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2023 PhysiCell Workshop and Hackathon Agenda

This is the official, full agenda for the 2023 PhysiCell Workshop and Hackathon.

Quick navigation: [Pre-Workshop] [Day 1] [Day 2] [Day 3] [Day 4] [Day 5] [Final presentations)]

All times are US Eastern Click here to see the current US Eastern date and time.

last updated: Sunday, July 22, 2023

Pre-Workshop Materials and Activities

To arrive prepared, all workshop participants should work through the pre-workshop materials prior to Monday.

Set up PhysiCell

MacOS Setup

Windows Setup

Linux Setup

Join the community!

Join the PhysiCell 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

Join the Gather space

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.

Watch introductory materials

Session 0: Introduction to agent-based modeling and PhysiCell

Session 1: Working with Projects in PhysiCell

4 Minute Lighting Self Introduction

User our template to prepare a short self-introduction, including your ideas for PhysiCell hackathon projects. Submit slides by email to Paul Macklin before the Sunday virtual social hour.

Meet your hackathon colleagues at virtual socials (optional)

Sunday (4:00-6:00 pm US Eastern Time) Virtual Social

Introduce yourself and meet your fellow participants in this virtual social. You will receive the link by email and in Gather. Submit slides by email to Paul Macklin in advance if at all possible.

Please prepare your 4 minute mini introduction using this template

Asynchronous Sessions in Preparation for Day 1.

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 1 activities.

Session 2: Working with PhysiCell Studio

Monday: Day 1 (All times US Eastern)

Asynchronous Sessions in Preparation for Day 1.

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 1 activities.

Session 2: Working with PhysiCell Studio

11:00-11:10. Welcome and Introduction

Welcome participants, give the overall format, and discuss goals for the week.

  • Presenter: Paul Macklin

11:10-12:30. Session 3: PhysiCell Signals, Behaviors, and Grammar

Introduce the standardized (reference) behavior models, signals, and a behavior grammar at the core of PhysiCell's new rules-based modeling approach.

12:30-13:00. Break (H)

Take a virtual coffee break in Gather to mix and meet with your fellow participants.

13:00-14:30. Session 4: First PhysiCell Model

We will create, run, visualize, and explore a full model of oxygen-dependent tumor growth with mechanofeedback.

14:30-15:00. Break (H)

Take a virtual coffee break in Gather to mix and meet with your fellow participants.

15:00-16:30. Session 5: Model Extensions 1

Building upon our first model (Session 4), we will add hypoxic responses, a cytotoxic drug, cellular debris, and macrophages.

16:30-17:00. Break

Take a virtual coffee break in GatherTown to mix and meet with your fellow participants.

17:00-17:35. Brainstorming Round 1

Start brainstorming for hackathon projects with your fellow workshop participants.

  • Facilitator: Paul Macklin
  • Format: 5 minute introduction + 3 x 10 minute discussions

17:35-17:45. Wrapup

Wrap up the day's activities, and outline plans for day 2.

  • Presenter: Paul Macklin

17:45-???. Virtual Social (Optional)

Please use Gathe to continue getting to know your fellow participants.

Advanced / Asynchronous / Optional

These are optional C++ based sessions intended for advanced users and PhysiCell developers.

Advanced Session 1: Boundary Conditions, Custom Variables, Parameters, and C++ searches

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.

Advanced Session 2: Functions in PhysiCell

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 hand-coded agent rules that can dynamicaly change cell phenotype in response to signals.

Advanced Session 3: PhysiCell Coloring Functions

Tuesday: Day 2 (All times US Eastern)

11:00-11:10. Welcome and Day's Goals

Summarize Day 1, and discuss Day 2 goals.

  • Facilitator: Paul Macklin

11:10-11:20 Day 2 Warmup Demo: Asymmetric Cell Division

Give a fast modeling demo on combination rules and logic that can yield asymmetric cell divsion without direct control of daughter cells.

  • Presenter: Paul Macklin
  • Slides:
  • Code:

11:20-12:40. Session 6: Model Extensions 2

Building upon our first models (Sessions 4-5), we will add inflammation, cytotoxic T cells, and mutations of tumor cells to evade immune responses.

12:40-13:00. Break

Take a virtual coffee break in Gather to mix and meet with your fellow participants.

13:10-14:00. Session 7: Working with PhysiCell Data in Python with Data Loader

Learn to load, manipulate, and explore full PhysiCell outputs in Python using PhysiCell Data Loader.

14:00-14:30. Break

Take a virtual coffee break in Gather to mix and meet with your fellow participants.

14:30-14:45. Summary of Day 1 Brainstorming

We will present clustering of main ideas generated in Round 1 brainstorming to prepare for continued project brainstorming.

  • Facilitator: Paul Macklin

14:45-15:15. Brainstorming Round 2

Choose a cluster and refine project ideas. Prepare to briefly present your refined project theme.

  • Facilitator: Paul Macklin

15:15-15:45. Present Brainstorming Round 2

Briefly summarize the refined brainstorming for each group.

  • Facilitator: Paul Macklin

15:45-16:00. Break

Take a virtual coffee break in Gather to mix and meet with your fellow participants.

16:00-16:45. Team Formation Round 1

Choose a refined project. Further refine your project idea and prepare to briefly present it.

  • Facilitator: Paul Macklin

16:45-17:15. Team Report Round 1

Briefly summarize team formation results. Choose whether to switch teams.

  • Facilitator: Paul Macklin

17:15-17:30. Break

Take a virtual coffee break in Gather to mix and meet with your fellow participants.

17:30-18:00. Team Formation Round 2

Continue refining your team's main idea, with a focus on a bite-sized preliminary result.

  • Facilitator: Paul Macklin

18:00-18:10 Day 2 wrap-up

Discuss the day's progress and set the stage for Day 3.

  • Facilitator: Paul Macklin

18:10-???. Virtual Social (Optional)

Please use Gather to continue getting to know your fellow participants.

Asynchronous in preparation for Day 3

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.

Session 8: PhysiBoSS Introduction

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.

Wednesday: Day 3 (All times US Eastern)

Asynchronous in preparation for Day 3

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.

Session 8: PhysiBoSS Introduction

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.

11:00-11:05. Welcome and Day's Goals

Discuss the day's goals

  • Facilitator: Paul Macklin

11:05-12:30. Session 9: PhysiBoSS Walk-Thru

Continue to learn to integrate Boolean signaling networks with PhysiCelll in this fully guided walk-thru.

12:30-13:00. Break

Take a virtual coffee break in Gather to mix and meet with your fellow participants.

13:05-14:30. Session 10: PhysiCell Modeling Example and Warm-Up 1

We present a full modeling example as a daily warmup.

14:30-15:00. Break

Take a virtual coffee break in Gather to mix and meet with your fellow participants.

15:00-16:00. Team Time 1

Work with your team on your project in Gather / Zoom breakout. Work on brief presentations of your team's plans

  • Facilitator: Paul Macklin
  • Presentation template: Click here

16:00-16:15. Break

Take a virtual coffee break in Gather to mix and meet with your fellow participants.

16:16-17:45. Cross-Pollination: Team Brief Presentations

Briefly present your team's plan and give/get feedback from workshop participants.

17:45-18:00. Day 3 wrap-up

Discuss the day's progress and set the stage for Day 3.

18:00-???. Virtual Social (Optional) (E).

Please use Gather to continue getting to know your fellow participants.

18:00-18:30. Feedback on instructional materials (optional)

Give feedback on improvements to the Day 0-3 training materials.

Advanced / Asynchronous / Optional

These are optional C++ based sessions intended for advanced users and PhysiCell developers.

Advanced Session 4: Intracellular with libRoadrunner (introduction)

Learn how to write intracellular models (systems of ODEs) in cancer cell agents. Work through a cancer metabolism example.

Advanced Session 5: Cell-Cell Interactions in PhysiCell

Learn how to make cells communicate by chemical and contact interactions.

  • Presenter: Paul Macklin
  • Slides:
  • Code:
  • Video:

Advanced Session 6: Sharing PhysiCell Models on nanoHUB

Learn about sharing PhysiCell models as cloud-hosted, "zero-install" models on nanoHUB.

13:45-14:00. Break (H)

Take a virtual coffee break in GatherTown to mix and meet with your fellow participants.

Thursday: Day 4 (All times US Eastern)

11:00-11:05. Welcome and Day's Goals

Discuss the day's goals

  • Facilitator: Paul Macklin

11:05-12:00. Advanced Session 7: Intracellular with libRoadrunner (interactive demo) (optional)

Continuing learning how to write intracellular models (systems of ODEs) in cancer cell agents. Work through a cancer metabolism example. This session is optional.

  • Dependencies:
    • Advanced Session 1
    • Advanced Session 2
    • Advanced Session 4
  • Presenter: Furkan Kurtoglu
  • Slides: Click Here
  • Code: Click Here
  • Video: Click Here

12:00-16:00. Team Time 2

Work with your team in Gather / Zoom.

12:00-13:30. PhysiCell Governance (optional and by invitation only)

Discuss transition to a community governance model.

16:00-18:00. Present Preliminary Results

Share your team's preliminary results in Gather / Zoom.

  • Facilitator: Paul Macklin

18:00-18:10. Wrap-Up

  • Presenter: Paul Macklin

18:10-???. Virtual Social (Optional)

Please use Gather to continue getting to know your fellow participants.

Friday: Day 5 (All times US Eastern)

11:00-11:05. Welcome and Day's Goals

Discuss the day's goals

  • Presenter: Paul Macklin

11:05-12:00. Session 11: PhysiCell Modeling Example and Warm-Up 2

We present a full modeling example as a daily warmup.

12:00-18:15. Team Time 3.

Work with your team in Gather / Zoom. Schedule breaks on your own as needed. Prepare presentations.

Presentation templates:

Adapt as you see best:

  • Presentation template (Modeling projects): click here
  • Presentation template (Tools projects): click here

12:00-13:30. PhysiCell Governance (optional and by invitation only)

Discuss transition to a community governance model.

18:15-18:30. Day 5 wrap-up

Discuss the day's progress and set the stage for group presentations.

18:30-???. Virtual Social (Optional).

Please use Gather to continue getting to know your fellow participants.

Saturday: Final Presentations (All times US Eastern)

11:00-12:00. Final Team Presentations.

Present your team's project results for the community and for feedback and scoring. Detailed schedule TBA.

25 minute presetation, with 5 minutes of Q&A.

Presentation templates:

Adapt as you see best:

  • Presentation template (Modeling projects): click here
  • Presentation template (Tools projects): click here

12:00-12:30. Judges' Discussion.

12:30-13:00. Announce results and farewell

  • Facilitator: Paul Macklin