Documentation Overview

Publications

Publications related to semanticSBML can be found here.

For users

User's manual This short description of semanticSBML will help you get started.

Exercises Suggestions for trying out some features of semanticSBML.

Limitations of the current version A list of SBML features that are not yet supported by semanticSBML.

Frequently asked questions Some facts about annotations and model merging.

For advanced users

Resource Files The program semanticSBML has several resource files that can be configured by a user to keep up with the development of the SBML format. These files can be found in the .semanticSBML directory which is located in the home directory of your user account.

For programmers

Annotation Classes Here you find additional documentation for the annotation classes. It also includes a short description of the SBML MIRIAM annotation.

Merge Classes Here you find additional documentation for the merge classes. The documentation describes the concept of the semanticSBML merge process.

Custom Interactive Console The console interface (not part of the beta release) is based on a module that creates an interactive shell (similar to the Python interactive shell). The interactive shell can be used independently of semanticSBML.

Source Code The source code has been documented using epydoc; an automatically generated documentation can be found here.