GENESIS: Documentation

Related Documentation:

The GENESIS Graphic User Interface

Introduction

The GENESIS graphic user interface (G-Tube) provides an interactive environment for the construction, modification, and simulation of computational models of subcellular mechanisms, neurons and neural circuits. A demonstration session that runs a simulation with the G-Tube can be found here.

G-Tube is developed according to the principles of the Computational Biology Initiative Federated Software Architecture which is described in the GENESIS Overview. The underlying philosophy of the GUI’s modular software design is that it follows the GENESIS user work flow and supports the work flow’s five basic steps:

1. Create/import, explore, and save model.
2. Define simulation constants, inputs, and outputs.
3. Check, run, reset simulation, and save model state.
4. Check simulation output.
5. Iterate.

The block diagram given below illustrates the relationships between the software components that support this GUI functionality.

User Interface Functions:

gtube can be initiated from a UNIX prompt.

• gtube.py: This refers to the initiation of the Python/Perl enabled G-Tube from the command line of a terminal window.
• NS-SLI: This refers to the Neurospaces Script Language Interpreter that provides backward compatibility with the Script Language Interpreter of earlier versions of GENESIS.

The Diagnostic Translator (Simulator Object) is a middle ware software component that enables interaction between the user (via a given GUI component–G-Tube, G-Shell, or NS-SLI) and the Model Container, Experiment Library, Heccer, or SSP.

G-Tube Installation

G-Tube is a GUI implemented in Python which simplifies the use of GENESIS. It is currently under development so functionality is limited. Bugs and feature requests should be reported to the authors to ensure users are satisfied with the end result. Details

G-Tube Developer Repository

G-Tube is verisoned in mercurial and has a repository served over the internet to show the status of the latest checkins at the following website. http://repo-genesis3.cbi.utsa.edu/hg/g-tube/

Dependencies

To install G-Tube you need the following packages installed on your machine.

• Python 2.5: You can check the version you have installed with

  “python -V”

• wxPython: Version 2.8 or higher from:
  • wxPython site
  • Direct link to Sourceforge
• PyYAML: For data and configuration handling.
• PyOpenGL: For 3D support.

Building wxPython from source

To use wxPython you must first build wxWidgets, which is included with the wxPython source tarball. To build wxWidgets you’ll need the following libraries installed. To compile you’ll need g++.

• zlib-dev
• libjpeg-dev
• libpng-dev
• libtiff-dev
• libgtk-dev

If you want 3D bindings you’ll need:

• libglut-dev

Once wxWidgets is built be sure to run ldconfig. After building and setting up wxWidgets go into the wxPython directory and use the Python script setup.py to build and install the wxPython bindings.