This document gives an overview of priorities for official releases of the GENESIS 3 simulator. Items required for proper functioning of the simulator appear in this document as TODO items, and they disappear when they have been implemented. We are currently working on the first alpha release of GENESIS 3.0.
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The first alpha release of GENESIS 3 will have a focus on single cell modeling. Single cell simulations include simulations based on complex morphologies, active channels, current injection, voltage and dynamic clamp, synaptic and endogenous stimulation. Output can be membrane potentials, currents or ion concentrations. The G-Tube, the official GENESIS 3 GUI, is an integral part of the alpha release. Other GUIs for model exploration and result visualization are not included, and undocumented (e.g. the Neurospaces studio and the Neurospaces project-browser)1 .
The most important functions of GENESIS 3 for single cell modeling are:
To foster community building, also included are:
GENESIS 3 comes with two shells. One offers backward compatibility. The second shell replaces the first one and has the advantages that it offers better performance and integrates with the GENESIS 3 GUI.
The GENESIS 2 backward compatibility module of GENESIS 3 (NS-SLI) currently includes:
The publicly availabe Purkinje cell scripts of the De Schutter and Bower model are supported by the NS-SLI module.
Models created from GENESIS 2 scripts can be exported to the GENESIS 3 NDF modeling format.
The GENESIS 3 command shell is a simple replacement for the GENESIS 2 SLI. The GENESIS 3 command shell allows the user to define simple models from scratch and save them to declarative model definition files. Building complex models is supported by glueing together existing declarative model definition files.
The GENESIS 3 command shell to be shipped with the alpha release, has all functions needed to instantiate and run single cell models. The shell talks directly to the Model Container and SSP, and the Model Container and SSP talk to the experiment package (Experiment) and the compartmental solver (Heccer) as required.
The GENESIS 3 shell can import and combine models from GENESIS 2 scripts, NDF files, SWC morphologies and Perl or Python scripts.
It is also possible to export the models to NDF files, and to export configurations to SSP files. This facilitates batch simulations for research projects.
The included documentation introduces GENESIS 3, describes tutorials, gives technical descriptions of commands, and documents the layout and APIs of the source code.
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The tutorials are based on the GENESIS 2 tutorials and demonstrate the use of the NS-SLI to run simulations based on GENESIS 2 SLI scripts. They also show how the model programmed into the script can be exported to declarative NDF files for use with the more advanced features of GENESIS 3 such as the project browser.
Some features of the compartmental solver are not documented yet, and for completeness we briefly mention them here. These include:
The technical documentation describes the use of the GENESIS 3 simulator from a UNIX shell command line and from the GENESIS 3 shell. It also outlines the NDF file format. Examples are given for a simple Hodgkin-Huxley model and for a model with Ca pools. Technical documentation bridges between user documentation and developer documentation.
The developer documentation is meant for people who are interested in software development or other technical aspects of the GENESIS 3 simulator. This documentation is not included in the alpha release, but instead made available over the internet.
An experimental feature is the use of a community tool to document user requirements and user workflows.
The GENESIS 3 simulator uses tools of professional quality for automated installation, testing and reporting. An outline of the use of these tools can be found on the Neurospaces wiki. Briefly, the installation tool enable and simplify installation and upgrade of source code, as well as initiation of your own development projects that (optionally) can be integrated with GENESIS 3.
The test framework is a higly dynamic environment for stand-alone software component testing and software component integration testing. It compares test specifications and expected output with the output produced by the software applications.
The test specifications are included in the alpha release and can be exported to HTML and mirrored on a web server. The Neurospaces website has an HTML version of all tests. The testing tool is integrated with the installation procedure. The Neurospaces wiki documents how to setup a testbot based on the installation scripts (neurospaces_build and neurospaces_cron).
The next release is planned for October 2009.