Agenda: Computational Methods for Spatially Realistic Microphysiological Simulations
This agenda is subject to change.
View a print version of this agenda (Adobe PDF, 12 KB).
DAILY SCHEDULE, JUNE 6-9, 2006
Breakfast at hotel
Morning session, PSC Lecture Room (Room 103)
- 8:00 - 8:30 Informal Discussion & Questions
- 8:30 - 10:00 Lecture & Demos
- 10:00 - 10:30 Break & Discussion
- 10:30 - 12:00 Lecture & Demos
Lunch, 12:00 - 1:00, PSC Lecture Room (103 South Craig)
Afternoon session, PSC Computer Training Center (adjoins Lecture Room)
- 1:00 - 2:00 Instructor-led Tutorials
- 2:00 - 2:15 Break
- 2:15 - 3:30 Instructor-led Tutorials
- 3:30 - 4:00 Break/Discussion
- 4:00 - 5:00 Individualized Practice
TUESDAY, JUNE 6:
- Introduction to Microphysiological Modeling
- Software Pipeline, Data Structures and Organization
- Overview of PSC_DX, DReAMM, and MCell Architectures
- Overview of Visual Programming for Data Analysis & Visualization
- Introduction to Command-line Interfaces
- Overview of PSC Machines and Accounts
- Installing PSC_DX, DReAMM, and MCell
- DReAMM Basics
- Stereoscopic Animation Demos
WEDNESDAY, JUNE 7:
- Introduction to Monte Carlo Methods for Diffusion and Reaction in Solution
- 1st and 2nd Order Reactions, Kinetics, and Molecular Lifetimes
- Overview of MCell3 Model Description Language (MDL)
- MDL & Tutorial Focus:
- Chemical Reactions in Solution
- Use of 3-D Partitioning and Spatial Subvolumes
- Checkpointing
- Reaction Data Output
- Visualization Data Output
THURSDAY, JUNE 8:
- Diffusion-Reaction Problems in Complex Spaces
- Concepts and Practices for Surface Meshes
- MDL & Tutorial Focus:
- Mesh Objects, Mesh Regions, Surface Classes
- Mesh editing and MDL Export with DReAMM
- Advanced Mesh Rendering with DReAMM
FRIDAY, JUNE 9:
- Advanced Topics
- Time-dependent Rate Constants
- Mesh Refinement and Simplification
- Region Extraction, Region and Mesh Merging
- Placement of Individual Molecules
- Advanced counting options
- Experimental MCell3 Features
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