1. Simulation Tools in Neuroscience
Ronald van Elburg
Neuroinformatics Group (A. van Ooyen)
11/26/2004
Simulation Tools in Neuroscience

2. Two Neuroscience Classifications
Organizational Levels
System
Connectivity
Maps
Networks
Neurons
Synapses
Channels
Transporters
Membrane
Proteins
Phenomena
Signaling
Computation
Plasticity
Learning
Development
11/26/2004
Simulation Tools in Neuroscience

3. Existing Simulation Environments
Organizational Level
Simulation Environment
System
Topographica
Catacomb
Morphology/Connectivity
L-Neuron
Neosim
Network
Matlab
NEST
Neuron
Neuron (110)
Genesis (3)
Surf-Hippo
SNNAP (15)
C/C++ (6)
XPP (2)
Synapses
CalC (Calcium Diffusion)
MCell (Molecular Dynamics)
11/26/2004
Simulation Tools in Neuroscience

4. Single Neuron: Compartmental Modeling
From "The Book of GENESIS" see:
11/26/2004
Simulation Tools in Neuroscience

5. Simulation Tools in Neuroscience
Neuron: Some Features
Implements Compartmental Modeling
Object Oriented Scripting Language (HOC)
Networks via Discrete Event Simulation
Extendable (NMODL)
IVTools based GUI
Basic Optimization (Praxis Algorithm)
107 Ready to Run Downloadable Models
11/26/2004
Simulation Tools in Neuroscience

6. Simulation Tools in Neuroscience
Model Invention I
High Dimensional Parameter Space
Ionic Currents
channel characteristics
channel densities
Morphology
lengths and diameters of cell substructures
pyramidal, interneuron and glial cell types
Connectivity
intercortical connections
intracortical connections
11/26/2004
Simulation Tools in Neuroscience

7. Simulation Tools in Neuroscience
Model Invention II
Resources
Databases
NeuronDB: Literature References
ModelDB: Complete Simulations
Literature
Mimicking Reality
Optimizer Tools
Heuristics
11/26/2004
Simulation Tools in Neuroscience

8. Neuroinformatics Challenges
Model Driven Simulations
Simulators for Changing Dimensions
Connectivity and/or Morphology Development in Interaction with Ionic Activity
Extracellular Space
Standardized Naming Conventions
Mixing Organizational and Abstraction levels
Visual Modeling
Heuristical Support in Simulation Environment
Optimization for Fast Changing Signals
11/26/2004
Simulation Tools in Neuroscience

9. Model Driven Simulations
Loosely Based on ideas from Model Driven Architecture ® by OMG®
Catacomb’s Specification with NeuroML has aspects of MDS
Neuroscience Objects and Protocols in
NeuroML
Mathematical Modeling
Mathematical Objects in
MathML
Discretization
Simulation Objects in
SimML?
Optimizer
Simulation Engines
Experimental Data
Data Analysis
Visualization
11/26/2004
Simulation Tools in Neuroscience

10. Simulation Tools in Neuroscience
Questions?
11/26/2004
Simulation Tools in Neuroscience