(click the above to download the class brochure.)

CompuCell3D 17th User Training Workshop July 31st - August 7th, 2022

Class Links

• Student Material (slides, readings, demos, etc.) are on Google drive here (individual sessions are listed below).

• The complete set of daily slides are here.

• The class video recordings are all here (individual sessions are listed below).

• There is also the Workshop Slack channel.

Class Material

28 June 2022 Orientation Session

• Orientation Slides, and Video 1, Video 2 (same information in the two sessions).

Sunday 31 July 2022 Python Day

The videos are in the Day 0 Folder.

• Module 0.0 Welcome

• Module 0.1 Python Getting Started

• Module 0.2 Python Sequence Types

• Module 0.3 Python Basic Functions

• Module 0.4 Python Object Oriented Programming

• Module 0.E CompuCell3D nanoHUB and Desktop Setup

Monday 1 August 2022 Basics of CC3D

The videos are in the Day 1 Folder.

• Module 1.0 Day 1 Welcome

• Module 1.1 Introduction to CC3D Glazier 2022

• Module 1.2 IntroToPotts EMT and Contact Energies Belmonte 2022

• Module 1.3 Cell Shape Determinants Belmonte 2022

• Module 1.4 Cell Growth and Cell Division Thomas 2022

• Module 1.5 Day 1 Questions Glazier 2022

• Module 1.E Sample CC3D Simulationsv2 Glazier

Tuesday 2 August 2022 Forces and Chemical Fields

The videos are in the Day 2 Folder.

• Module 2.0 Day 2 Welcome

• Module 2.1 CC3D Applications and Modeling Approaches Glazier 2022

• Module 2.2 Chemical Fields 2022

• Module 2.3 Chemical Fields Secretion and Absorption

• Module 2.4 Cell Movement Under External Forces Thomas 2022

• Module 2.5 Day 2 Questions

• Module 2.E Hackathon Teaming Session

Wednesday 3 August Network Modeling in CC3D

The videos are in the Day 3 Folder.

• Module 3.0 Day 3 Welcome

• Module 3.1 Secretion Absorption Avascular Tumor

• Module 3.2 Coupling Cells and Fields Chemotaxis 2022

• Module 3.3 Introduction to Network Modeling with Antimony

• Module 3.4 Advanced Antimony Using Network Models in a MultiCellular Context

• Module 3.E Hackathon Teaming Session Day 3

Thursday 4 August Title Compartments and Links

The videos are in the Day 4 Folder.

• Module 4.0 Day 4 Welcome

• Module 4.1 Using Network Models in a MultiCellular Context Glazier 2022

• Module 4.2 Cell Compartments Belmonte 2022

• Module 4.3 Breakout Session Intermission Slide

• Module 4.3 Intro Slides

• Module 4.3.1 Cell Competition Banerjee and Carpenter 2022

• Module 4.3.2 Germinal Center Response Modeling Mu 2022

• Module 4.4 FPPLinks and ConvergetExtension

• Module 4.7 Releasing CompuCell3D Models in NanoHUb

• Module 4.E Hackathon Teaming Session Day 4

Friday 5 August 2022 Advanced Topics in CC3D

The videos are in the Day 5 Folder.

• Module 5.0 Day 5 Welcome

• Module 5.1 Links Epithelial Cells Tissue Folding Belmonte 2022

• Module 5.3.1 Palate Model Polarized Epithelium Hutson 2022

• Module 5.3.2 Cluster Size Distribution in Tumors Mukherjee 2022

• Module 5.3.3 Deploying CC3D Simulations as nanoHUB Tools Gianlupi 2022

• Module 5.3.4 Cell Lineage Tracking Adhyapok 2022

• Module 5.4 Dynamic Compartments and PCP Belmonte 2022

• Module 5.E Hackathon Teaming Session Day 5

Saturday 6 August 2022 Hackathon to Build Your Own Model Day 1

The videos are in the Day 6 Folder.

• Module 6.0 Hackathon Introduction

Sunday 7 August 2022 Hackathon to Build Your Own Model Day 2

The videos are in the Day 7 Folder.

• Module 7.0 Hackathon Introduction

Class announcement for the CompuCell3D 17th User Training Workshop (Online)

July 31st - August 7th, 2022

• The entire set of YouTube videos for the 2021 workshop are available here.

• The slides and other information are available on 2021 class's Google drive here.

Zoom links:

• Python class on Sunday: Zoom link

• Workshop Monday - Friday: Zoom link

• Hackathon Saturday (Sunday): Zoom link

Please make sure that the email address Compucell3d.iu@gmail.com is on your whitelist so it doesn't get marked as spam!

Pre-workshop Events:

Orientation meetings for the 2022 CC3D Workshop will be held in advance of the workshop on June 28th at 9:00 AM, 12:00 PM, and 6:00 PM (EST). If you are unable to attend one of these sessions, you can view the recordings on YouTube and download the slides at your convenience. The orientation will include a number of important links, a step-by-step tutorial on using CompuCell3D on nanoHub, as well as a preliminary course schedule.

A recording of the orientation meeting can be found on YouTube at the following link: https://youtu.be/lHlYHw8QxzU

Two hackathon discussion and teaming meetings will be held in advance of the workshop on July 13th and July 25th from 12:00–2:00 PM (EST). If you are planning to attend the hackathon, these meetings will be a good way to start thinking of a topic and find potential teammates with similar interests.

We recommend joining the Workshop's Slack group to discuss the course and hackathon ideas. Join here.

Page Index

• Contacts and Registration

• Intro to Python Class (optional)

• Tissue Modeling with CompuCell3D

• Model-Building Hackathon

• Class Announcement, fliers, etc.

• Supported by

Registration and Contacts:

To register please fill out the registration form.

If you have any questions please contact <compucell3d DOT iu AT gmail DOT com>

CompuCell3D.org | twitter: @CompuCell3D

Related workshops to consider:
July 18–11: Network Modeling Virtual Summer School & Symposium (link)
July 24–30: PhysiCell Workshop and Hackathon (link)

Intro to Python:

July 31st, 2022. 10:30 AM - 5:30 PM US Eastern time.

We will have a one day Python training class on Sunday August 1st. This class is optional and meant as an introduction and refresher course for programming in Python. if you are comfortable using Python this can be skipped.
The meeting is via Zoom here.

• Python Cheat Sheet

Tissue Modeling with CompuCell3D:

August 1nd - 5th, 2021. 10:30 AM - 5:30 PM US Eastern time.
The class is via Zoom here.

Model-Building Hackathon:

August 6th - 7th, 2021. 10:30 AM - 5:30 PM US Eastern time.
The class is via Zoom here.

Class Announcement, fliers, etc.:

(click to download)

Supported by:

• The Biocomplexity Institute of Indiana University
• The NIH (U24EB028887, R01GM122424)
• The NSF (NSF 1720625)