1 General Introduction

1.1 Why Modeling?

What is so special about modeling and why do we think we need computational modeling in neuroscience? What is the relationship with experimental neuroscience?

1.2 History of GENESIS

1. G-2 architecture.
2. Models and software extensions (technologies).
3. Purkinje cell model lineage.
4. How do we advance the formal records of neuroscience? What is required for the next generation simulator? What impact will this have on scientific communication and publication?

1.3 Simulator Archetypes

1. Technical Axis
   • Open vs Closed & Extensibility: how easy is to contribute to the simulator code?
   • Future orientation: who easy is it to interface with future technologies?
2. Community Axis
   • Level of support for Biological modeling as opposed to purely mathematical modeling?
   • Workflow Orientation: is model development well structured ? how easy is it to disassemble model descriptions? how clear is the separation between the model of the biology and periphery code?
   • Model Sharing: how open-minded / protective is the user-community?

2 Basic Concepts

1. Using the G-3 User Workflow for single-compartment and multi-compartment modeling and simulation.
2. Advanced use:
   1. Querying a model.
   2. Setting up the simulation.
   3. Running batch simulations.

3 What is currently in G-3?

See release notes.

4 Setting up Collaborations

4.1 An Architecture for a Heterogeneous Community

See CBI Architecture.

1. New Software Components as CBI Architecture Extensions allow third parties to develop new components independently.
2. Coarsely grained extension: SSP plugins and simulation objects.
3. Finely grained extensions:
   1. Extending the Model Container (for more details see here).
   2. Extending the compartmental solver.
   3. Extending the G-3 Shell.

4.2 The Documentation and Publishing System

• Documentation Framework: Levels of Documentation
• Documentation separation for separate software systems / components. Third party software and documentation can be maintainted independently, and integrated into the G-3 software and documentation system by correct configuration of G-3.
• Documentation Integration
  • Document Creation.
  • Dynamic Integration.
  • External documents are declared using document descriptors.
  • Documentation Maintenance.

5 The Graphical User Interface

Presenters: Hugo Cornelis, Allan D. Coop, Mando Rodriguez, David Beeman, and James M. Bower.
Additional information:
G-3: http://www.genesis-sim.org/userdocs/documentation-homepage/documentation-homepage.html