Systems Biology Research Tool 2.0.0 API Specification

This document is the API specification for the Systems Biology Research Tool.

See:
          Description

Packages
plug_in_example.kernel  
plug_in_example.shell  
sbrt Provides the class used to run the Systems Biology Research Tool.
sbrt.ext Provides classes that allow the Systems Biology Research Tool to encapsulate external software.
sbrt.ext.cplex Provides a class that allows communication with CPLEX.
sbrt.ext.glpk Provides a class that allows communication with GLPK.
sbrt.ext.mma Provides classes that allow communication with Mathematica.
sbrt.ext.mma.algebra Provides classes that allow communication with Mathematica for the purposes of algebra.
sbrt.ext.R Provides classes that allow communication with R.
sbrt.ext.R.stat Provides classes that allow communication with R for the purposes of statistics.
sbrt.kernel Provides interfaces to define processes.
sbrt.kernel.fba Provides classes and interfaces for creating objects relevant to Flux Balance Analysis.
sbrt.kernel.fba.analysis Provides classes and interfaces for analyzing Flux Balance Analysis data.
sbrt.kernel.fba.comp Provides classes and interfaces for performing Flux Balance Analysis computations.
sbrt.kernel.fba.proc Provides classes and interfaces for executing Flux Balance Analysis processes.
sbrt.kernel.io Provides classes and interfaces used to perform kernel-level I/O.
sbrt.kernel.math Provides classes and interfaces for creating objects relevant to mathematics.
sbrt.kernel.math.algebra Provides classes and interfaces for creating objects relevant to algebra.
sbrt.kernel.math.algebra.proc Provides classes and interfaces for executing algebra-related processes.
sbrt.kernel.math.comb.comp Provides classes and interfaces for performing combinatorial analysis-related computations.
sbrt.kernel.math.comb.proc Provides classes and interfaces for performing combinatorial analysis-related processes.
sbrt.kernel.math.geom Provides classes and interfaces for creating objects relevant to computational geometry.
sbrt.kernel.math.geom.comp Provides classes and interfaces for performing geometry-related computations.
sbrt.kernel.math.geom.proc Provides classes and interfaces for performing geometry-related processes.
sbrt.kernel.math.graph_theory Provides classes and interfaces for creating objects relevant to graph theory.
sbrt.kernel.math.graph_theory.comp Provides classes and interfaces for performing graph theoretical computations.
sbrt.kernel.math.graph_theory.proc Provides classes and interfaces for performing graph theoretical processes.
sbrt.kernel.math.optimization Provides classes and interfaces for creating objects relevant to solving optimization problems.
sbrt.kernel.math.stat Provides classes and interfaces for creating objects relevant to statistics.
sbrt.kernel.math.stat.comp Provides classes and interfaces for performing statistical computations.
sbrt.kernel.math.stat.proc Provides classes and interfaces for performing statistical processes.
sbrt.kernel.utilities Provides classes and interfaces for performing utility functions.
sbrt.kernel.utilities.proc Provides classes and interfaces for performing utility processes.
sbrt.shell Provides classes used by shell-level software.
sbrt.shell.gui Provides classes for creating graphical user interfaces for the SBRT.
sbrt.shell.io Provides classes and interfaces for reading and writing files.
sbrt.shell.io.fba Provides classes and interfaces for reading and writing files relevant to Flux Balance Analysis.
sbrt.shell.mng Provides classes and interfaces for creating process managers.
sbrt.shell.mng.algebra Provides classes for creating algebra process managers.
sbrt.shell.mng.comb Provides classes for creating combinatorics process managers.
sbrt.shell.mng.fba Provides classes and interfaces for creating Flux Balance Analysis process managers.
sbrt.shell.mng.geom Provides classes and for creating geometry process managers.
sbrt.shell.mng.graph_theory Provides classes and for creating graph theoretical process managers.
sbrt.shell.mng.stat Provides classes and interfaces for creating statistical process managers.
sbrt.shell.mng.utilities Provides classes and interfaces for creating mathematical process managers.
sbrt.shell.proc.fba Provides classes for converting FBA-related files of different formats.
sbrt.shell.text Provides classes and interfaces for defining formats for basic objects.
sbrt.shell.text.chem Provides classes and interfaces for defining formats for chemistry related objects.
sbrt.shell.text.fba Provides classes and interfaces for defining formats for objects relevant to Flux Balance Analysis.
sbrt.shell.text.math Provides classes and interfaces for defining formats for mathematical objects.

 

This document is the API specification for the Systems Biology Research Tool.