Agenda: Cell Modeling Workshop 2018
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, March 7 | |
|---|---|
| 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, March 8 | |
| 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, March 9 | |
| 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 |