCitation

htmlCitation[string,URL->value,opt] returns an html formatted citation as <p>string</p><a href=URL>URL</a>. Options: indent->\"\"

htmlModelDescription

Returns html for the <notes> section of html, and optionally generates an html file.\n ... eir names\ndescription->optional string text to be included \nhtmlfile->optional file name

icDistance

icDistance[g,{n1,n2}] or icDistance[g,n1,n2] gives the distance (a number) between the initi ... in two nodes in a graph even if they are not linked.See also distance, linkLength, linkDistance.

identifySBMLVariableParameters

identifySBMLVariableParameters[options] determines which Cellerator variables are really sbm ... ..];\nidentifySBMLparameters[r,exclude->{...}\nidentifySBMLparameters is called by writeSBML.

include

include is an option to run[graph,options] and writeSBML[graph,options] that gives a list of ... t;False then this option is ignored.If include is specified, then the option exclude is ignored.

indexDomain

indexDomain[x] represents a list where each element is either an integer or an indexSet. An indexDomain is instantiated by expandDomain.  See also indexSetQ.

indexedSpecieDefinitions

indexedSpecieDefinitions[{variable,list-of-compartment-numbers, list-of-indices},options] r ... ...</domain>\", \"<specie name=\"K[..domains...]\"... />\"}

indexSetQ

indexSetQ[x] returns True if x is an indexSet and False otherwise. An indexSet is a a list where each element is either an integer or a list containing integers and indexSets (recursively).

initializeSBMLReactions

initializeSBMLReactions reinitializes the counters and globals used to generate SBML reactions:$SBMLReactionCounter, $reactionSpecies

initialMass

initialMass is an option for standardNode, organism or meristem the defines the desired init ...  2.0} and the values are randomized with a uniform distribution over a range of +/- 15%.

initTimeChecker

initTimeChecker[] initializes the CPU counter used by timeChecker.

intDomain

intDomain[m], intDomain[m,n], intDomain[m,n,p] are Domain objects represents the lists Range[m], Range[m,n], Range[m,n,p]. Use expandDomain to instantiate these domains.

integerform

integerform[i,n] returns a string of length n that is padded in front by zeroes. Only really works for integers.

integrateGraph

integrateGraph[graph, step, options] formats and executes the call NDSolve and generates any ... ay also be used.\nNote:integrateGraph is called by runStep and is not intended for the end user.

intermediateCompound

intermediateCompound[x,y] returns a list containing the name (as a symbol) of the compound f ... joining x and y.See also compoundName, intermediateCompoundName, dash, complexLeft, complexRight

intermediateCompoundName

intermediateCompound[x,y] returns the name (as a symbol) of the compound formed by joining x and y.See also compoundName, intermediateCompound, dash

interpret

... at each reaction must be enclosed in curly brackets:\ninterpret[{{AB,k1}, {CF}}]

interpretArrowType

... b b

interpretedSystemQ

interpretedSystemQ[x] returns True if x is syntacticaly equivalent to the output of interpre ... ..}, {var,var,...}} where ode is a Mathematica differential equation and var is a variable name.

interpretReaction

interpretReaction[r] returns a string indicating the type of reaction.

interpretTree

interpretTree[tree] returns the tree as an option List.

intersects

intersects[options] determines if a line segment defined by two points intersects a circle w ... 62754;1\nendPoints{{x1,y1},{x2,y2}}\nplot->False\nSee also: findIntersection, blocks.

intersperse

intersperse[list1, list2] returns a list with the elements interspersed. Both lists must be ... ange[5],{A,B,C,D,F}] returns {1,A,2,B,3,C,4,D,5,F}. See also multsperceBefore, multisperceAfter.

isAPartialRateList

isAPartialRateList[x] returns True if x is a list composed of a combination of Cellerator reactions with and without rates, or if it is a rate list.

isARateList

isARateList[x] returns True if x is a list of Celllerator reactions including rate  constants, and False otherwiase.

isAReaction

isAReaction[x] returns True if x is a Cellerator Reaction and False otherwise.

isAReactionList

isAReactionList[x] returns True if x is a list of Cellerator Reactions and False otherwise. ... False if any of the reactions have rate constants specified. See isARateList, isAPartialRateList

isFlat

isFlat[g] returns True if graphDomain g is 2-dimensional AND only in the x-y plane.

jacobianMatrix

jacobianMatrix[sys] returns the Jacobian of sys, where sys is either a signal transduction network (interpretable); an interpreted signal transduction network; or a list of first order ODEs

jog

jog is another name for predictTransferFunction]

LambdaApproximation

... roximation[Km,Kcat,Λ]} returns the value { A⇄B, Λ*Kcat/Km, (Λ-1)Kcat, Kcat}

lambdaMatrixMode

... ult, e.g., Sqrt[ab]) or averagearithmetic (e.g., (a+b)/2) \nShadow: same as default. \n

leavesIn

leavesIn[tree] returns the number of leaves in a tree

leftBracketHolder

leftBracketHolder is a global symbol used during Cellerator output translation to hold the desired text symbol used for a left bracket.

leftParenHolder

leftParenHolder is a global symbol used during Cellerator output translation to hold the desired text symbol used for a left parenthesis.

lhsShortRightArrow

lhsShortRightArrow[ab] returns a list of the reactants a, e.g., lhsShortRightArrow[a+b+cx+y+z] returns {a,b,c}

limitedRandomNumber

limitedRandomNumber[size] returns a random number between -size and +size

lineageTree

A lineage tree is a binary tree containing the integers 1,...,n,in the leaves,representing t ... he left,and n+1 on the right,where n is the number of leaves in t.The modified tree is returned.

lineageTreeQ

lineageTreeQ[t] returns True only when t is a properly formatted lineage tree

link

link[g,n] is the same as linkDomain[g,n] where g is a graphDomain and n an integer.

linkData

linkData[linkDomain[...]] returns the link data\nlinkData[graphDomain[...],n] returns the link data for the nth link

linkDistance

linkDistance[g,n] gives the length of link n in graph g using the initial conditions on the ... he two ends of the linke (i.e., it returns a number). See also linkLength, distance, icDistance.

linkDistances

linkDistances[g] returns an ordered list of the lengths of thelinks in g using the initial conditions of the embeddings of the two ends of the links.

linkDomain

linkDomain[options] represent a linkDomain in a graph\nlinkDomain[linkDomain[...], options] ... kedNodes, linkData, linkType, linkSpring, linkDistance, linkLength, springConstant, springLength

linkedNodes

linkedNodes[linkDomain[...]] returns the pair of integer node numbers {n1, n2} representing ... n a list of all node pairs that are linked {{n1,n2},{n1,n2},{n1,n2},...}\n See also linkNodePair

linkLength

linkLength[g,n] returns the length of link n in graph g as a formula based on the variables ... he enmbedding variables of the two ends of the link. See also linkDistance, distance,icDistance.

linkNodePair

linkNodePair[graphDomain[...],n] returns the node pair {n1,n2} for the nth link of the graph

linksIn

linksIn[g] returns an integer, the number of links in g.

linkSpring

linkSpring[linkDomain[...]] returns the Spring\nlinkData[graphDomain[...],n] returns the Spring for the nth link

linkType

linkType[linkDomain[...]] returns the link type\nlinkType[graphDomain[...],n] returns the link type for the nth link

localDensity

localDensity[g,n] returns the local density of a graph at a given node based on the node's d ... neighborsMass^1/3)/((4/3)*Pi*separation). If a node has no neighbors a density of 1 is returned.

lowLevel

lowLevel[reactions] counts the number of low level reactions in reactions. To display the reactions, see lowLevelReactions or lowLevelReactionTable.

lowLevelReactions

lowLevelReactions[circuit] gives a list of the low-level reactions in circuit. circuit has the same format as the input to interpret. See also LowLevelReactionTable

lowLevelReactionTable

lowLevelReactionTable[circuit] lists the low-level reactions as a table rather than a Mathematica list. See also lowLevelReactions.

makeConditional

makeConditional[{condition,result,default}] returns the SBML level 2 conditional string \&qu ... ue is always enclosed in parenthesis so that conditionals can be easily (and correctly) nested.

makeConditionals

makeConditionals[{ {c1,r1}, {c2,r2},...,{cn,rn,d} }] returns the nested SBML level two condi ... return \"c1?r1:(c2?r2:(c3?r3:(c4?r4:(d4))))\".Warning: No error checking is performed.

makeIndexed

makeIndexed[x,i] returns x[i]

makeList

makeList[expression] replaces all function f[x] by lists {f, lists-in-x} where lists-in-x is ... bly nested list of arguments where each function call is also replaced by a list, to all depths.

makeMovie

makeMovie[s, {tstart, tend, dt}] creates a move from a list of graphs and solutions generated by runFixedInterval. s is the list produced by runFixedInterval.

MAPKCascade

MAPKCascade[options] generates the biochemical reactions for an n-stage MAP-Kinase phosphory ... on,rates},...}, an optional list of rate constants to use for specific reactions in the cascade.

mapTimeVariable

mapTimeVariable[{x1,x2,...},t] returns a list{x1[t],x2[t],...}

massGrowth

massGrowth is an Option for mass$formula that selects a particular massGrowth model. Both ru ... eans dmdt=massGrowthRate*m(1-m/steadyStateMass),\nmassGrowthNone or False: means dm/dt=0

massGrowthRate

massGrowthRate is an option for standardNode and organism as well as a subfield of a nodeDom ... 065, Floor 0.065}, and the values are randomized with a uniform distribution by +/- 15%.

mass$formula

mass$formula[options] returns a Mathematica pure function of a single argument that represen ... 54; 99.3,massGrowth logistic, massGrowthRate 0.01][m]\nreturns: 0.01*(1 - m/5)*m

mergeIndices

mergeIndices[x[i,...][j,...]...[k,...] returns a symbol with a single index list x[i,...,j,...,k,,,], for example, mergeIndices[a[1,2,3,4,5][3][5,12]] returns a[1,2,3,4,5,3,5,12]

mergeModelDomains

mergeModelDomains[m1, m2] or mergeModelDomain[{m1,m2}] creates a single modelDomain by merging the two modelDomains m1 and m2.

meristem

meristem[n,options] generates a simulated meristem of hemispherical radius n cells.\nOptions ... be used: such as mitoticOscillator, force, shape,species,speciesIC,speciesodes,speciesReactions

mitosis

mitosis is an option for run[graph,...] that indicates whether or not cell division is allow ... resent and working; it will not create an oscillator in each cell if one is not already present.

mitoticOscillator

mitoticOscillator is an option for organism and standardNode that indicates which mitotitic ... \nUser: to create a user-defined model. Any option allowed to createUserModel may be specified.

MM

... EReverse

model

model is an option for writeSBML that specifies the name be used for the SBML model.If unspecified,a unique model name is generated automatically.

modelDomain

modelDomain[options] represents a model within a cell;\nmodelDomain[modelDomain[...], option ... default is zero\n\nOperations on modelDomains include:modelODEs[m],modelMOLECULES[m],modelIC[m]

modelDomains

modelDomains[nodeDomain[...] gives a list of all the modelDomains in the specified nodeDomain.

modelIC

modelIC[m] gives a list of the initial conditions in m.

modelMOLECULES

modelMOLECULESs[m] gives a list of the molecules in m.

modelODEs

modelODEs[m] gives a list of the differential equations in m.

modeltime

modeltime[m] gives the value of the time field of m.

modifyNode

modifyNode[n, options] returns a modified node based on options, where options are any valid ... for either a nodeDomain, an embeddingDomain, or a modelDomain, and are applied in that sequence.

movieKey

movieKey[nodeColorscolor - list] returns a list of the form {{⁃Graphics⁃ ... e:movieKey is not an end-user function. It is called by showGraph, showFlatGraph, and makeMovie.

multiplot

multiplot[x] is plots a variable from a cellerator run sequence that may be composed of seve ... multiplot directly but should use runPlot. The plot option in run produces a call to multiplot.

multisperseAfter

multisperseAfter[list1, {list2a, list2b, list2c, ...}] intersperses each of list 2a, 2b, ... ... ; {{A,1,B,2,C,3,D,4,F,5},{P,1,Q,2,R,3,S,4,T,5},{alpha,1,beta,2,gamma,3,delta,4,epsilon,5}}.

multisperseBefore

multisperseBefore[list1, {list2a, list2b, list2c, ...}] intersperses list 1 into each of lis ... ; {{1,A,2,B,3,C,4,D,5,F},{1,P,2,Q,3,R,4,S,5,T},{1,alpha,2,beta,3,gamma,4,delta,5,epsilon}}.

myPadRight

myPadRight is a work-around a bug in PadRight in Mathematica version 4.1.5.\n myPadRight[lis ... nts PadRight[list,n,{x}]\n other versions of PadRight are not implemented and may lead to error.

neighborFunctionSBML

neighborFunctionSBML[cm, options] generates the level-2 SBML for a function that is true when the square matrix cm[[i,j]] is nonzero, and is false when the i,j element of cm is zero.

neighbors

neighbors[g,n] returns a list of the (node numbers of the) neighbors of node n in graph g.\nneighbors[g] returns a list {{1, neighbors of 1}, {2, neighbors of 2},...} for the whole graph

newCompartment

newCompartment will return a string \"Compartmentnnn\"  where nnn is the current value of $CompartmentNumber, which is then incremented. See also resetSBML.

newDomain

newDomain will return a string \"Domainnnn\"  where nnn is the current v ... be \"foo00001\",\"foo00002\",\"foo00003\",... See also resetSBML.

newModel

newModel will return a string \"Modelnnn\"  where nnn is the current value of $ModelNumber, which is then incremented. See also resetSBML

newRateConstant

newRateConstant[x] returns a rate constant xnnn where nnn is the value of $rateConstantNumber, and is incremented during interpret when rate constants are defined.

news

The news command is no longer supported by Cellerator. To learn about a particular command, enter ?command

NHCA

... i i i

NHCARatesQ

NHCARatesQ[k] returns True if k is a valid rate constant list for a NHCA reaction, i.e., it ... recisely the form NHCA[options], or is an option list that contains the option typeNHCA.

node

node[g,n] is the same as nodeDomain[g,n] where g is a graphDomain and n an integer.

nodeDomain

nodeDomain[options] represents a node (cell) in a Cellerator Graph.\nnodeDomain[nodeDomain, ... omain see: nodeODEs, nodeVariables, nodeIC, getNodeType, getNodeTypes,getNodeData, getNodeModels

nodeIC

nodeIC[n] returns a list of all the initial conditions for all variables in node n (a nodeDo ... eIC[g,n] returns the the initial conditions for all variables in node n (an integer) of graph g.

nodeModels

nodeModels[n] returns a list of the models (modelDomains) in node n.\nnodeModels[g,n] returns a list of the models in the nth nodeDomain of graph g.

nodeODEs

nodeODEs[n] returns a list of all the differential equations for all variables in node n (a ... Es[g,n] returns the differentnial equations for all variables in node n (an integer) of graph g.

nodesIn

nodesIn[g] retursn an integer, the number of nodes in g.

nodeVariables

nodeVariables[n] returns a list of all the variables in node n (a nodeDomain), including all ... position variables.\nnodeVariables[g,n] returns the variables in node n (an integer) of graph g.

node$Shape

node$Shape is a global variable that stores the most recently selected value of shape->\& ... PHERE\",\"DISK\"; this value is used unless it is overridden by the shape option.

nonOptionQ

nonOptionQ[x] returns True if x is not an Option and false if x is an Option

note

note is an option for writeSBML that specifies the contents of the SBML <notes> field. ... on number, operating system, date/time file written, and a reference to the cellerator web site.

notListQ

notListQ[x] returns True if x is not a list and False if x is a list.

Now

Now[] prints the curent date and time in the format \n\"February 15, 2002 10:55:22\"; compare with dhmsDate.

nullQ

nullQ[x] returns True if x is {}

numberQ

numberQ is the same as NumberQ but also allows +/- Infinity to be a number.

odeCounter

odeCounter counts the number Cellerator ODE pointers that have been allocated

odeQ

odeQ[x] returns True if x is a single differential equation or list of differential equations.

ODEsin

ODEsin[g] returns an integer, the number of differential equations in the graph g.

offsetEmbedding

embeddingDomain[emb, {value1, value2, value3}] adds the specified vector of valuess to the initial conditions of the embeddingDomain emb and returns the modified embeddingDomain

offsetNode

offsetNode[nodeDomain,{x, y, z}] returns a node with the initial conditions moved by the vector {x, y, z}. See also putNode.

optionPairs

optionPairs[opt1val1, opt2val2, opt3val3,...] returns a list {{opt1,val1},{opt2,val2},...}; opt may be either a list or a sequence of rules and/or options.

organism

organism[options] creates a Cellerator graph object based on the input provided.\n\nOptions ... passed to interpret.\nstatsFalse, if True, prints statistics on CPU use and graph size.

parameterNames

parameterNames[GRNEQ[x]] retrieves a list of the names of parameters in the GRN equations.

parameters

parameters[GRNEQ[options]] retrieves the list of parameters in the GRN equations.

parametricRunPlot

parametricRunPlot[r,{x,y}] plots y[t] as a function of x[t] for the entire cellerator run r. ... imeCourse)\n(2) not implemented for graph runs.\n(3) Any valid option for Plot may be specified.

performEvent

performEvent[graph, solution] returns a modified graph with new initial conditions and start ... ed new cells and corresponding links added to it. performEvent is not intended for end-user use.

phasePlot

phasePlot[x,...] is another name for parametricRunPlot[x,...]

phasePortrait

phasePortrait[stn,{xvar,xmin,xmax,xdelta},{yvar,ymin,ymax,ydelta}] returns a phase portrait ... ait plots only a two-dimensional projection of the full phase spase onto the plane {xvar,yvar}.

plotColumns

plotColumns->n is an option for run[...] that indicates the number of columns to used in generating plots (default = 3). Ignored if plotVariables->None.

plotCoordinates

plotCoordinates->True (Default: False) is an option for run[graph,...] that will produce plots of the x,y, and z coordinates for each node at the end of each call to NDSolve.

plotGraphRun

plotGraphRun[variable, solution, {tstart, tend}, options] plots a variable or list of variab ... ;\"Linear\"(Default) ,\"Log\" ,\"LogLinear\" ,\"LogLog\"

plotLinks

plotLinks[r], where r is the output of r[graph,...], will plot the lengths of the links as a ... )\nValid plot options can be specified, e.g., p=plotLinks[r,PlotRange{{9,15},Automatic}]

plotSTNrun

plotSTNrun is equivalent to runPlot for signal transduction (non graph) run.  See runPlot for allowed syntax and options.

plotTrajectories

plotTrajectories-> True (default=False) is an option for run[graph,...] that will produce ... the embedding of each node to be plotted in a three-dimensional grid after each call to NDSolve.

plotVariables

plotVariables->{variable, variable,...} is an option for run[...] that specifies a list o ... arning messages if cell division occurs because it attempts to plot all variables for all times.

pointer

Cellerator pointers are uninstantiated functions pointer[s], where s is a string that gives the name of an actual globally defined data structure.

powerToRepeat

powerToRepeat[x] replaces expressions of the form x^n with lists {x,x,...} of length n. If m ... a list\npowerToRepeat[A^3] returns {A,A,A}\npowerToRepeat[A,B^2,C^4] returns {A,{B,B},{C,C,C,C}}

predictTimeCourse

predictTimeCourse[s,options] is a smart wrapper for run. The first argument must be a Celler ... ions and rate constants will be produced. If conciseTrue, this option will be supressed.

predictTransferFunction

predictTransferFunction[c,options] is an extension of predictTimeCourse that performs multip ... ,S[500]},{3,S[500]},{4,S[500]},{5,S[500]}}}\nGraphics`MultipleListPlot[s] will plot the results.

prepReactionsForSBML

prepReactionsForSBML[reactions] prepares a reaction list for generation of SBML code. It is ... of the form A⊕B⊕C⊕...↦product, as required by SBMLLevel1ArrowReaction.

processParameters

processParameters[parameters,options] will generate an sbml level 2 string for a set of Cell ... returned will include a list of domain definitions followed by a list of parameter definitions.

processSumsOverDomains

processSumsOverDomains[expression,options] returns a list {newexpr,domains} domains is a str ... ession with sumOverDomain expressed as sumOverDomain[expression, domainSymbol, domainSymbol,...]

protectAll

protectAll will protect every defined symbol in the context Global that does not have an attribute of Temporary.

proteins

proteins[node,options] returns a list of proteins in the the specified nodeDomain.\nproteins ... variables to include in the list. If the include option is used, the exclude option is ignored.

pulse

pulse[t] returns a unitPulse\npulse[t,magnitude] returns magnitude if -1/2≤t≤1/2 ... within width/2 of tcenter, and zero otherwise\nSee also: unitPulse, unitPulseTrain, pulseTrain.

pulseTrain

pulseTrain[t,magnitude,n] delivers a train of n pulses of the given magnitude and unit time ... delivers a train of n pulses of the given magnitude, pulseWidth, and center-to-center spacing.\n

putNode

putNode[nodeDomain,{xvalue, yvalue, zvalue}] returns a node with the embedding initial condition modified to {xvalue, yvalue, zvalue}. See also offsetNode.

rand

rand returns a random number between 0 and 1

randomEmbedding

randomEmbedding[options] returns an embeddingDomain with random initial conditions on the po ... variables in the (0,1)×(0,1)×(0,1) cube. Options are otherwise the same as for embeddingDomain.

randomGraph

randomGraph[n,options] returns a graph with n nodes at randomly placed locations in the unit ... t element.\nsymmetric True, if True, the links are two-way; otherwise they are directed.

randomIC

randomIC[] returns a held expression for a random number between 0 and 1\nrandomIC[x] return ... f {x1, x2} and the larger of {x1, x2}\nExample: randomIC[5,12] returns Hold[Random[Real,{5,12}]]

randomize

randomize[list, fraction] returns list with every element perturbed by a random number in th ... riginal value. If list is a number, a number is returned; if list is a list, a list is returned.

randomSign

randomSigns returns either 1 or -1, randomly.

rateConstant

rateConstant generates a new rate constant (as a symbol, not a string) of the form kxxx wher ... tinues to be incremented until a rate constant of the form kxxx has not been previously defined)

rateDB

rateDB is a database that contains definitions of the rate constants needed by Cellerator. I ... ants supplied to interpret. It is not user-modifiable. To reinitialize the database use setDB[];

reactionType

reactionType[reaction] returns an integer indicating the  type of reaction. Note t ... )\n24 Michaelis-Menten (Enzyme Explicit Form)\n25 enzymatic (mass action, SE and PE complexes)\n

realRandom

realRandom[a,b] returns a random real number between a and b

recoverSolution

recoverSolution retrives the global solutions and graphs generated by the most recent call to runFixedInterval.

rectangularGrid

rectangularGrid[nx,ny] generates an nx by ny rectangular grid of points in the xy plane betw ... {x2,y2}] uses (x1,y1) for the upper left hand corner and (x2,y2) for the lower right hand corner

regularPolygon

regularPolygon[n] generates the coordinates of a regular polygon centered at the origin with ... e of radius\nregularPolygon[n, radius, offset] rotates the polygon by an angle offset in radians

relax

relax->True (default) is an option for run[graph,...] that indicates that graph relaxation is supposed to be performed when new nodes are added to the graph.

relaxGraph

relaxGraph[graph,options] relaxes an unrelaxed graph by allowing all springs to relax toward ... tercellular distances as a function of time\ntimeStep1, duration of each call to NDSolve

releaseRules

releaseRules inverts holderRules.

removeLink

removeLink[g,n1,n2] or removeLink[g,{n1,n2}] returns graph g with the link from n1 to n2 rem ... nkBothways. Options are:\nexception->Floor (only allow exception cells to move horizontally).

removeLinkBothWays

removeLinkBothWays[g,n1,n2] returns graph g with links {n1,n2} aned {n2,n1} both removed. See also removeLink.

removeLinks

removeLinks[g, {{from,to},{from,to},...}] returns a new graph with the specified nodes removed.

replaceArrows

replaceArrows[x] returns a string version of x with Cellerator arrows convertged to their AS ... esentations, as , become ->, ↦ becomes|->, ⇄ becomes <=>

resetGraphIC

resetGraphIC[g, initialConditions {name1val1, name2val2,name3 ... resetVariables (for unindexed varialbes) and resetSpecificVariables (for the indexed variables).

resetNodeType

resetNodeType[g,n,newType] returns a modification of the graph g, with the nodeType of node n changed to newType.

resetSBML

resetSBML[] resets the values of $CompartmentNumber, $DomainNumber, and $ModelNumber to 1. r ... values of these globals to n. writeSBML invokes resetSBML[1] prior to generating an SBML model.

resetSpecificVariables

resetSpecificVariables[graph, options] resets the values (initial conditions) of specific va ... ...} list of variavble names\nvalues{var1value, var2value,...} values for each variable

resetVariables

resetVariables[graph, options] resets the values (initial conditions) of variables to specif ... ...} list of variavble names\nvalues{var1value, var2value,...} values for each variable.

rhsShortRightArrow

rhsShortRightArrow[ab] returns a list of the products b, e.g., lhsShortRightArrow[a+b+cx+y+z] returns {x,y,z}

rightBracketHolder

rightBracketHolder is a global symbol used during Cellerator output translation to hold the desired text symbol used for a right bracket.

rightParenHolder

rightParenHolder is a global symbol used during Cellerator output translation to hold the desired text symbol used for a right parenthesis.

rmvItem

rmvItem[{item1, item2, ...,itemn}, form ] returns a list with with the specified item or items in form removed; form may be either a single item or a list of times.

ruleListQ

ruleListQ[x] returns True if x has is a list of Rules; the difference between ruleListQ and OptionQ is that OptionQ does not allow indexed options, such as k[5]-> 12; see also RuleQ,rulesQ

rulePairs

rulePairs[x] is identical to optionPairs[x]\noptionPairs[opt1val1, opt2val2, ... t {{opt1,val1},{opt2,val2},...}; opt may be either a list or a sequence of rules and/or options.

RuleQ

RuleQ[x] returns True if x is a rule and False otherwise. Compare with OptionQ. See also ruleListQ.

rulesQ

rulesQ[x,...] returns True if x is a sequence or list of Rules and False otherwise. Thus it ... , which is not an option because of the function (index) argument. Compare with ruleQ, ruleListQ

run

run[celleratorSystem,options] will solve the system of differential equations produced by in ... accuracy of the interpolating Function.\nIn addition, any valid option for NDSolve may be used.

runFixedInterval

runFixedInterval[duration, step, options] returns a list of the form {{solution1, solution2, ... accuracy of the interpolating Function.\nIn addition, any valid option for NDSolve may be used.

runFixedIntervalWrapper

runFixedIntervalWrapper[g,options] is used by run[] to format a call to runFixedInterval. g ... lid option to runFixedInterval can also be specified.\nNOTE:Not intended for end user execution.

runGRN

runGRN[G, T, options] executes NDSolve and returns the list of interpolating functions for all proteins in a graph.

runPlot

runPlot[variable, solution, {tstart, tend}, options] plots a variable or list of variables a ... ;\"Linear\"(Default) ,\"Log\" ,\"LogLinear\" ,\"LogLog\"

runStep

runstep[graph, step, options] formats a call of duration step to NDSolve for a growing organ ... \n\nNote:runStep is called by runFixedInterval and is not designed to be called by the end user.

samePlot

samePlot[variables, sys, options] will plot a set of variables from a Cellerator run on the ... gives the name of variable containing the Cellerator System or the actual variable name itself.

samePlots

samePlots[{{var, var,...}, {var, var, ...},...}, sys, opt] plots each set of variables together on a single plot. Each sublist of varibables is plotted using samePlot.

sbml2ODEs