= CompuCell3D 15th User Training Workshop =

=== August 3rd - August 9th, 2020 ===

------

== Quick Start Guides and Cheat Sheets ==
 1. Python Cheat Sheet: [[attachment:python_cheat_sheet_py3.pdf|(get) |&do=get]] [[attachment:python_cheat_sheet_py3.pdf|(view)|target=_blank]]

 1. CompuCell3D (CC3D) Python Quick Reference Guide: [[attachment:cc3d_quick_reference_guide.pdf|(get)|&do=get]]  [[attachment:cc3d_quick_reference_guide.pdf|(view)|target=_blank]]

 1. [[attachment:Twedit menus.pdf|Twedit menus.pdf|&do=get]]

 1. [[attachment:cc3d menus.pdf|CC3D menus.pdf (aka Player)|&do=get]]

 1. Tellurium and libRoadRunner Quick Reference Guide: [[attachment:TellRoadCheatSheet.pdf| (get)|&do=get]] [[attachment:TellRoadCheatSheet.pdf|(view)|target=_blank]]

------

== On Line Help Pages ==
 1. CompuCell3D:
  1. [[https://pythonscriptingmanual.readthedocs.io/en/4.1.1/|CompuCell3D Python Manual|target=_blank]]
  1. [[https://compucell3d.org/Manuals|Other CompuCell3D Manuals|target=_blank]]

 1. Tellurium:
  1. [[https://tellurium.readthedocs.io/en/latest/quickstart.html|Tellurium Quick Start|target=_blank]]
  1. [[https://tellurium.readthedocs.io/en/latest/index.html|Tellurium Full Manual|target=_blank]]

------

== Class Files ==
==== A. General ====
 1. [[attachment:CC3D class schedule 2020 BRIEF.pdf|Preliminary Class Schedule|&do=get]]
 1. [[https://multiscalemod-ags3330.slack.com/archives/C018H1EPUBB|Slack student material channel]]
 1. [[https://drive.google.com/drive/folders/18b5lTDBQrAe765wddu_eMw3PgLYTEvKz?usp=sharing|Google Drive]]

==== B. YouTube Play Lists ====

 1. [[https://www.youtube.com/playlist?list=PLmj-KAP6Sc2TjGWCNabKk6-wRw05MLriC|Day 1 Lecture Videos|target=_blank]]
 1. [[https://www.youtube.com/playlist?list=PLmj-KAP6Sc2RpKeNxIGVhIJvWomSImzc7|Day 2 Lecture Videos|target=_blank]]
 1. [[https://www.youtube.com/playlist?list=PLmj-KAP6Sc2S4w3h6Te_6cMeNSnHXQvx7|Day 3 Lecture Videos|target=_blank]]
 1. [[https://www.youtube.com/playlist?list=PLmj-KAP6Sc2R3JHGyL2UDuhlsoJve9sXI|Day 4 Lecture Videos|target=_blank]]
 1. Links to individual !YouTube videos are given in the listing below.


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

  1. [[attachment:CC3D Course Lectures--Module 1.0 Welcome.pptx|CC3D Course Lectures--Module 1.0 Welcome.pptx|&do=get]]  ([[https://www.youtube.com/watch?v=TtKwwb6G4KQ&list=PLmj-KAP6Sc2TjGWCNabKk6-wRw05MLriC&index=2&t=0s|YouTube|target=_blank]])

  1. [[attachment:CC3D Course Lectures--Module 1.1 Getting Tools to Run.pptx|CC3D Course Lectures--Module 1.1 Getting Tools to Run.pptx|&do=get]]  ([[https://www.youtube.com/watch?v=FTHJTWXEf48&list=PLmj-KAP6Sc2TjGWCNabKk6-wRw05MLriC&index=3&t=0s|YouTube|target=_blank]])
    * [[attachment:Angiogenesis.zip|Angiogenesis.zip|&do=get]]
    * [[attachment:Twedit menus.pdf|Twedit menus.pdf|&do=get]]
    * [[attachment:cc3d menus.pdf|CC3Dmenus.pdf (aka Player)|&do=get]]
    * [[attachment:Uploading & Downloading Files to NanoHub.pdf|Uploading & Downloading Files to NanoHub.pdf|&do=get]]
    * [[attachment:example_colonic_crypt.zip|example_colonic_crypt.zip|&do=get]]

  1. [[attachment:CC3D Course Lectures--Module 1.2 Sample CC3D Simulationsv2.pptx|CC3D Course Lectures--Module 1.2 Sample CC3D Simulationsv2.pptx|&do=get]] (very large file)  ([[https://www.youtube.com/watch?v=KdQs0_i88l4&list=PLmj-KAP6Sc2TjGWCNabKk6-wRw05MLriC&index=4&t=0s|YouTube|target=_blank]])

  1. [[attachment:CC3D Course Lectures--Module 1.3 CC3D COVID Model.pptx|CC3D Course Lectures--Module 1.3 CC3D COVID Model.pptx|&do=get]]  ([[https://www.youtube.com/watch?v=pz_aW0Dfq20&list=PLmj-KAP6Sc2TjGWCNabKk6-wRw05MLriC&index=5&t=0s|YouTube|target=_blank]])
    * [[https://nanohub.org/tools/cc3dcovid19|Link to the Covid-19 model in nanoHUB|target=_blank]]<<BR>>(This opens a new window. You may need to click the link a couple times to get through <<BR>>the login process and to get to the screen with the '''Launch Tool''' button.)

  1. [[attachment:CC3D Course Lectures--Module 1.4 CC3D COVID Model.pptx|CC3D Course Lectures--Module 1.4 CC3D COVID Model.pptx|&do=get]]  ([[https://www.youtube.com/watch?v=Ff-ogXc1EjM&list=PLmj-KAP6Sc2TjGWCNabKk6-wRw05MLriC&index=6&t=0s|YouTube|target=_blank]])
    *  Download a simple version in a zip file to run on your local machine: [[attachment:Model.zip|Download this model in a zip file|&do=get]].
    * Download the complete model repository from !GitHub as of 3 Aug 2020: [[attachment:covid-tissue-response-models-master.zip|covid-tissue-response-models-master.zip|&do=get]] 

  1. [[attachment:CC3D Course Lectures--Module 1.5 ODE Viral Infection Model in Tellurium.pptx|CC3D Course Lectures--Module 1.5 ODE Viral Infection Model in Tellurium.pptx|&do=get]]  ([[https://www.youtube.com/watch?v=Qxngw-ZWYfA&list=PLmj-KAP6Sc2TjGWCNabKk6-wRw05MLriC&index=7&t=0s|YouTube|target=_blank]])
    * The simple ODE model in Tellurium for nanoHUB as an iPython Notebook:  [[attachment:Exercise1.5.0.ipynb|Exercise1.5.0.ipynb|&do=get]] 
    * The complete and annotated processes of building the simple viral replication model in an iPython Notebook: [[attachment:How_to_write_viral_infection_model.ipynb|How_to_write_viral_infection_model.ipynb|&do=get]] 

  1. [[attachment:CC3D Course Lectures--Module 1.end QA.pptx|CC3D Course Lectures--Module 1.end QA.pptx|&do=get]]

  1. [[https://www.youtube.com/playlist?list=PLmj-KAP6Sc2TjGWCNabKk6-wRw05MLriC|Day 1 Lecture Videos play list|target=_blank]]


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

  1. [[attachment:CC3D Course Lectures--Module 2.0 Welcome to Day 2.pptx|CC3D Course Lectures--Module 2.0 Welcome to Day 2.pptx|&do=get]] ([[https://www.youtube.com/watch?v=kQXfDIL5rkU&list=PLmj-KAP6Sc2RpKeNxIGVhIJvWomSImzc7&index=1|YouTube|target=_blank]])
  
  1. '''Continuing''' [[attachment:CC3D Course Lectures--Module 1.5 ODE Viral Infection Model in Tellurium Part II.pptx|CC3D Course Lectures--Module 1.5 ODE Viral Infection Model in Tellurium Part II.pptx|&do=get]] ([[https://www.youtube.com/watch?v=9URBFpwEDzA&list=PLmj-KAP6Sc2RpKeNxIGVhIJvWomSImzc7&index=3&t=0s|YouTube|target=_blank]])
    * The complete and annotated processes of building the simple viral replication model in an iPython Notebook: [[attachment:How_to_write_viral_infection_model.ipynb|How_to_write_viral_infection_model.ipynb|&do=get]] 

  1. [[attachment:CC3D Course Lectures--Module 1.6 ODE to Spatial Models Running ODEs in CC3D and Plotting.pptx|CC3D Course Lectures--Module 1.6 ODE to Spatial Models, Running ODEs in CC3D and Plotting.pptx|&do=get]] '''(moved from Monday)'''. ([[https://www.youtube.com/watch?v=geR_vODZqOU&list=PLmj-KAP6Sc2RpKeNxIGVhIJvWomSImzc7&index=3|YouTube|target=_blank]])
   * [[attachment:CC3D Course Lectures--Module 1.6 CC3D Models.zip|Zip file containing the various versions of Josua's models|&do=get]] including the examples for modules 1.6, 2.1, 2.2, 2.3, 2.4 and 3.1.
   * [[attachment:Module_1.6.Version0.zip|Module_1.6.Version0.zip|&do=get]]

  1. [[attachment:CC3D Course Lectures--Module 2.1 ODE to Spatial Models Creating Epithelial Layer and Cell Type Transitions v2(1).pptx|CC3D Course Lectures--Module 2.1 ODE to Spatial Models Creating Epithelial Layer and Cell Type Transitions v2(1).pptx|&do=get]] ([[https://www.youtube.com/watch?v=IuH6idsmH8U&list=PLmj-KAP6Sc2RpKeNxIGVhIJvWomSImzc7&index=4|YouTube|target=_blank]])
   * [[attachment:Module_2.1.Version1.zip|Module_2.1.Version1.zip|&do=get]]
  
  1. [[attachment:CC3D Course Lectures--Module 2.end QA.pptx|CC3D Course Lectures--Module 2.end QA.pptx|&do=get]]

  1. [[attachment:CC3D Course Lectures--Module 3.5 How CC3D Does Calculations and Cell Division.pptx|CC3D Course Lectures--Module 3.5 How CC3D Does Calculations and Cell Division.pptx|target=_blank]]

  1. [[https://www.youtube.com/playlist?list=PLmj-KAP6Sc2RpKeNxIGVhIJvWomSImzc7|Day 2 Lecture Videos play l list|target=_blank]]


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

  1.  [[attachment:CC3D Course Lectures--Module 3.0 Welcome to Day 3.pptx|CC3D Course Lectures--Module 3.0 Welcome to Day 3.pptx|&do=get]]. ([[https://www.youtube.com/watch?v=wGXEYAbQTHI&list=PLmj-KAP6Sc2S4w3h6Te_6cMeNSnHXQvx7&index=2&t=0s|YouTube|target=_blank]])

  1. [[attachment:CC3D Course Lectures--Module 2.1 ODE to Spatial Models Creating Epithelial Layer and Cell Type Transitions v2(1).pptx|CC3D Course Lectures--Module 2.1 ODE to Spatial Models Creating Epithelial Layer and Cell Type Transitions v2(1).pptx|&do=get]] '''(continued)''' ([[https://www.youtube.com/watch?v=uj31CYiuCC0&list=PLmj-KAP6Sc2S4w3h6Te_6cMeNSnHXQvx7&index=2|YouTube|target=_blank]])
   *  [[attachment:Module_2.1.Version1.zip|Module_2.1.Version1.zip|&do=get]]

  1. [[attachment:CC3D Course Lectures--Module 2.2 ODE to Spatial Part 2 Spatializing the Virus Diffusion Solver.pptx|CC3D Course Lectures--Module 2.2 ODE to Spatial Part 2 Spatializing the Virus Diffusion Solver.pptx|&do=get]]. ([[https://www.youtube.com/watch?v=pXM7smSvi3I&list=PLmj-KAP6Sc2S4w3h6Te_6cMeNSnHXQvx7&index=3|YouTube|target=_blank]])
   *  [[attachment:Module_2.2.Version2.zip|Module_2.2.Version2.zip|&do=get]]

  1. [[attachment:CC3D Course Lectures--Module 2.3 ODE to Spatial Part 3 Adding Active Immune Cells Creating Cells Volume Adhesion.pptx|CC3D Course Lectures--Module 2.3 ODE to Spatial Part 3 Adding Active Immune Cells Creating Cells Volume Adhesion.pptx|&do=get]]. ([[https://www.youtube.com/watch?v=GTq4n26EXGs&list=PLmj-KAP6Sc2S4w3h6Te_6cMeNSnHXQvx7&index=4|YouTube|target=_blank]])
   * [[attachment:Module_2.3.Version3.zip|Module_2.3.Version3.zip|&do=get]]

  1. [[attachment:CC3D Course Lectures--Module 3.5 How CC3D Does Calculations and Cell Division.pptx|CC3D Course Lectures--Module 3.5 How CC3D Does Calculations and Cell Division.pptx|&do=get]] (M. Swat)
   *  All of the demo simulations in a zip  [[attachment:CC3D_Theory_Simulation_Files.zip|CC3D_Theory_Simulation_Files.zip|&do=get]]

  1. [[https://www.youtube.com/playlist?list=PLmj-KAP6Sc2S4w3h6Te_6cMeNSnHXQvx7|Day 3 Lecture Videos play list|target=_blank]]


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

  1. [[attachment:CC3D Course Lectures--Module 4.0 Welcome to Day 4.pptx|CC3D Course Lectures--Module 4.0 Welcome to Day 4.pptx|&do=get]]. ([[https://www.youtube.com/watch?v=GTq4n26EXGs&list=PLmj-KAP6Sc2S4w3h6Te_6cMeNSnHXQvx7&index=4|YouTube|target=_blank]])

  1. [[attachment:CC3D Course Lectures--Module 4.0 Welcome to Day 4 From Single Cell to Avascular Tumor_MaciekSwat.pptx|CC3D Course Lectures--Module 4.0 Welcome to Day 4 From Single Cell to Avascular Tumor_MaciekSwat.pptx|&do=get]] ([[https://www.youtube.com/watch?v=QaWtgyFlzJQ&list=PLmj-KAP6Sc2R3JHGyL2UDuhlsoJve9sXI&index=2|YouTube|target=_blank]])
   * [[attachment:CC3D Course Lectures--Module 4.1 From Single Cell to Avascular Tumor_MaciekSwat.pptx|Version 2 of PPT|&do=get]]
   * All of the demo simulations in a zip  [[attachment:CC3D_Theory_Simulation_Files.zip|CC3D_Theory_Simulation_Files.zip|&do=get]]

  1. [[attachment:CC3D Course Lectures--Module 2.4 ODE to Spatial Part 4 Controlling Cell Movement Chemotaxis and Random Motility.pptx|CC3D Course Lectures--Module 2.4 ODE to Spatial Part 4 Controlling Cell Movement Chemotaxis and Random Motility.pptx|&do=get]] Exercises on cell motility, chemotaxis and random motility and dependence on parameters (Dr. TJ Sego) ([[https://www.youtube.com/watch?v=0fh166Rmn1Q&list=PLmj-KAP6Sc2R3JHGyL2UDuhlsoJve9sXI&index=3|YouTube|Target=_blank]])
   * [[attachment:Module_2.4.Version4.zip|Module_2.4.Version4.zip|&do=get]]

  1. [[attachment:CC3D Course Lectures--Module 3.1 ODE to Spatial Part 5 Contact Killing.pptx|CC3D Course Lectures--Module 3.1 ODE to Spatial Part 5 Contact Killing.pptx|&do=get]]  (Dr. TJ Sego) ([[https://www.youtube.com/watch?v=ChjFU-hMJFU&list=PLmj-KAP6Sc2R3JHGyL2UDuhlsoJve9sXI&index=4|YouTube|target=_)blank]])
   * [[attachment:Module_3.1.Version5.zip|Module_3.1.Version5.zip|&do=get]]

  1. [[attachment:CC3D Course Lectures--Module 4.1 - Delta-Notch Models.pptx|CC3D Course Lectures--Module 4.1 - Delta-Notch Models.pptx|&do=get]] (Dr. Julio M. Belmonte) ([[https://www.youtube.com/watch?v=4GLSeaJ00YY&list=PLmj-KAP6Sc2R3JHGyL2UDuhlsoJve9sXI&index=5|YouTube|target=_blank]]) 
   * [[attachment:Julio's lecture examples.zip|Julio's lecture examples.zip|&do=get]]

  1. [[attachment:CC3D Course Lectures--Module 4.2 Embryonic Segmentation and Links.ppt|CC3D Course Lectures--Module 4.2 Embryonic Segmentation and Links.ppt|&do=get]] (Dr. Priyom Adhyapok) ([[https://www.youtube.com/watch?v=Demyr4XQYdI&list=PLmj-KAP6Sc2R3JHGyL2UDuhlsoJve9sXI&index=6|YouTube|target=_blank]]) 
   * [[attachment:priyom exercises.zip|Priyom's exercises.zip|&do=get]]

  1. [[attachment:CC3D Course Lectures--Module 4.3 CellCrawling.pptx|CC3D Course Lectures--Module 4.3 CellCrawling.pptx|&do=get]] (Dr. Gilberto L. Thomas)
   * [[attachment:Cell Crawling -- Compartmental Cells.zip|Cell Crawling -- Compartmental Cells.zip|&do=get]]
   * [[attachment:G_Thomas_crawling_cell.mp4|The crawling cell animation|&do=get]].

  1.  [[attachment:CC3D Course Lectures--Module 4.3 Parameter Scans and Cluster Execution_Maciek Swat.pptx|CC3D Course Lectures--Module 4.4 Parameter Scans and Cluster Execution_Maciek Swat.pptx|&do=get]] (Dr. Maceik Swat)
   *  [[attachment:ParameterScan.zip|ParameterScan.zip|&do=get]]

  1. [[attachment:CC3D Course Lectures--Module 4.5 Best Practices and Parameters.pptx|CC3D Course Lectures--Module 4.5 CC3D Best Practices and Parameters.pptx|&do=get]] (Dr. James Sluka)
   * Zip file with an example CC3D model  [[attachment:CC3D_parameters_example.zip|CC3D_parameters_example.zip|&do=get]]
   * [[attachment:Module 4.6 Best Practices and Parameters Excercise.pdf|Module 4.6 Best Practices and Parameters Excercise.pdf|&do=get]]

  1. Unitary model to modules (Dr. TJ Sego)

  1. [[attachment:CC3D Course Lectures--Module 4.7 Releasing CompuCell3D Models in NanoHUb.pptx|CC3D Course Lectures--Module 4.7 Releasing CompuCell3D Models in NanoHUb.pptx|&do=get]]

  1. [[https://www.youtube.com/playlist?list=PLmj-KAP6Sc2R3JHGyL2UDuhlsoJve9sXI|Day 4 Lecture Videos play list|target=_blank]]

==== G. Friday Aug. 7, 2020,  11AM - 6PM EDT Hackathon ====
  1. [[attachment:CC3D Hackathon--Module 5.0 Welcomev2_JAG.pptx|CC3D Hackathon--Module 5.0 Welcomev2_JAG.pptx|&do=get]]
   * [[attachment:Model Definition & Roadmapping Guide.docx|Model Definition & Roadmapping Guide.docx|&do=get]]
   *  [[attachment:Workflow for Developing Mechanism-Based Computational Biology Models (Article).docx|Workflow for Developing Mechanism-Based Computational Biology Models (Article).docx|&do=get]]

==== H. Saturday Aug. 8, 2020,  11AM - 6PM EDT Hackathon ====
  1.  [[attachment:CC3D Hackathon--Module 6.0 Welcome.pptx|CC3D Hackathon--Module 6.0 Welcome.pptx|&do=get]]

==== I. Sunday Aug. 9, 2020,  11AM - 6PM EDT Hackathon ====
  1.  [[attachment:CC3D Hackathon--Module 7.0 Welcome.pptx|CC3D Hackathon--Module 7.0 Welcome.pptx|&do=get]]