PhysiCell Project.
@physicell.bsky.social
Major PhysiCell paper in Cell using a new, intuitive model grammar to create complex multicellular systems models with "plain language" cell hypotheses! 🧪
@cellpress.bsky.social @cp-cell.bsky.social @mathcancer.bsky.social @fertiglab.bsky.social #mathonco #mathbio #abm #opensource
@cellpress.bsky.social @cp-cell.bsky.social @mathcancer.bsky.social @fertiglab.bsky.social #mathonco #mathbio #abm #opensource
Really excited to share our new @cellpress.bsky.social Cell paper with @fertiglab.bsky.social and colleagues. 1/n
www.cell.com/cell/fulltex...
@jktgfoundation.bsky.social @itcrtraining.bsky.social @smbmathbiology.bsky.social #mathbio #mathonco @mathonco.bsky.social @deniswirtz.bsky.social
www.cell.com/cell/fulltex...
@jktgfoundation.bsky.social @itcrtraining.bsky.social @smbmathbiology.bsky.social #mathbio #mathonco @mathonco.bsky.social @deniswirtz.bsky.social
Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories
We developed a plain text modeling language—a cell behavior hypothesis grammar—to
easily build virtual cell models and connect them to data, helping scientists to unlock
the hidden dynamics of tissues...
www.cell.com
July 29, 2025 at 4:02 PM
Major PhysiCell paper in Cell using a new, intuitive model grammar to create complex multicellular systems models with "plain language" cell hypotheses! 🧪
@cellpress.bsky.social @cp-cell.bsky.social @mathcancer.bsky.social @fertiglab.bsky.social #mathonco #mathbio #abm #opensource
@cellpress.bsky.social @cp-cell.bsky.social @mathcancer.bsky.social @fertiglab.bsky.social #mathonco #mathbio #abm #opensource
Reposted by PhysiCell Project.
Nice writeup of our new @cp-cell.bsky.social article on an intuitive, plain language "grammar" to make simulation modeling of complex multicellular systems more accessible. Huge thx to Forest Ray and @genomeweb.bsky.social !
Joint work by @fertiglab.bsky.social, Genevieve Stein-O'Brien & team! 🧪
Joint work by @fertiglab.bsky.social, Genevieve Stein-O'Brien & team! 🧪
Computational Model Predicts Tissue-Specific Cell Activity Over Time
Computational Model Predicts Tissue-Specific Cell Activity Over Time
www.genomeweb.com
July 29, 2025 at 10:43 AM
Nice writeup of our new @cp-cell.bsky.social article on an intuitive, plain language "grammar" to make simulation modeling of complex multicellular systems more accessible. Huge thx to Forest Ray and @genomeweb.bsky.social !
Joint work by @fertiglab.bsky.social, Genevieve Stein-O'Brien & team! 🧪
Joint work by @fertiglab.bsky.social, Genevieve Stein-O'Brien & team! 🧪
Reposted by PhysiCell Project.
Today’s morning plenary and John Jungck Prize lecture is from @smbmathbiology.bsky.social former president, Fred Adler (@dendroicap.bsky.social) on "Education, Bureaucracy and Corruption". He manages to discuss some of his virus work with former @mathonco.bsky.social member Anna Miller! #SMB2025
July 15, 2025 at 3:43 PM
Today’s morning plenary and John Jungck Prize lecture is from @smbmathbiology.bsky.social former president, Fred Adler (@dendroicap.bsky.social) on "Education, Bureaucracy and Corruption". He manages to discuss some of his virus work with former @mathonco.bsky.social member Anna Miller! #SMB2025
Hello, #SMB2025!
If you’d like PhysiCell stickers, please find Paul Macklin (@mathcancer.bsky.social). I’ll try to get stickers to Randy Heiland ( @rheiland.bsky.social ) and John Metzcar (@jmetzcar.bsky.social) as well.
If you’d like PhysiCell stickers, please find Paul Macklin (@mathcancer.bsky.social). I’ll try to get stickers to Randy Heiland ( @rheiland.bsky.social ) and John Metzcar (@jmetzcar.bsky.social) as well.
July 15, 2025 at 12:41 PM
Hello, #SMB2025!
If you’d like PhysiCell stickers, please find Paul Macklin (@mathcancer.bsky.social). I’ll try to get stickers to Randy Heiland ( @rheiland.bsky.social ) and John Metzcar (@jmetzcar.bsky.social) as well.
If you’d like PhysiCell stickers, please find Paul Macklin (@mathcancer.bsky.social). I’ll try to get stickers to Randy Heiland ( @rheiland.bsky.social ) and John Metzcar (@jmetzcar.bsky.social) as well.
Reposted by PhysiCell Project.
Really fantastic ECM and spheroid modeling in @physicell.bsky.social. Great work! 🧪
Congrats Margherita for her new paper, where she investigated how cancer spheroids grow in collagen matrices with varying stiffness, implementing varying ECM properties in @physicell.bsky.social Thanks Tom Susan John and Pradeep for the collaboration
www.frontiersin.org/journals/bio...
www.frontiersin.org/journals/bio...
Frontiers | A hybrid computational model of cancer spheroid growth with ribose-induced collagen stiffening
www.frontiersin.org
April 9, 2025 at 2:03 PM
Really fantastic ECM and spheroid modeling in @physicell.bsky.social. Great work! 🧪
Reposted by PhysiCell Project.
"Patients should be their own control"
- great & pithy takeaway from @sandyanderson.bsky.social in his talk on the adoption of adaptive therapies in the clinic #SMB2025 #MathOnco
- great & pithy takeaway from @sandyanderson.bsky.social in his talk on the adoption of adaptive therapies in the clinic #SMB2025 #MathOnco
July 14, 2025 at 11:17 PM
"Patients should be their own control"
- great & pithy takeaway from @sandyanderson.bsky.social in his talk on the adoption of adaptive therapies in the clinic #SMB2025 #MathOnco
- great & pithy takeaway from @sandyanderson.bsky.social in his talk on the adoption of adaptive therapies in the clinic #SMB2025 #MathOnco
Reposted by PhysiCell Project.
Unexpected treat today @moffittnews.bsky.social Innovator's of Tomorrow symposium with Jeanette Johnson, working with @fertiglab.bsky.social and developing on @physicell.bsky.social to create an #ABM for #pancreatic #cancer forecasting
April 4, 2025 at 3:17 PM
Unexpected treat today @moffittnews.bsky.social Innovator's of Tomorrow symposium with Jeanette Johnson, working with @fertiglab.bsky.social and developing on @physicell.bsky.social to create an #ABM for #pancreatic #cancer forecasting
Reposted by PhysiCell Project.
Congrats Margherita for her new paper, where she investigated how cancer spheroids grow in collagen matrices with varying stiffness, implementing varying ECM properties in @physicell.bsky.social Thanks Tom Susan John and Pradeep for the collaboration
www.frontiersin.org/journals/bio...
www.frontiersin.org/journals/bio...
Frontiers | A hybrid computational model of cancer spheroid growth with ribose-induced collagen stiffening
www.frontiersin.org
April 9, 2025 at 12:41 PM
Congrats Margherita for her new paper, where she investigated how cancer spheroids grow in collagen matrices with varying stiffness, implementing varying ECM properties in @physicell.bsky.social Thanks Tom Susan John and Pradeep for the collaboration
www.frontiersin.org/journals/bio...
www.frontiersin.org/journals/bio...
New paper for new PhysiCell capabilities!
John Metzcar et al. (2025) created a very accessible framework to integrate ECM structure into cell agent behaviors, particularly including contact guidance.
Give it a look! 🧪
John Metzcar et al. (2025) created a very accessible framework to integrate ECM structure into cell agent behaviors, particularly including contact guidance.
Give it a look! 🧪
Congratulations to John Metzcar for his new paper modeling cell-ECM interactions in @physicell.bsky.social ! 🧪
This work helps provide an accessible means to have an intermediate level of ECM detail (density, orientation, anisotropy) affect cell migration and behavior.
dx.doi.org/10.1007/s115...
This work helps provide an accessible means to have an intermediate level of ECM detail (density, orientation, anisotropy) affect cell migration and behavior.
dx.doi.org/10.1007/s115...
A Simple Framework for Agent-Based Modeling with Extracellular Matrix - Bulletin of Mathematical Biology
Extracellular matrix (ECM) is a key component of the cellular microenvironment and critical in multiple disease and developmental processes. Representing ECM and cell-ECM interactions is a challenging...
dx.doi.org
February 13, 2025 at 5:57 PM
New paper for new PhysiCell capabilities!
John Metzcar et al. (2025) created a very accessible framework to integrate ECM structure into cell agent behaviors, particularly including contact guidance.
Give it a look! 🧪
John Metzcar et al. (2025) created a very accessible framework to integrate ECM structure into cell agent behaviors, particularly including contact guidance.
Give it a look! 🧪
PhysiCell 1.14.2 is released! 🧪
* bug fixes
* better support for the cell behavior grammar / rules
* prep work for future PhysiGym
* new script to more easily add PhysiCell Studio
See download links at:
physicell.org/Downloads.html
* bug fixes
* better support for the cell behavior grammar / rules
* prep work for future PhysiGym
* new script to more easily add PhysiCell Studio
See download links at:
physicell.org/Downloads.html
PhysiCell Project Website: Downloads
PhysiCell Project Website
physicell.org
January 21, 2025 at 5:29 PM
PhysiCell 1.14.2 is released! 🧪
* bug fixes
* better support for the cell behavior grammar / rules
* prep work for future PhysiGym
* new script to more easily add PhysiCell Studio
See download links at:
physicell.org/Downloads.html
* bug fixes
* better support for the cell behavior grammar / rules
* prep work for future PhysiGym
* new script to more easily add PhysiCell Studio
See download links at:
physicell.org/Downloads.html
Continuing our 10-year celebration of PhysiCell with some more project history! :-)
Today we'll talk about choosing a name 🧪
On Thanksgiving Day in 2014, I was with family at Disneyland sitting for the parade. I'm not as super big into the parade, so I started searching for our project name ...
Today we'll talk about choosing a name 🧪
On Thanksgiving Day in 2014, I was with family at Disneyland sitting for the parade. I'm not as super big into the parade, so I started searching for our project name ...
January 16, 2025 at 1:58 PM
Continuing our 10-year celebration of PhysiCell with some more project history! :-)
Today we'll talk about choosing a name 🧪
On Thanksgiving Day in 2014, I was with family at Disneyland sitting for the parade. I'm not as super big into the parade, so I started searching for our project name ...
Today we'll talk about choosing a name 🧪
On Thanksgiving Day in 2014, I was with family at Disneyland sitting for the parade. I'm not as super big into the parade, so I started searching for our project name ...
Reposted by PhysiCell Project.
Another nice benefit of our approach is that we can combine the model grammar with graphical interfaces to easily write and test new models without writing code. This opens the world of simulation modeling to new communities. (Preprint by @rheiland soon!) 16/19
September 22, 2023 at 1:17 AM
Another nice benefit of our approach is that we can combine the model grammar with graphical interfaces to easily write and test new models without writing code. This opens the world of simulation modeling to new communities. (Preprint by @rheiland soon!) 16/19
Reposted by PhysiCell Project.
New in our PhysiCell Ecosystem series is a GUI for building, simulating, and visualizing PhysiCell models.
PhysiCell Studio: a graphical tool to make agent-based modeling more accessible doi.org/10.46471/gig...
See also the introductory video: youtu.be/jkbPP1yDzME?...
PhysiCell Studio: a graphical tool to make agent-based modeling more accessible doi.org/10.46471/gig...
See also the introductory video: youtu.be/jkbPP1yDzME?...
PhysiCell Studio: a graphical tool to make agent-based modeling more accessible
PhysiCell Studio: a graphical tool to make agent-based modeling more accessible
doi.org
July 3, 2024 at 8:00 AM
New in our PhysiCell Ecosystem series is a GUI for building, simulating, and visualizing PhysiCell models.
PhysiCell Studio: a graphical tool to make agent-based modeling more accessible doi.org/10.46471/gig...
See also the introductory video: youtu.be/jkbPP1yDzME?...
PhysiCell Studio: a graphical tool to make agent-based modeling more accessible doi.org/10.46471/gig...
See also the introductory video: youtu.be/jkbPP1yDzME?...
Reposted by PhysiCell Project.
I'm so thankful for this post! I saw it just as two different collaborators were asking us to do things with our ABMs that we hadn't done before. Your tutorials and demos were so clear! Coupling with MaBoSS and PhysiCell Studio is also great and intuitive!
November 25, 2024 at 11:02 PM
I'm so thankful for this post! I saw it just as two different collaborators were asking us to do things with our ABMs that we hadn't done before. Your tutorials and demos were so clear! Coupling with MaBoSS and PhysiCell Studio is also great and intuitive!
Reposted by PhysiCell Project.
Start&Stop - a PhysiCell and PhysiBoSS 2.0 add-on for interactive simulation control https://www.biorxiv.org/content/10.1101/2024.12.13.628298v1
December 18, 2024 at 5:55 AM
Start&Stop - a PhysiCell and PhysiBoSS 2.0 add-on for interactive simulation control https://www.biorxiv.org/content/10.1101/2024.12.13.628298v1
Reposted by PhysiCell Project.
At the #Hanami High Level Symposium, my friend and colleagues Adam Smelko is presenting our new @PhysiCell formulation that allows for stretchable cellular membrane! We are still working on this, but I hope we will be able to give you updates vero soon!
January 14, 2025 at 11:02 AM
At the #Hanami High Level Symposium, my friend and colleagues Adam Smelko is presenting our new @PhysiCell formulation that allows for stretchable cellular membrane! We are still working on this, but I hope we will be able to give you updates vero soon!
A fun FYI: PhysiCell was first publicly presented in 2015, with first open source release in 2016.
So let's call 2025 our 10th anniversary! 🧪
So let's call 2025 our 10th anniversary! 🧪
January 15, 2025 at 4:58 PM
A fun FYI: PhysiCell was first publicly presented in 2015, with first open source release in 2016.
So let's call 2025 our 10th anniversary! 🧪
So let's call 2025 our 10th anniversary! 🧪
Reposted by PhysiCell Project.
My lectures are freely available on YouTube: www.youtube.com/playlist?lis...
Nonlinear Dynamics and Chaos - Steven Strogatz, Cornell University - YouTube
This course of 25 lectures, filmed at Cornell University in Spring 2014, is intended for newcomers to nonlinear dynamics and chaos. It closely follows Prof. ...
www.youtube.com
January 2, 2025 at 5:07 PM
My lectures are freely available on YouTube: www.youtube.com/playlist?lis...
Reposted by PhysiCell Project.
Welcome to the Science feed!
Please read our FAQs for instructions for how to be added as a contributor: bossett.io/science-feed/
Mod introductory posts linked below⬇️
Use the test tube emoji on posts you want to appear in the feed🧪
Please like the feed and make sure you follow our feed rules:
Please read our FAQs for instructions for how to be added as a contributor: bossett.io/science-feed/
Mod introductory posts linked below⬇️
Use the test tube emoji on posts you want to appear in the feed🧪
Please like the feed and make sure you follow our feed rules:
February 10, 2024 at 3:08 PM
Welcome to the Science feed!
Please read our FAQs for instructions for how to be added as a contributor: bossett.io/science-feed/
Mod introductory posts linked below⬇️
Use the test tube emoji on posts you want to appear in the feed🧪
Please like the feed and make sure you follow our feed rules:
Please read our FAQs for instructions for how to be added as a contributor: bossett.io/science-feed/
Mod introductory posts linked below⬇️
Use the test tube emoji on posts you want to appear in the feed🧪
Please like the feed and make sure you follow our feed rules:
Fantastic new paper by @fordversyptlab.bsky.social lab using @physicell.bsky.social !! 🧪
Our newest paper is now online. Mohammad Aminul Islam, Ph.D. developed this followup to our earlier COVID-19 agent-based model and resulting lung fibrosis. Here, we studied COVID-19 with the renin-angiotensin system and patient-specific differences: www.sciencedirect.com/science/arti...
Mathematical modeling of impacts of patient differences on renin-angiotensin system and applications to COVID-19 lung fibrosis outcomes
Patient-specific premorbidity, age, and sex are significant heterogeneous factors that influence the severe manifestation of lung diseases, including …
www.sciencedirect.com
January 3, 2025 at 12:45 AM
Fantastic new paper by @fordversyptlab.bsky.social lab using @physicell.bsky.social !! 🧪
PhysiCell 1.14.1 is released!
This introduced asymmetric cell division (thanks, @danielrbergman.bsky.social!), improved handling of conserved cell contents in phagocytosis and transformation, and numerous bug fixes. 🧪 #mathbio #mathonco #opensource
github.com/MathCancer/P...
This introduced asymmetric cell division (thanks, @danielrbergman.bsky.social!), improved handling of conserved cell contents in phagocytosis and transformation, and numerous bug fixes. 🧪 #mathbio #mathonco #opensource
github.com/MathCancer/P...
Release 1.14.1 · MathCancer/PhysiCell
PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D Multicellular Systems
Versions: 1.14.0 -
Release dates: 15 September 2024 -
1.14.0 : 15 September 2024
1.14.1 : 13 December 2024
Ove...
github.com
December 13, 2024 at 11:29 PM
PhysiCell 1.14.1 is released!
This introduced asymmetric cell division (thanks, @danielrbergman.bsky.social!), improved handling of conserved cell contents in phagocytosis and transformation, and numerous bug fixes. 🧪 #mathbio #mathonco #opensource
github.com/MathCancer/P...
This introduced asymmetric cell division (thanks, @danielrbergman.bsky.social!), improved handling of conserved cell contents in phagocytosis and transformation, and numerous bug fixes. 🧪 #mathbio #mathonco #opensource
github.com/MathCancer/P...
PhysiCell 1.14.0 is released!
Key features include improved cell behavior grammar (including better phagocytosis, effector attack, and cell damage), better initialization, and more! 🧪
Release notes and downloads:
github.com/MathCancer/P...
Key features include improved cell behavior grammar (including better phagocytosis, effector attack, and cell damage), better initialization, and more! 🧪
Release notes and downloads:
github.com/MathCancer/P...
Release Version 1.14.0 · MathCancer/PhysiCell
PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D Multicellular Systems
Versions: 1.14.0 -
Release dates: 15 September 2024 -
1.14.0 : 15 September 2024
Overview:
PhysiCell is a flex...
github.com
September 16, 2024 at 2:43 PM
PhysiCell 1.14.0 is released!
Key features include improved cell behavior grammar (including better phagocytosis, effector attack, and cell damage), better initialization, and more! 🧪
Release notes and downloads:
github.com/MathCancer/P...
Key features include improved cell behavior grammar (including better phagocytosis, effector attack, and cell damage), better initialization, and more! 🧪
Release notes and downloads:
github.com/MathCancer/P...
Reposted by PhysiCell Project.