Module Hierarchy

fastSBMLCreator
- fastSBMLCreator.fastSBMLCreator
libModelSimilarity
- libModelSimilarity.bicluster
- libModelSimilarity.calc_bimatrix
- libModelSimilarity.cluster
- libModelSimilarity.compareModels
- libModelSimilarity.eTVSM
- libModelSimilarity.fake_annotations
- libModelSimilarity.hand_curated_clusters
- libModelSimilarity.html
- libModelSimilarity.okapicluster
- libModelSimilarity.qualifiers
- libModelSimilarity.similarity_query: Class implementing the wishes of Ron to query the libSBAnnotation in such a way, that it will return related resource entries having a certain similarity to the initially provided one.
- libModelSimilarity.stats
- libModelSimilarity.wolfscluster
libPyless
- libPyless.pyless
- libPyless.pyless2
- libPyless.pylessDerivVar: This module provides automatic differentiation for functions with any number of variables.
- libPyless.pylessOdeCompare
- libPyless.pylessPyscesStoich: PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net) Copyright (C) B.G.
libSBAnnotation
- libSBAnnotation.annotate
- libSBAnnotation.buildDB
- libSBAnnotation.config
- libSBAnnotation.database
- libSBAnnotation.database_new
- libSBAnnotation.file: custom file class with read progress
- libSBAnnotation.indexedTables
- libSBAnnotation.mydifflib
- libSBAnnotation.sbannotationSOAPserver: SOAP server for libSBAnnotation
- libSBAnnotation.sbannotationSOAPserver2: SOAP server for libSBAnnotation
- libSBAnnotation.sbo
- libSBAnnotation.stderr
- libSBAnnotation.tables: Classes implementing the tables of the semanticSBML database.
- libSBAnnotation.xmlobject: XMLObject - Allows XML files to be operated on like Python objects.
libSBtab
- libSBtab.Column
- libSBtab.Document
- libSBtab.Exception
- libSBtab.GenerateSBtab
- libSBtab.Helper: Module that provides some helping methods that do not really belong to one class alone but can be used in this central place
- libSBtab.IDMerge
- libSBtab.Parser: Parser Module
- libSBtab.Row
- libSBtab.Table: Table class for storing Rows
- libSBtab.Validator: Classes for Row validations
- libSBtab.Value
- libSBtab.Warning
- libSBtab.convert
libTI2
- libTI2.aa: Script to test the new version of TIde with the arachnoic acid pathway.
- libTI2.add_new_kinetics
- libTI2.add_sboterms_to_sbml
- libTI2.global_options
- libTI2.laotide
- libTI2.model
  - libTI2.model.additional_information_handler
  - libTI2.model.flat_formula_database_parser
  - libTI2.model.function_manipulation
  - libTI2.model.model: Class for holding the model structure of an SBML file.
  - libTI2.model.pre_defined_formulas
  - libTI2.model.rre_generator
  - libTI2.model.sboreader
- libTI2.optimize
  - libTI2.optimize.nnca
- libTI2.results
  - libTI2.results.consolewriter
  - libTI2.results.simulation_data_handler
- libTI2.solvers
  - libTI2.solvers.abstract_fortran_solver
  - libTI2.solvers.bestfortransolver
  - libTI2.solvers.copasisolver
  - libTI2.solvers.csolver
  - libTI2.solvers.dopri5solver
  - libTI2.solvers.eulsimsolver
  - libTI2.solvers.limexsolver
  - libTI2.solvers.lsodasolver
  - libTI2.solvers.lsodesolver
  - libTI2.solvers.radausolver
  - libTI2.solvers.seulexsolver
  - libTI2.solvers.solver
semanticSBML
- semanticSBML.Model: Interface to all functions in the semanticSBML core for one document actions
- semanticSBML.annotate: MIRIAM annotation manipulation this module provides classes for the manipulation of MIRIAM annotations of an SBML model or single SBML elements
- semanticSBML.balance
- semanticSBML.kegg2sbml
- semanticSBML.kineticizer
- semanticSBML.merge: Merging of Multiple SBML Models this module enables the merging of sbml models to merge two models an internal representation of the model is created the elements of the internal representatin are compared a list of matching elements is created interfaces for modyfieing the match list are provided matching elements can be in conflict interfaces for conflict resolution are provided if there are no conflicts or all conflicts are resolved the internal representation of the model is translated back into a new sbml model
- semanticSBML.merge_datamodel: Datamodel used for the merging
- semanticSBML.merge_logic
- semanticSBML.sbml2dot: Sbml2Dot converts a SBMLDocument into a .dot file.
- semanticSBML.sbmlcheck
- semanticSBML.sbmlmisc
- semanticSBML.sbo
- semanticSBML.xmlobject: XMLObject - Allows XML files to be operated on like Python objects.
semanticSBMLgui
- semanticSBMLgui.gui_main_ui
- semanticSBMLgui.gui_resources
- semanticSBMLgui.gui_view_annotate
- semanticSBMLgui.gui_view_balance
- semanticSBMLgui.gui_view_build
- semanticSBMLgui.gui_view_check
- semanticSBMLgui.gui_view_graph
- semanticSBMLgui.gui_view_merge: GUI views need for merging of models.
- semanticSBMLgui.gui_view_semanticSBML
- semanticSBMLgui.gui_views: B{Graphical User Interface Views} This module contains all views of a semanticSBML model.
- semanticSBMLgui.semanticSBML_gui_resource_rc
semanticSBMLui
- semanticSBMLui.CustomInteractiveConsole: Interactive Console a generic Interactive Console it is used for the console userinterface of semanticSBML
- semanticSBMLui.console_views: Console User Interface Views all views on a SBML file relevant for semantiSBML the views also contain the connection to the cotrollers that modifiy a SBML file
- semanticSBMLui.docmanager: Document-View-Manager actions on multiple documents
- semanticSBMLui.ui_resources