This is the official, full agenda for the 2021 PhysiCell Workshop and Hackathon.
last updated: Sunday, July 18, 2021
Events marked "E" are exclusive to accepted participants. All others are publicly accessible. Wherever possible, we will post full slides and video recordings for all sessions.
Read and follow the appropriate guide for your operating system, found at:
https://github.com/physicell-training/ws2021
Linux users can most likely skip setup g++ and Python setup, but should download PhysiCell 1.9.0 to test that they can compile and run the sample projects. See either the Windows or MacOS guide for details.
We will continue to hold virtual office hours for testing your setup as noted in the workshop email. You can also 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 GatherTown as our virtual conference space, particularly to help navigate between zoom rooms for the virtual hackathon and breakout sessions. Details sent by email to full participants.
- Slides: click here
- Video: click here
- Slides: click here
- Video: click here
Introduce yourself and meet your fellow participants in this virtual social.
Please prepare your 4 minute mini introduction using this template
Introduce yourself and meet your fellow participants in this virtual social.
Please prepare your 4 minute mini introduction using this template
Welcome participants, give the overall format, and discuss goals for the week.
- Slides: click here
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: click here
- Video: click here
Take a virtual coffee break in GatherTown 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.
- Slides: click here
- Video: click here
Take a virtual coffee break in GatherTown 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.
- Slides: click here
- Video: click here
Take a virtual coffee break in GatherTown to mix and meet with your fellow participants.
Work through a complete modeling example from start to finish. This session will focus on defining multiple cell definitions in a model of clonal competition in a tumor. This model 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.
- Slides: click here
Discuss the day's progress and set the stage for Day 2.
- Slides: click here
Please use GatherTown to continue getting to know your fellow participants.
Learn about how to work with custom cell variables and user 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 custom cell variables and user 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.
- Slides: click here
Learn how to write custom C++ cell functions in PhysiCell, and use them to write dynamical cell phenotype that varies 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
- Video: click here
Take a virtual coffee break in GatherTown to mix and meet with your fellow participants.
Learn how to use diffusible signals for chemical communication and coordination between cell agents.
- Slides: click here
- Code: click here
- Video: click here
Take a virtual coffee break in GatherTown 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 GatherTown 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 GatherTown 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.
Please use GatherTown to continue getting to know your fellow participants.
Learn about testing for cell-cell contact and pressure in PhysiCell C++ projects
- 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 testing for cell-cell contact and pressure in PhysiCell C++ projects
- 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.
Arnau Montagud (Barcelona Supercomputing Center) will present a tuturial on PhysiBoSS: the first official PhysiCell plug-in, which supports Boolean signaling models (via MaBoSS) in PhysiCell agents.
- Slides: click here
- Video: click here
Discuss the day's goals.
- Slides: click here
- Slides: click here
Explore coding examples that use cell-cell contacts, including a "predator-prey" example and a "worm" example.
- Slides: click here
- Code: click here
- Video: click here
Take a virtual coffee break in GatherTown 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.
- Slides: click here
- Video: click here
Take a virtual coffee break in GatherTown 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.
- Slides: click here
- Video: click here
Take a virtual coffee break in GatherTown to mix and meet with your fellow participants.
Work with your team on your project in GatherTown / Zoom breakout. Work on brief presentations of your team's plans
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 GatherTown to continue getting to know your fellow participants.
Learn about sharing PhysiCell models as cloud-hosted, "zero-install" models on nanoHUB.
- 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 sharing PhysiCell models as cloud-hosted, "zero-install" models on nanoHUB.
- 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.
Work with your team in GatherTown / Zoom.
Share your team's preliminary results in GatherTown / Zoom.
Please use GatherTown to continue getting to know your fellow participants.
Work with your team in GatherTown / Zoom. Schedule breaks on your own as needed.
Discuss the day's progress and set the stage for group presentations.
Please use GatherTown 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.
30 minute presetation, with 10 minutes of Q&A.
Adapt as you see best:
- Model presentation template click here
- Toll presentation template click here