Agenda: Computational Methods for Spatially Realistic Microphysiological Simulations 2015

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Monday, April 27
8:30 - 9:00 Welcome and Introduction
9:00 - 10:00 Introduction to Spatial Modeling with MCell (part 1) (PDF, video)
10:00 - 10:15 Break
10:15 - 11:15 Introduction to Spatial Modeling with MCell (part 2) (PDF, video)
11:15 - 12:00 CellBlender Introduction and Demo (video)
12:00 - 1:00 Lunch Break (lunch will be provided)
1:00 - 5:00 Hands-on tutorials in PSC's Computer Training Center
 
Tuesday, April 28
8:30 - 9:15 Introduction to Rule-Based Modeling (PDF, video)
9:15 - 10:15

Short Talks on Atomizer, Visualization, and Rare Event Sampling Using the Weighted Ensemble Method

(PDF, pptx, PDF, video)

10:15 - 10:30 Break
10:30 - 11:15 Hands-on with RuleBender - Specifying a model, visualization, simulation, parameter scans
11:15 - 12:00 Extending rule-based models into space
12:00 - 1:00 Lunch Break (lunch will be provided)
1:00 - 5:00 Hands-on tutorials in Computer Training Center and/or work on your own projects (PDF)
 
Wednesday, April 29
8:30 - 9:30 Introduction to Generative Modeling with CellOrganizer (PDF, video)
9:30 - 10:00 Working with Diffeomorphic Models (pptx, video)
10:00 - 10:30 Break
10:30 - 11:00 Training of Ratio Model and Protein Patterns
11:00 - 12:00 Training of CellOrganizer Models - From Images to Models (pptx, video)
12:00 - 1:00 Lunch Break (lunch will be provided)
1:00 - 5:00 Hands-on tutorials in Computer Training Center and/or work on your own projects ( pptx )