GENESIS: Documentation

Related Documentation:

Backward Compatibility

G-2 is a complicated software application, therefore being compatible with G-2 is a challenge. Clarity plays an important role in addressing any challenge, so let’s define what we mean with G-2 compatibility.

• G-2 is a simulator that is useful for batch jobs, taking input and producing output on a filesystem. A software application is G-2 black-box compatible when it produces the same output files as G-2, given the same input files.
• G-2 can be used as an interactive application, where the user issues commands, checks the output on the screen and takes further actions that depends on the output on the screen. An application is G-2 interactive compatible when it allows the user to issue those same commands and it prints the same information onto the screen.
• G-2 can be extended by users at the source code level. An application is G-2 extensible when it can be extended with the same source code as for G-2.

We currently have nice examples in the ns-sli test specification of G-2 black-box compatibility. For example, given the SLI scripts of the purkinje cell, they produce ascii output files with complex spikes and typical somatic responses to current injections. Some of the output files were generated using G-2 and are used by the regression tester to test the functionality G-3.

GENESIS-3 is fully backward compatible with GENESIS Release 2.3 for all functionality of Tutorial 9–The Purkinje Tutorial. In doing this, backward compatibility supports the major functionalities of the GENESIS Script Language Interpreter.

Scope

Importantly, backward compatibility is provided to enable GENESIS 2 scripts to be used in association with the reconfigured GENESIS. It is not designed to extend a pre-existing GENESIS 2 script with new functionality provided by GENESIS 3. Although this may be possible is some cases, the results are not currently guaranteed. Contact GENESIS Support if you require further details.

New Graphic Functionality

Functionality for the graphical objects of the XODUS library is now provided by the Studio and Project Browser in conjunction with the new GENESIS GUI.

Application

Backward compatibility is provided by NS-SLI (the Neurospaces Scripting Language Interpreter).

Functional and Unit Regression Tests

Regression test specification for backward compatibility can be found here.

Recognized GENESIS 2 Commands

The following commands are also recognized but exhibit a reduced functionality:

Unrecognized Commands

The following commands are not backward compatible with GENESIS 2. There are typically three reasons for this:

1. Commands are obsolete.
2. Equivalent commands are implemented in the Model Container.
3. Commands are associated with GENESIS 2 network implementation and control.

Regression Tests of Specific Functionality

• list_objects
• copy
• copy2
• copy3
• copy4
• foreachloop
• forendloop
• function_iftest
• ifelse
• setfield

Regression Tests of GENESIS 2 Functionality in Heccer

Regression tests of of the following functions in the Model Container can be found at here.

• c1c2p2
• channel1-nernst1
• channel2-nernst1
• double
• heccerreset
• kc
• passive
• pool-feedback
• pool-nernst
• pools
• springmass
• table-kc
• table-kdr
• tables

Regression Tests of Tools

• asc_file
• Purkinje Cell Model
• readcell
• Simplifying a Model with the Model Container

Further Documentation

Further documentation is available in Regression Testing of Backward Compatibility. For the output of regression testing of backward compatibility see here.