Computational Systems Biology
Sauro Lab
University of Washington
Home  |   Downloads  |   News  |   Research  |   Papers  |   About Us  |   Contact Us  |   SBW Help   |   Jobs
     


What is SBW 
Research Impact 
Published Papers 
Lab Members 
Available Positions 
CSB Links 
Courses 
 
 
 
Software Downloads:

1. SBW
2. JDesigner
3. Jarnac
4. WinSCAMP
5. Matlab Interface
6. Optimization
6. Bifurcation
 
maintained by Frank Bergmann
 
 
 
 

Structural Analysis Module API

Service: StructAnalysis

string loadSBML(string)

Initialization method, takes SBML as input

string loadSBMLwithTests(string)

Initialization method, takes SBML as input

string analyzeWithLU()

Uses LU Decomposition for Conservation analysis

string analyzeWithLUandRunTests()

Uses LU Decomposition for Conservation analysis

string analyzeWithFullyPivotedLU()

Uses fully pivoted LU Decomposition for Conservation analysis

string analyzeWithFullyPivotedLUwithTests()

Uses fully pivoted LU Decomposition for Conservation analysis

double[][] getL0Matrix()

Returns L0 Matrix

double[][] getNrMatrix()

Returns Nr Matrix

double[][] getN0Matrix()

Returns N0 Matrix

double[][] getLinkMatrix()

Returns L, the Link Matrix

double[][] getK0Matrix()

Returns K0

double[][] getNullSpace()

Returns Nullspace

string[] getReorderedSpecies()

Returns the reordered list of species

string[] getReorderedSpeciesNamesList()

Returns the actual names of the reordered species

string[] getIndependentSpecies()

Returns the list of independent species

string[] getIndependentSpeciesNamesList()

Returns the actual names of the independent species

string[] getDependentSpecies()

Returns the list of dependent species

string[] getDependentSpeciesNamesList()

Returns the actual names of the dependent species

string[] getReactions()

Returns the list of Reactions

string[] getReactionsNamesList()

Returns actual names of the Reactions

double[][] getConservationLawArray()

Returns Gamma, the conservation law array

string[] getConservedEntities()

Returns algebraic expressions for conserved cycles

double[] getConservedSums()

Returns values for conserved cycles using Initial conditions

{} getInitialConditions()

Returns Initial Conditions used in the model

double[][] getStoichiometryMatrix()

Returns the original stoichiometry matrix

double[][] getReorderedStoichiometryMatrix()

Returns reordered stoichiometry matrix

string[] testConservationLaws()

Tests if conservation laws are correct

string getTestDetails()

Return Details about conservation tests

string getModelName()

Returns the name of the model

int getNumSpecies()

Returns the total number of species

int getNumIndSpecies()

Returns the number of independent species

int getNumDepSpecies()

Returns the number of dependent species

int getNumReactions()

Returns the total number of reactions

int getRank()

Returns rank of stoichiometry matrix

double getNmatrixSparsity()

Returns the number of nonzero values in Stoichiometry matrix

void setTolerance(double)

Set user specified tolerance

string getName()

Returns the name of the module

string getVersion()

Returns the version of the module

string getAuthor()

Returns the author of the module

string getDescription()

Returns the description of the module

string getDisplayName()

Returns the display name of the module

string getCopyright()

Returns the copyright of the module

string getURL()

Returns the URL of the module

 
sbw/structanalysis/api.txt · Last modified: 2007/01/12 07:20 (external edit)
 

    Home  |   About Us  |   Contact Us  |   Statistics
Recent changes RSS feed Creative Commons License Donate Powered by PHP Valid XHTML 1.0 Valid CSS Driven by DokuWiki