CompuCell3D 15th User Training Workshop

August 3rd - August 9th, 2020

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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)

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On Line Help Pages

1. CompuCell3D:

   1. CompuCell3D Python Manual

   2. Other CompuCell3D Manuals

2. Tellurium:

   1. Tellurium Quick Start

   2. Tellurium Full Manual

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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)

   • Angiogenesis.zip

   • Twedit menus.pdf

   • CC3Dmenus.pdf (aka Player)

   • Uploading & Downloading Files to NanoHub.pdf

   • example_colonic_crypt.zip

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)

   • Download a simple version in a zip file to run on your local machine: Download this model in a zip file.

   • Download the complete model repository from GitHub as of 3 Aug 2020: covid-tissue-response-models-master.zip

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

   • The simple ODE model in Tellurium for nanoHUB as an iPython Notebook: Exercise1.5.0.ipynb

   • The complete and annotated processes of building the simple viral replication model in an iPython Notebook: How_to_write_viral_infection_model.ipynb

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)

   • The complete and annotated processes of building the simple viral replication model in an iPython Notebook: How_to_write_viral_infection_model.ipynb

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

   • Zip file containing the various versions of Josua's models including the examples for modules 1.6, 2.1, 2.2, 2.3, 2.4 and 3.1.

   • Module_1.6.Version0.zip

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

   • Module_2.1.Version1.zip

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)

   • Module_2.1.Version1.zip

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

   • Module_2.2.Version2.zip

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

   • Module_2.3.Version3.zip

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

   • All of the demo simulations in a zip CC3D_Theory_Simulation_Files.zip

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)

   • Version 2 of PPT

   • All of the demo simulations in a zip CC3D_Theory_Simulation_Files.zip

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)

   • Module_2.4.Version4.zip

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

   • Module_3.1.Version5.zip

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

   • Julio's lecture examples.zip

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

   • Priyom's exercises.zip

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

   • Cell Crawling -- Compartmental Cells.zip

   • The crawling cell animation.

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

   • ParameterScan.zip

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

   • Zip file with an example CC3D model CC3D_parameters_example.zip

   • Module 4.6 Best Practices and Parameters Excercise.pdf

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

   • Model Definition & Roadmapping Guide.docx

   • Workflow for Developing Mechanism-Based Computational Biology Models (Article).docx

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