GENESIS: Documentation

Related Documentation:

Documentation Overview

There are currently seven levels of GENESIS documentation which can be accessed from the following links. These levels range from documentation required by the user to technical detail of a specific implementation.

Each level can include specifics about compatibility and portability. Because backward compatibility is defined as a user requirement, the documentation for backward compatibility falls under the first two levels.

• Level 1: Introductory Material
  Provides a comprehensive introduction to the use of the GENESIS software system. Documentation includes an introduction to Unix and the Linux Graphical Desktop, fundamentals of Computational Neuroscience, and basic tutorials on the concepts and use of GENESIS. Documentation at this level also guides the user in the choice of documentation necessary to implement research and educational models and simulations. Tutorials at this level are short and contain links to the user documentation required for specific types of projects.
• Level 2: User Guides and Documentation
  In depth documentation about specific functions of GENESIS in the context of advanced research projects.
• Level 3: Automated Use Cases
  Common use cases and examples of workflows. Provides a bridge between the functions visible to a user and the way those functions are implemented in the code. This level of documentation also guides technical developers through the code and defines a framework for communication between users and developers. Currently, this level of documentation is automatically generated from test cases.

  The following GENESIS software components have output defined for regression testing. Most of these tests are defined by use cases.

  • G-Shell (Interactive Command Line Shell)
  • Experiment (Experimental Protocols)
  • Heccer (Compartmental Solver)
  • Exchange (NeuroML and NineML Interchange)
  • Model Container
  • NS-SLI (GENESIS 2 Backward Compatibility SLI)
  • SSP (Simple Scheduler in Perl)
  • Studio (Visual Model Explorer)
  • Documentation System
• Level 4: Technical Guide Specification
  Technical outline and specification of the use of all GENESIS functions, commands and components.

  The tools related to software development such as the Neurospaces installer, can be documented via the Neurospaces wiki.

• Level 5: Algorithm Documentation
  This type of documentation contains outlines of the algorithms used in an implementation, their theoretical analysis and behavior, their edge cases, and an outline of the expected application programmers interface (API). Links to various publications and external documents are provided for most of the algorithms used.

  At a practical level, this documentation also includes the specification of basic unit tests. At present, there are no plans to implement these tests due to the maintenance cost for the developer.

• Level 6: Algorithm API Documentation This documentation includes source code documentation typically generated by Doxygen or a similar documentation extraction system. Documentation is focused on how to interface to the specific implementations of low-level algorithms. Doxygen also allows inclusion of implementation documentation.
• Level 7: Inline Source Code Documentation Typically this documentation is provided by inline source code comments with a focus on how a function or algorithm is implemented. It provides extensive cross referencing between implementation and the API of the same and other functions. Both the Doxygen system and Xrefactory provide this functionality.