Scientific Program
Thursday March 23rd
10:30am - 4pm: Open Workshop on the future development of the GENESIS
simulation system.
The format of the workshop will be several short presentations on the status
and the design issues of various aspects of GENESIS 3 development. Each one
will followed by a period of moderated open discussion on related topics. The
purpose will be to solict opinions, ideas, and suggested development priorities
from GENESIS users and developers.
10:30 AM: Introduction to the Workshop:
Dr. James Bower: Overview - where we have been, where we are going
Dr. David Beeman: Planning the Development of GENESIS 3.0
Presentations and Moderated Open Discussion:
11:00 AM: Dr. Upinder Bhalla: The Design, Capabilities, and Status of MOOSE
Suggested discussion topics:
- GENESIS 2 non-graphical simulation objects and commands to re-implement
- Which ones can we omit?
- Development of documentation that will allow user/programmers to do some of this work, without detailed knowledge of the MOOSE code.
- Binary file format compatibility, Netcdf or alternatives
New features for GENESIS 3?
Adding various specialized commands
Markov Channels
Environment (e.g. rat maze, human arm ...)
Real-time hooks (for interaction with dynamic clamping)
Compilation for real time implementations, notably FPGAs
Script Language Interpreter
Completion of reimplementation started by Upi - any compatibility issues?
Removing UNIX-dependencies from parser commands (e.g, "more", "cd", etc.)
Alternate parsers - totally new (Python, Java, etc.) or improved SLI2 without curly brackets and other GENESIS 2 eccentricities.
Technical issues - how to "plug in" another parser?
12:00 - 1:00 PM: Break for lunch
1:00 PM: Mr. Josef Svitak: Graphical Interface Design
Suggested discussion topics:
GUI development to replace XODUS - design issues
What XODUS 2 widgets to reimplement, and how faithfully?
Degree of backwards compatibility with GENESIS 2 XODUS scripting language
(will be difficult to achieve full compatibility - how hard to try?)
SWING/non-SWING, JAVA version, etc.
(compromises betweeen usablility in a web browser and features available with standalone operation)
Interfaces between JAVA code and MOOSE/computational core
Source code maintenance, development process, etc.
Coordination of MOOSE and GENESIS repositories
- Modularization of MOOSE and GENESIS code development
- Do we need a separate Windows code base.
CVS or Subversion for version control?
Use of GNU autoconfigure instead of editing Makefiles?
- How would this apply to Windows?
Can we have automatic upgrades like Linux distros do?
Test scripts
IDE (Integrated Design Environment) for constructing and debugging simulations
Automatic code generation?
Equivalents for Neurokit, Kinetikit, and Netkit.
Total environment for generating simulation scripts, including widget layout?
2:00 PM: Dr. Sharon Crook: NeuroML, the XML for neuronal simulation project
Suggested discussion topics:
* Model representation
Transition from readcell to NeuroML representation
Channel representation
Signaling model representation using SBML
Network representation
Automatic loading of model parts from internet
Database of channels and models.
Simulation database management
3:00 Dr. Greg Hood: HPC and Neural Simulation: Capacity for large scale models
Suggested discussion topics:
Parallel/Scheduling issues
Major design decision to make: Should we restrict SMP to solvers?
Need to set up queue-based API for parsers, shell and GUI to run on threads.
Implicit solvers for compartmental models
Should be fast, transparent, easy to use - no chanmodes!
Should also be flexible: easy to add new channels that solver does not know.
Design of multiple solvers
Design and development toward wrappers for other simulators.
Who will do the implementation?
4:00 - 4:30 PM: Wrapup discussion (moderated by Dave Beeman)
5:00 pm - 7:00 pm: Grand opening of the San Antonio Computational Biology
Initiative
(transportation provided to UTSA).
Friday March 24th
9:00 am - 5:00 pm: General session on realistic modeling (program to be announced
shortly)
5:00 pm: Special presentation commemorating the contribution of Wil Rall to
computational neuroscience
7:00 pm - 12:00 pm: Poster session
Saturday March 25th
9:00 am - 5:00 pm: Special session on computation in the olfactory system
7:00 pm - whenever: Banquet at the Buckhorn
Museum and Salon
Schedule with Titles and Abstracts
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