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 | |
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8:30 - 9:00 | Welcome and Introduction - (student intros, short overview of MMBioS) |
9:00 - 10:30 | RuleBender Introduction and Hands-On Example (James Faeder) |
10:30 - 10:45 | Break |
10:45 - 12:00 | CellBlender Introduction and Hands-On Example (Thomas Bartol) |
12:00 - 1:00 | Lunch Break (lunch will be provided) |
1:00 - 2:00 | CellOrganizer Introduction and Hands-On Example (Ivan Cao-Berg) |
2:00 - 5:00 |
Afternoon Exercises GAMer stuff - geometry repair |
Thursday, May 9 | |
8:30 - 9:30 | Introduction to Rule-Based Modeling (James Faeder) |
9:30 - 10:30 | Introduction to MCell's Algorithms (Thomas Bartol) |
10:30 - 10:45 | Break (Group Photo) |
10:45 - 12:00 | More examples from BNGTutorial (James Faeder) |
12:00 - 1:00 | Lunch |
1:00 - 2:00 | Introduction to MCell-R |
2:00 - 4:00 | Lab projects (problem solving at the drop of a hat) |
4:00 - 5:00 | Project presentations |
Friday, May 10 | |
8:30 - 9:30 | Introduction to Generative Modeling with CellOrganizer |
9:30 - 10:00 | Introduction to Cell Shape Modeling |
10:00 - 10:30 | Break |
10:30 - 11:00 | Simulations and the Generation of SBML Instances |
11:00 - 11:30 | CellOrganizer for Galaxy |
11:30 - 12:00 | CellOrganizer for Jupyter |
12:00 - 1:00 | Lunch Break (lunch will be provided) |
1:00 - 2:00 | CellOrganizer basics |
2:00 - 5:00 | Lab projects |
Additional topics:
CellBlender Geometry Construction (via Blender’s GUI) - 1 day
CellBlender Geometry Construction (algorithmic and imported) - 1/2 day
CellBlender Molecule-Reaction Basics - 1/2 day
CellBlender Counting/Plotting - 1/2 day
CellBlender Surface Classes - 1/2 day
CellBlender Dynamic Geometry - 1 day
Basic MDL - The language of MCell - 1 day
MDL Scripting in CellBlender - 1/2 day
Data Model Representation in CellBlender - 1/2 day
Data Model Scripting - How to build anything - 1/2 day
Neuron / MCell Coupling Demonstration - 1/4 day
Alternate Simulation Engines and Runners - 1/4 day
Galaxy Interface for Large Scale Processing - 1/4 day