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.

Instructional materials

Wednesday, May 8
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
Annotating region on cell surface
Overview of CellBlender examples
Lipid raft model
Lotka-Volterra model

 
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

Copyright © 2019 National Center for Multiscale Modeling of Biological Systems. All Rights Reserved.

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