Looking forward to building the next chapter at @michiganstateu.bsky.social! More on this in the coming week!
10/10
#academia #DeanLife #DigitalTwins #mathonco #mathbio #OpenSource #PhysiCell
10/10
#academia #DeanLife #DigitalTwins #mathonco #mathbio #OpenSource #PhysiCell
November 1, 2026 at 5:06 PM
Looking forward to building the next chapter at @michiganstateu.bsky.social! More on this in the coming week!
10/10
#academia #DeanLife #DigitalTwins #mathonco #mathbio #OpenSource #PhysiCell
10/10
#academia #DeanLife #DigitalTwins #mathonco #mathbio #OpenSource #PhysiCell
Friday was my last day at IU Luddy School of Informatics, Computing, and Engineering.
I'm so grateful for the opportunities I had to build and grow here in the past ten years. 1/10
#academia #DeanLife #DigitalTwins #mathonco #mathbio #OpenSource #PhysiCell 🧪
I'm so grateful for the opportunities I had to build and grow here in the past ten years. 1/10
#academia #DeanLife #DigitalTwins #mathonco #mathbio #OpenSource #PhysiCell 🧪
November 1, 2026 at 5:06 PM
Friday was my last day at IU Luddy School of Informatics, Computing, and Engineering.
I'm so grateful for the opportunities I had to build and grow here in the past ten years. 1/10
#academia #DeanLife #DigitalTwins #mathonco #mathbio #OpenSource #PhysiCell 🧪
I'm so grateful for the opportunities I had to build and grow here in the past ten years. 1/10
#academia #DeanLife #DigitalTwins #mathonco #mathbio #OpenSource #PhysiCell 🧪
We built phenomenal collaborations to create a thriving international community focused around understanding multiscale cancer-immune interactions.
journals.plos.org/ploscompbiol...
I got to explore academic leadership while working as Associate Dean of Undergraduate Education (ADUE).
4/10
journals.plos.org/ploscompbiol...
I got to explore academic leadership while working as Associate Dean of Undergraduate Education (ADUE).
4/10
PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems
Author summary This paper introduces PhysiCell: an open source, agent-based modeling framework for 3-D multicellular simulations. It includes a standard library of sub-models for cell fluid and solid ...
journals.plos.org
November 1, 2026 at 5:06 PM
We built phenomenal collaborations to create a thriving international community focused around understanding multiscale cancer-immune interactions.
journals.plos.org/ploscompbiol...
I got to explore academic leadership while working as Associate Dean of Undergraduate Education (ADUE).
4/10
journals.plos.org/ploscompbiol...
I got to explore academic leadership while working as Associate Dean of Undergraduate Education (ADUE).
4/10
It was really fun to talk with eisensteinium.bsky.social for his piece in @nature.com about #VirtualCells and #VirtualTissues.
Thanks for including #PhysiCell and joint work with @fertiglab.bsky.social & others!
Please do give this terrific piece a read!
www.nature.com/articles/d41...
Thanks for including #PhysiCell and joint work with @fertiglab.bsky.social & others!
Please do give this terrific piece a read!
www.nature.com/articles/d41...
‘Virtual cells’ aim to turn raw data into predictive models of biology
Simulations of biological systems could transform biomedical research, but researchers are still learning how to reproduce life’s complexity without drowning in data.
www.nature.com
June 3, 2026 at 1:36 PM
It was really fun to talk with eisensteinium.bsky.social for his piece in @nature.com about #VirtualCells and #VirtualTissues.
Thanks for including #PhysiCell and joint work with @fertiglab.bsky.social & others!
Please do give this terrific piece a read!
www.nature.com/articles/d41...
Thanks for including #PhysiCell and joint work with @fertiglab.bsky.social & others!
Please do give this terrific piece a read!
www.nature.com/articles/d41...
Paper is in Cell at www.cell.com/cell/fulltex...
@genomeweb.bsky.social
@cp-cell.bsky.social @physicell.bsky.social #mathonco #mathbio #grammar #PhysiCell #multicellular
@genomeweb.bsky.social
@cp-cell.bsky.social @physicell.bsky.social #mathonco #mathbio #grammar #PhysiCell #multicellular
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 10:43 AM
We have been striving to find the commonalities in mathematical models of cancer and tissue ecosystems, simplify the process of creating these models, and unlock the methods to everyone. 2/n
@galaxyproject.bsky.social @physicell.bsky.social
@galaxyproject.bsky.social @physicell.bsky.social
July 28, 2025 at 2:20 PM
We have been striving to find the commonalities in mathematical models of cancer and tissue ecosystems, simplify the process of creating these models, and unlock the methods to everyone. 2/n
@galaxyproject.bsky.social @physicell.bsky.social
@galaxyproject.bsky.social @physicell.bsky.social
Cell won't allow us to update the preprint, but we have even better versions already in PhysiCell. ;-)
February 14, 2025 at 4:55 PM
Cell won't allow us to update the preprint, but we have even better versions already in PhysiCell. ;-)
In the future, elements of this will likely be introduced into PhysiCell core, with the broader package incorporated as an official PhysiCell Extension.
Way to go, John!
Way to go, John!
February 13, 2025 at 5:56 PM
In the future, elements of this will likely be introduced into PhysiCell core, with the broader package incorporated as an official PhysiCell Extension.
Way to go, John!
Way to go, John!
@elmarbucher.bsky.social is now on BlueSky!
He's doing some fantastic work on PhysiCell modeling of breast cancer and cancer immunology, and core contributions on reinforcement learning other cool things in the @physicell.bsky.social ecosystem.
Keep on eye on that account! Welcome, Elmar!
He's doing some fantastic work on PhysiCell modeling of breast cancer and cancer immunology, and core contributions on reinforcement learning other cool things in the @physicell.bsky.social ecosystem.
Keep on eye on that account! Welcome, Elmar!
January 20, 2025 at 9:22 PM
@elmarbucher.bsky.social is now on BlueSky!
He's doing some fantastic work on PhysiCell modeling of breast cancer and cancer immunology, and core contributions on reinforcement learning other cool things in the @physicell.bsky.social ecosystem.
Keep on eye on that account! Welcome, Elmar!
He's doing some fantastic work on PhysiCell modeling of breast cancer and cancer immunology, and core contributions on reinforcement learning other cool things in the @physicell.bsky.social ecosystem.
Keep on eye on that account! Welcome, Elmar!
Hmm, seem to be stuck here for last 20 minutes on 104 queued checks. Messages like these:
Requested labels: macos-13
Job defined at: MathCancer/PhysiCell/.github/workflows/build_binaries.yml@refs/pull/354/merge
Waiting for a runner to pick up this job...
Requested labels: macos-13
Job defined at: MathCancer/PhysiCell/.github/workflows/build_binaries.yml@refs/pull/354/merge
Waiting for a runner to pick up this job...
January 20, 2025 at 9:12 PM
Hmm, seem to be stuck here for last 20 minutes on 104 queued checks. Messages like these:
Requested labels: macos-13
Job defined at: MathCancer/PhysiCell/.github/workflows/build_binaries.yml@refs/pull/354/merge
Waiting for a runner to pick up this job...
Requested labels: macos-13
Job defined at: MathCancer/PhysiCell/.github/workflows/build_binaries.yml@refs/pull/354/merge
Waiting for a runner to pick up this job...
Kudos to @vincent-noel.fr and @rheiland.bsky.social for major work on automated PR quality checks.
January 20, 2025 at 9:01 PM
Kudos to @vincent-noel.fr and @rheiland.bsky.social for major work on automated PR quality checks.
PhysiCell 1.14.2 will release later this afternoon.
Mostly bugfixes and minor refinements, but also exciting new work by Elmar Bucher prepping for a future "PhysiGym" addon for RL etc.
Major thanks to @danielrbergman.bsky.social for numerous PRs! Watch @physicell.bsky.social for the release.
Mostly bugfixes and minor refinements, but also exciting new work by Elmar Bucher prepping for a future "PhysiGym" addon for RL etc.
Major thanks to @danielrbergman.bsky.social for numerous PRs! Watch @physicell.bsky.social for the release.
January 20, 2025 at 8:56 PM
PhysiCell 1.14.2 will release later this afternoon.
Mostly bugfixes and minor refinements, but also exciting new work by Elmar Bucher prepping for a future "PhysiGym" addon for RL etc.
Major thanks to @danielrbergman.bsky.social for numerous PRs! Watch @physicell.bsky.social for the release.
Mostly bugfixes and minor refinements, but also exciting new work by Elmar Bucher prepping for a future "PhysiGym" addon for RL etc.
Major thanks to @danielrbergman.bsky.social for numerous PRs! Watch @physicell.bsky.social for the release.
More PhysiCell history, as part of our 10-year celebration!
See the thread below. ;-)
@physicell.bsky.social #OpenSource #mathonco @smbmathbiology.bsky.social @bcrfcure.bsky.social
See the thread below. ;-)
@physicell.bsky.social #OpenSource #mathonco @smbmathbiology.bsky.social @bcrfcure.bsky.social
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 2:13 PM
More PhysiCell history, as part of our 10-year celebration!
See the thread below. ;-)
@physicell.bsky.social #OpenSource #mathonco @smbmathbiology.bsky.social @bcrfcure.bsky.social
See the thread below. ;-)
@physicell.bsky.social #OpenSource #mathonco @smbmathbiology.bsky.social @bcrfcure.bsky.social
I say PhysiCell *community* because we've grown to be more than a software framework.
* We have an growing ecosystem of addons, like Boolean networks in PhysiBoSS, and training materials.
* We have an amazing, active community!
* Core devs in USA, Europe and Brazil are regularly contributing!
* We have an growing ecosystem of addons, like Boolean networks in PhysiBoSS, and training materials.
* We have an amazing, active community!
* Core devs in USA, Europe and Brazil are regularly contributing!
January 15, 2025 at 5:10 PM
I say PhysiCell *community* because we've grown to be more than a software framework.
* We have an growing ecosystem of addons, like Boolean networks in PhysiBoSS, and training materials.
* We have an amazing, active community!
* Core devs in USA, Europe and Brazil are regularly contributing!
* We have an growing ecosystem of addons, like Boolean networks in PhysiBoSS, and training materials.
* We have an amazing, active community!
* Core devs in USA, Europe and Brazil are regularly contributing!
Did you know that PhysiCell--our #OpenSource community for multicellular systems biology--is celebrating its 10 year anniversary this year?
Read below (and follow @physicell.bsky.social) to see more of the project history! 🧪
Read below (and follow @physicell.bsky.social) to see more of the project history! 🧪
January 15, 2025 at 5:10 PM
Did you know that PhysiCell--our #OpenSource community for multicellular systems biology--is celebrating its 10 year anniversary this year?
Read below (and follow @physicell.bsky.social) to see more of the project history! 🧪
Read below (and follow @physicell.bsky.social) to see more of the project history! 🧪
OK, looks like WordPress on GoDaddy went berserk, and PhysiCell.org went down.
I took this a sign to start over with GitHub pages. Hated WordPress anyway.
I'm rebuilding a SUPER BASIC page with static HTML5 & CSS and nothing else. No script libraries. No server-side crap. Very fast.
I took this a sign to start over with GitHub pages. Hated WordPress anyway.
I'm rebuilding a SUPER BASIC page with static HTML5 & CSS and nothing else. No script libraries. No server-side crap. Very fast.
PhysiCell Project Website
PhysiCell Project Website
PhysiCell.org
January 3, 2025 at 7:25 PM
OK, looks like WordPress on GoDaddy went berserk, and PhysiCell.org went down.
I took this a sign to start over with GitHub pages. Hated WordPress anyway.
I'm rebuilding a SUPER BASIC page with static HTML5 & CSS and nothing else. No script libraries. No server-side crap. Very fast.
I took this a sign to start over with GitHub pages. Hated WordPress anyway.
I'm rebuilding a SUPER BASIC page with static HTML5 & CSS and nothing else. No script libraries. No server-side crap. Very fast.
Thanks for this!
I *think* I'm already in, but here's my google scholar just in case. Thanks!!
scholar.google.com/citations?us...
I *think* I'm already in, but here's my google scholar just in case. Thanks!!
scholar.google.com/citations?us...
Paul Macklin
Associate Dean for Undergraduate Education - Luddy School - Indiana University - Cited by 6,275 - PhysiCell - mathematics - cancer - computational modeling - digital cell lines
scholar.google.com
November 28, 2024 at 4:52 PM
Thanks for this!
I *think* I'm already in, but here's my google scholar just in case. Thanks!!
scholar.google.com/citations?us...
I *think* I'm already in, but here's my google scholar just in case. Thanks!!
scholar.google.com/citations?us...
Congratulations to Cicely Macnamara, Robyn Shuttleworth, @vincent-noel.bsky.social, and Marco Ruscone for publishing PhysiMeSS in @gigabytejournal.bsky.social!
A beautiful community contribution to the @physicell.bsky.social ecosystem! Tremendous work!! 🧪
gigabytejournal.com/articles/136
A beautiful community contribution to the @physicell.bsky.social ecosystem! Tremendous work!! 🧪
gigabytejournal.com/articles/136
PhysiMeSS - a new physiCell addon for extracellular matrix modelling
PhysiMeSS - a new physiCell addon for extracellular matrix modelling
gigabytejournal.com
October 16, 2024 at 7:55 PM
Congratulations to Cicely Macnamara, Robyn Shuttleworth, @vincent-noel.bsky.social, and Marco Ruscone for publishing PhysiMeSS in @gigabytejournal.bsky.social!
A beautiful community contribution to the @physicell.bsky.social ecosystem! Tremendous work!! 🧪
gigabytejournal.com/articles/136
A beautiful community contribution to the @physicell.bsky.social ecosystem! Tremendous work!! 🧪
gigabytejournal.com/articles/136
Animation of simple "5-minute" tumor-immune model (created in PhysiCell via PhysiCell Studio) I presented at #smb2024 last week.
Grey: tumor (black = dead)
Red: macrophages
Yellow: effector T cells #mathonco 🧪
OK, evidently no video on bluesky yet. I'll post a link at the end of the thread.
Grey: tumor (black = dead)
Red: macrophages
Yellow: effector T cells #mathonco 🧪
OK, evidently no video on bluesky yet. I'll post a link at the end of the thread.
July 9, 2024 at 7:35 PM
Excited to share that our OpenAccess PhysiCell article is among the most cited papers in PLOS Computational Biology in 2022. 🧪
This really speaks to our vibrant community! Thank you all!
Read it at journals.plos.org/ploscompbiol...
This really speaks to our vibrant community! Thank you all!
Read it at journals.plos.org/ploscompbiol...
PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems
Author summary This paper introduces PhysiCell: an open source, agent-based modeling framework for 3-D multicellular simulations. It includes a standard library of sub-models for cell fluid and solid ...
journals.plos.org
September 15, 2023 at 10:16 PM
Excited to share that our OpenAccess PhysiCell article is among the most cited papers in PLOS Computational Biology in 2022. 🧪
This really speaks to our vibrant community! Thank you all!
Read it at journals.plos.org/ploscompbiol...
This really speaks to our vibrant community! Thank you all!
Read it at journals.plos.org/ploscompbiol...
This is our third year teaching the workshop.
Each year, we've introduced new tools, infrastructure, and advances to make PhysiCell easier and faster to master.
We want to get past learning and straight to hands-on projects as fast as we can.
Each year, we've introduced new tools, infrastructure, and advances to make PhysiCell easier and faster to master.
We want to get past learning and straight to hands-on projects as fast as we can.
August 6, 2023 at 6:28 AM
This is our third year teaching the workshop.
Each year, we've introduced new tools, infrastructure, and advances to make PhysiCell easier and faster to master.
We want to get past learning and straight to hands-on projects as fast as we can.
Each year, we've introduced new tools, infrastructure, and advances to make PhysiCell easier and faster to master.
We want to get past learning and straight to hands-on projects as fast as we can.
At this workshop, we teach how to build agent-based models of multicellular systems in PhysiCell, our open source ABM simulation framework for multicellular systems biology.
After initial instruction, we pause for brainstorming to clear the way for team building and a hackathon.
After initial instruction, we pause for brainstorming to clear the way for team building and a hackathon.
August 6, 2023 at 6:25 AM
At this workshop, we teach how to build agent-based models of multicellular systems in PhysiCell, our open source ABM simulation framework for multicellular systems biology.
After initial instruction, we pause for brainstorming to clear the way for team building and a hackathon.
After initial instruction, we pause for brainstorming to clear the way for team building and a hackathon.
Very excited to start the 2023 PhysiCell Virtual Workshop and Hackathon later today!
main agenda:
https://github.com/physicell-training/ws2023/blob/main/agenda.md
I'll use this opportunity to introduce my science and lab to BlueSky. Watch this space! 🧪
main agenda:
https://github.com/physicell-training/ws2023/blob/main/agenda.md
I'll use this opportunity to introduce my science and lab to BlueSky. Watch this space! 🧪
github.com
August 6, 2023 at 6:22 AM
Very excited to start the 2023 PhysiCell Virtual Workshop and Hackathon later today!
main agenda:
https://github.com/physicell-training/ws2023/blob/main/agenda.md
I'll use this opportunity to introduce my science and lab to BlueSky. Watch this space! 🧪
main agenda:
https://github.com/physicell-training/ws2023/blob/main/agenda.md
I'll use this opportunity to introduce my science and lab to BlueSky. Watch this space! 🧪
Ooh, I'd be happy to do a scientific sticker exchange! :-)
July 31, 2023 at 10:33 PM
Ooh, I'd be happy to do a scientific sticker exchange! :-)