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PhysiCell is an open source, agent-based simulation framework for simulating complex multicellular systems. It simulates the chemical environment (diffusion of substrates and signaling factors), individual cell behaviors, and cell-cell interactions. It can be tailored to a broad variety of problems in cancer, infectious diseases, developmental biology, immunology, micro-ecosystems, and more.
PhysiCell won the 2019 PLoS Computational Biology Research Prize for Public Impact.
The workshop is open to all without participation limits. The hackathon is closely mentored and will be open to a selected cohort of up to 30 participants. Applicants should have prior experience in C++ or Python, with an interest in multicellular modeling.
- Build multiscale agent-based multicellular simulations in PhysiCell
- Integrate SBML network models in PhysiCell agents
- Share models online on nanoHUB
- Attend morning sessions to learn PhysiCell
- Form a team in afternoon hackathon sessions to build a model or a tool
- Join and help drive the PhysiCell community as future leaders
- Direct mentoring by experienced modelers
- PhysiCell swag mailed ot your home (upon request)
- Awards for the best model and best tool
The full agenda and materials--including setup guides--are here.
- Try PhysiCell models online on nanoHUB (these may be useful for education!)
- Learn to build and explore PhysiCell models
- Form a new team and build one of:
- A PhysiCell model of a multicellular system. Examples could include clonal expansion and competition in colorectal carcinoma, immunotherapy, nanotherapy, angiogenesis, or something completely new by your team!
- A PhysiCell tool that helps the community. Examples could include improved Python 3D visualization, new tools to configure models, an extension to link dynamic flux balance models, calibration tools, a plugin for reinforcement learning, or something completely new!
- Make new connections across the cancer modeling community
- Identify new leaders in the PhysiCell community
We coordinated with other workshops to prevent overlapping schedules. You may be interested in:
- Herbert Sauro’s Network Modeling Virtual Summer School and Hackathon
- July 18-24
- Learn to build network models in Python, such as metabolism and signaling.
- https://reproduciblebiomodels.org/dissemination-training/workshops/
- James Glazier’s CompuCell3D Workshop and Hackathon
- August 1-7
- Learn to build multiscale, multicellular models in CompuCell3D
- https://compucell3d.org/Workshop21