Agenda: Cell Modeling Workshop 2019

Workshop details: Home Apply | Agenda | Instructors

A laptop with the ability to install cell modeling software is required for the tutorial sessions. Instructions on how to install the workshop software will be posted soon.

 This agenda is tentative and subject to change.

 

Wednesday, May 8
8:30 - 9:00 Welcome and Introduction
9:00 - 10:00 Hands-on with CellBlender
10:00 - 10:15 Break
10:15 - 11:15 Basic models with CellBlender
11:15 - 12:00 Advanced models and parameter sweeps with CellBlender
12:00 - 1:00 Lunch Break (lunch will be provided)
1:00 - 2:00 Optimizing geometry with GAMer
3:00 - 5:00 Overview of MDL and pyMCell
 
Thursday, May 9
8:30 - 9:15 Introduction to Rule-Based Modeling (James Faeder)
9:15 - 10:15 Hands-on intro to RuleBender with basic models
10:15 - 10:30 Break
10:30 - 11:00 Continuing work with RuleBender
11:00 - 12:00 Developing a detailed model of CaMKII activation
12:00 - 1:00 Lunch Break (lunch will be provided)
1:00 - 1:30 Atomizer demo and hands-on
1:30 - 2:00 Visualization demo
2:00 - 2:30 Parameter estimation demo
3:00-5:00 Using MCell-R to perform spatial simulation of rule-based models
 
Friday, May 10
8:30 - 9:20 Introduction to Generative Modeling with CellOrganizer
9:20 - 10:00 Shape Modeling in CellOrganizer
10:00 - 10:30 Break
10:30 - 11:00 CellOrganizer Basics
11:00 - 12:00 Using CellOrganizer through Galaxy
12:00 - 1:00 Lunch Break (lunch will be provided)
1:00 - 5:00 Hands-on tutorials and/or work on your own projects

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