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
1.2 History of GENESIS
- G-2 architecture.
- Models and software extensions (technologies).
- Purkinje cell model lineage.
- 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
- Technical Axis
- Open vs Closed & Extensibility: how easy is to contribute to the
- Future orientation: who easy is it to interface with future
- Community Axis
- Level of support for Biological modeling as opposed to purely
- 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
2 Basic Concepts
- Using the G-3 User Workflow for single-compartment and
multi-compartment modeling and simulation.
- Advanced use:
- Querying a model.
- Setting up the simulation.
- 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.
- New Software Components as CBI Architecture Extensions allow
third parties to develop new components independently.
- Coarsely grained extension: SSP plugins and simulation objects.
- Finely grained extensions:
- Extending the Model Container (for more details see here).
- Extending the compartmental solver.
- 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.