This is the official, full agenda for the 2022 PhysiCell Workshop and Hackathon.
All times are US Eastern Click here to see the current US Eastern date and time.
last updated: Sunday, July 24, 2022
Events marked "H" are exclusive to accepted hackathon participants. All others are publicly accessible. Wherever possible, we will post full slides and video recordings for all sessions.
To arrive prepared, all workshop participants should work through the pre-workshop materials prior to Monday, July 25th.
- Slides: click here
- Video: click here
- Slides: click here
- Video: click here
Linux users can most likely skip setup g++ and Python setup, but they should download PhysiCell 1.10.4 (or later) to test that they can compile and run the sample projects. See either the Windows or MacOS guide for details.
You can get setup help in our dedicated Slack workspace.
We use a dedicated Slack workspace for annoucements, troubleshooting, and other (asynchronous) community activities. Join at:
https://join.slack.com/t/physicellcomm-sf93727/shared_invite/zt-qj1av6yd-yVeer8VkQaNDjDz7fF00jA
We will use Gather as our virtual conference space, particularly to help navigate between zoom rooms for the virtual hackathon and breakout sessions. Details will be sent by email to full participants.
- Slides: click here
- Video: click here
- Slides: click here
- Video: click here
Template slide deck to introduce yourself in the virtual social hours.
- Slides: click here
Introduce yourself and meet your fellow participants in this virtual social. You will receive the link by email and in Gather.
Please prepare your 4 minute mini introduction using this template
Introduce yourself and meet your fellow participants in this virtual social. You will receive the link by email and in Gather.
Please prepare your 4 minute mini introduction using this template
Welcome participants, give the overall format, and discuss goals for the week.
Give an introduction to modeling with PhysiCell using built-in sample projects, including basic data visualization and data access in Jupyter notebooks.
- Slides: click here
- Code:
- Example 1 config file: click here
- Example 2 config file: click here
- Jupyter notebook: click here
- Video: click here
Take a virtual coffee break in Gather to mix and meet with your fellow participants.
Learn about cell phenotype in PhysiCell. Modulating cell phenotype in response to microenvironmental and other signals is key to agent-based modeling in PhysiCell. We will also introduce cell signal and behavior dictionaries for more intuitive model development.
- Slides: click here
- Video: click here
Take a virtual coffee break in Gather to mix and meet with your fellow participants.
Work through two complete modeling examples from start to finish. This session will focus on defining multiple cell definitions in a model of clonal competition in a tumor. It will also define a model of innate immune response to invading bacteria. These intermediate-level models can be built completely through XML markup via a graphical interface with no additional C++.
- Slides: click here
- Code: click here
- Video: click here
Take a virtual coffee break in GatherTown to mix and meet with your fellow participants.
Start brainstorming for hackathon projects with your fellow workshop participants.
Join two of last year's teams for brief demonstrations and Q&A on their projects.
Please use Gathe to continue getting to know your fellow participants.
Learn about how to work with boundary conditions, custom cell variables, and users parameters. Learn how to search for and access custom variables, user parameters, cell definitions, and microenvironment substrates from within C++ in a PhysiCell project.
- Slides: click here
- Video: click here
To reduce Zoom fatigue sessions like this have been moved to asynchronous to watch at your own convenience. Please watch prior to the start of synchronous Day 2 activities.
Learn about how to work with boundary conditions, custom cell variables, and users parameters. Learn how to search for and access custom variables, user parameters, cell definitions, and microenvironment substrates from within C++ in a PhysiCell project.
- Slides: click here
- Video: click here
To reduce Zoom fatigue sessions like this have been moved to asynchronous to watch at your own convenience. Please watch prior to the start of synchronous Day 2 activities.
Discuss the day's goals.
Learn how to write custom C++ cell functions in PhysiCell, and use them to write dynamical cell phenotypes that vary with microenvironmental conditions. This is the basis for turning your cell biological hypotheses into agent rules that can dynamicaly change cell phenotype in response to signals.
- Slides: click here
- Code: click here
- Zoom: https://iu.zoom.us/j/83603978310
Take a virtual coffee break in Gather to mix and meet with your fellow participants.
Learn how to make cells communicate by chemical and contact interactions.
- Slides: click here
- Code: click here
- Zoom: https://iu.zoom.us/j/83603978310
Take a virtual coffee break in Gather to mix and meet with your fellow participants.
We will present clustering of main ideas generated in Round 1 brainstorming to prepare for continued project brainstorming.
Continue to generate and refine project ideas.
Briefly summarize the refined brainstorming for each group.
Take a virtual coffee break in Gather to mix and meet with your fellow participants.
Start forming teams for your hackathon project.
Briefly summarize team formation results.
Take a virtual coffee break in Gather to mix and meet with your fellow participants.
Continue forming teams for the hackathon projects.
Discuss the day's progress and set the stage for Day 3.
Learn to interactively visualize 3-D simualtion data with Simularium (Allen Cell Institute).
- Slides: click here
- Code: click here
- Zoom: https://iu.zoom.us/j/83603978310
Please use Gather to continue getting to know your fellow participants.
Learn about 3-D visualization with the FURY framework.
- Slides: click here
- Code: click here
- Video:
Learn about the PhysiBoSS extension (Barcelona Supercomputing Center and Institute Curie) to PhysiCell that lets you incorporate Boolean signaling networks in each cell agent, and connect these with signals in the tissue environment and the cell's behavioral phenotype. Please note that this session is necessary for the next day's content.
- Slides: click here
- Video: click here
To reduce Zoom fatigue sessions like this have been moved to asynchronous to watch at your own convenience. Please watch prior to the start of synchronous Day 3 activities.
Learn about the PhysiBoSS extension to PhysiCell that lets you incorporate Boolean signaling networks in each cell agent, and connect these with signals in the tissue environment and the cell's behavioral phenotype. Please note that this session is necessary for the next day's content.
- Slides: click here
- Video: click here
To reduce Zoom fatigue sessions like this have been moved to asynchronous to watch at your own convenience. Please watch prior to the start of synchronous Day 3 activities.
Discuss the day's goals.
Continue to learn to integrate Boolean signaling networks with PhysiCelll in this fully guided walk-thru.
- Slides: click here
- Code: click here
- Zoom: message Paul Macklin or Furkan Kurtoglu for details
Take a virtual coffee break in Gather to mix and meet with your fellow participants.
Learn how to write intracellular models (systems of ODEs) in cancer cell agents. Work through a cancer metabolism example.
- Zoom: message Paul Macklin or Furkan Kurtoglu for details
Take a virtual coffee break in GatherTown to mix and meet with your fellow participants.
Continuing learning how to write intracellular models (systems of ODEs) in cancer cell agents. Work through a cancer metabolism example.
- Zoom: message Paul Macklin or Furkan Kurtoglu for details
Take a virtual coffee break in Gather to mix and meet with your fellow participants.
Work with your team on your project in Gather / Zoom breakout. Work on brief presentations of your team's plans
- Instructions: click here
Take a virtual coffee break in Gather to mix and meet with your fellow participants.
Briefly present your team's plan and get feedback from workshop participants.
Discuss the day's progress and set the stage for Day 3.
Please use Gather to continue getting to know your fellow participants.
Learn about sharing PhysiCell models as cloud-hosted, "zero-install" models on nanoHUB.
See additional examples of more advanced cell-cell contacts and interactions, such as spring interactions and juxtacrine signaling.
To reduce Zoom fatigue sessions like this have been moved to asynchronous to watch at your own convenience. Please watch prior to the start of synchronous Day 4 activities.
See additional examples of more advanced cell-cell contacts and interactions, such as spring interactions and juxtacrine signaling.
To reduce Zoom fatigue sessions like this have been moved to asynchronous to watch at your own convenience. Please watch prior to the start of synchronous Day 4 activities.
Discuss the day's goals
Work with your team in Gather / Zoom.
Share your team's preliminary results in Gather / Zoom.
Please use Gather to continue getting to know your fellow participants.
Discuss the day's goals
Work with your team in Gather / Zoom. Schedule breaks on your own as needed.
Discuss the day's progress and set the stage for group presentations.
Please use Gather to continue getting to know your fellow participants.
Brielfy present your team's project results for the community and for consideration for prizes. Detailed schedule TBA.
25 minute presetation, with 5 minutes of Q&A.
Adapt as you see best:
- Model presentation template click here
- Tool presentation template click here