CompuCell3D:

CompuCell3D 15th User Training Workshop

August 3rd - August 9th, 2020


Quick Start Guides and Cheat Sheets

  1. Python Cheat Sheet: (get) (view)

  2. CompuCell3D (CC3D) Python Quick Reference Guide: (get) (view)

  3. Twedit menus.pdf

  4. CC3D menus.pdf (aka Player)

  5. Tellurium and libRoadRunner Quick Reference Guide: (get) (view)


On Line Help Pages

  1. CompuCell3D:
    1. CompuCell3D Python Manual

    2. Other CompuCell3D Manuals

  2. Tellurium:
    1. Tellurium Quick Start

    2. Tellurium Full Manual


Class Files

A. General

  1. Preliminary Class Schedule

  2. Slack student material channel

  3. Google Drive

B. YouTube Play Lists

  1. Day 1 Lecture Videos

  2. Day 2 Lecture Videos

  3. Day 3 Lecture Videos

  4. Day 4 Lecture Videos

  5. Links to individual YouTube videos are given in the listing below.

C. Monday Aug. 3, 2020, 11AM - 6PM EDT

  1. CC3D Course Lectures--Module 1.0 Welcome.pptx (YouTube)

  2. CC3D Course Lectures--Module 1.1 Getting Tools to Run.pptx (YouTube)

  3. CC3D Course Lectures--Module 1.2 Sample CC3D Simulationsv2.pptx (very large file) (YouTube)

  4. CC3D Course Lectures--Module 1.3 CC3D COVID Model.pptx (YouTube)

    • Link to the Covid-19 model in nanoHUB
      (This opens a new window. You may need to click the link a couple times to get through
      the login process and to get to the screen with the Launch Tool button.)

  5. CC3D Course Lectures--Module 1.4 CC3D COVID Model.pptx (YouTube)

  6. CC3D Course Lectures--Module 1.5 ODE Viral Infection Model in Tellurium.pptx (YouTube)

  7. CC3D Course Lectures--Module 1.end QA.pptx

  8. Day 1 Lecture Videos play list

D. Tuesday Aug. 4, 2020, 11AM - 6PM EDT

  1. CC3D Course Lectures--Module 2.0 Welcome to Day 2.pptx (YouTube)

  2. Continuing CC3D Course Lectures--Module 1.5 ODE Viral Infection Model in Tellurium Part II.pptx (YouTube)

  3. CC3D Course Lectures--Module 1.6 ODE to Spatial Models, Running ODEs in CC3D and Plotting.pptx (moved from Monday). (YouTube)

  4. CC3D Course Lectures--Module 2.1 ODE to Spatial Models Creating Epithelial Layer and Cell Type Transitions v2(1).pptx (YouTube)

  5. CC3D Course Lectures--Module 2.end QA.pptx

  6. CC3D Course Lectures--Module 3.5 How CC3D Does Calculations and Cell Division.pptx

  7. Day 2 Lecture Videos play l list

E. Wednesday Aug. 5, 2020, 11AM - 6PM EDT

  1. CC3D Course Lectures--Module 3.0 Welcome to Day 3.pptx. (YouTube)

  2. CC3D Course Lectures--Module 2.1 ODE to Spatial Models Creating Epithelial Layer and Cell Type Transitions v2(1).pptx (continued) (YouTube)

  3. CC3D Course Lectures--Module 2.2 ODE to Spatial Part 2 Spatializing the Virus Diffusion Solver.pptx. (YouTube)

  4. CC3D Course Lectures--Module 2.3 ODE to Spatial Part 3 Adding Active Immune Cells Creating Cells Volume Adhesion.pptx. (YouTube)

  5. CC3D Course Lectures--Module 3.5 How CC3D Does Calculations and Cell Division.pptx (M. Swat)

  6. Day 3 Lecture Videos play list

F. Thursday Aug. 6, 2020, 11AM - 6PM EDT

  1. CC3D Course Lectures--Module 4.0 Welcome to Day 4.pptx. (YouTube)

  2. CC3D Course Lectures--Module 4.0 Welcome to Day 4 From Single Cell to Avascular Tumor_MaciekSwat.pptx (YouTube)

  3. CC3D Course Lectures--Module 2.4 ODE to Spatial Part 4 Controlling Cell Movement Chemotaxis and Random Motility.pptx Exercises on cell motility, chemotaxis and random motility and dependence on parameters (Dr. TJ Sego) (YouTube)

  4. CC3D Course Lectures--Module 3.1 ODE to Spatial Part 5 Contact Killing.pptx (Dr. TJ Sego) (YouTube)

  5. CC3D Course Lectures--Module 4.1 - Delta-Notch Models.pptx (Dr. Julio M. Belmonte) (YouTube)

  6. CC3D Course Lectures--Module 4.2 Embryonic Segmentation and Links.ppt (Dr. Priyom Adhyapok) (YouTube)

  7. CC3D Course Lectures--Module 4.3 CellCrawling.pptx (Dr. Gilberto L. Thomas)

  8. CC3D Course Lectures--Module 4.4 Parameter Scans and Cluster Execution_Maciek Swat.pptx (Dr. Maceik Swat)

  9. CC3D Course Lectures--Module 4.5 CC3D Best Practices and Parameters.pptx (Dr. James Sluka)

  10. Unitary model to modules (Dr. TJ Sego)
  11. CC3D Course Lectures--Module 4.7 Releasing CompuCell3D Models in NanoHUb.pptx

  12. Day 4 Lecture Videos play list

G. Friday Aug. 7, 2020, 11AM - 6PM EDT Hackathon

  1. CC3D Hackathon--Module 5.0 Welcomev2_JAG.pptx

H. Saturday Aug. 8, 2020, 11AM - 6PM EDT Hackathon

  1. CC3D Hackathon--Module 6.0 Welcome.pptx

I. Sunday Aug. 9, 2020, 11AM - 6PM EDT Hackathon

  1. CC3D Hackathon--Module 7.0 Welcome.pptx

CompuCell3D: CC3D_2020_class_files (last edited 2020-08-09 15:05:36 by JamesSluka)