Hybrid Automata Library is a Java library for hybrid agent-based reaction diffusion modeling both on & off lattice in 2 & 3D developed by the #AndersonLab
Tampa, FL
Joined September 2018
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It’s been a long time coming but HAL is finally published in @PLOSCompBiol check out our software paper journals.plos.org/ploscompbi… and our website halloworld.org for more details on how to get started with our quick prototyping agent based platform! #AndersonLab – at Tampa, FL
HAL retweeted
Exciting News! Lenia-in-HAL! 🚨
We released Lenia in the Hybrid Automata Library (@HybridAutomata) and everyone can implement Lenia using this link
github.com/MathOnco/Lenia-in…
"Spatial interactions modulate tumor growth and immune infiltration"
Our latest preprint:
@S_Marzban in collab w/ @AmelioLab!
We apply methods from artificial life, @BertChakovsky's #Lenia, as a model of tumor-immune:
- spatial growth dynamics
- cell-cell competition &
- cell migration
Application to head & neck squamous cell carcinomas to elucidate the role of collagen on immune infiltration
biorxiv.org/content/10.1101/…
HAL retweeted
It's so cool to use @HybridAutomata to run the same simulation, but color-code and visualize many different ways:
HAL retweeted
Immune escape is a logical setting to implement an investigation into collective/group phenotypes (e.g. metaphenotypes, if you will)
Tumor-immune interactions are by a definition, a collective phenomenon by requiring the presence of two cell types interacting in close proximity: tumor and immune.
HAL retweeted
A thread on our #metaphenotypes paper:
frontiersin.org/journals/imm…
🧵🧵🧵
Excited to share the #AndersonLab 1st #Metaphenotype paper: frontiersin.org/journals/imm… Years in the making with many of @mathonco but @mathoncbro drove it to the finish line! Emerging in 2016 from @markrt_ work on cancer metabolic evolution, we observed the phenomena in this movie:
HAL retweeted
"Spatial interactions modulate tumor growth and immune infiltration"
Our latest preprint:
@S_Marzban in collab w/ @AmelioLab!
We apply methods from artificial life, @BertChakovsky's #Lenia, as a model of tumor-immune:
- spatial growth dynamics
- cell-cell competition &
- cell migration
Application to head & neck squamous cell carcinomas to elucidate the role of collagen on immune infiltration
biorxiv.org/content/10.1101/…
HAL retweeted
Super chuffed to see @mathoncbro artwork generated with @HybridAutomata on the cover of @TrendsCellBio for our recent article with @markrt_ on how, Agent-based methods facilitate integrative science in cancer. cell.com/trends/cell-biology…
HAL retweeted
Re-sharing this old blog post on combining @HybridAutomata with #EvoFreq:
mathematical-oncology.org/bl…
even though i wrote it, i still refer to it myself when building models 😅
HAL retweeted
This is so cool, our theoretical work led by @mathoncbro with @markrt_ using @HybridAutomata comes to similar conclusions but we use a buffer agent to modulate acidity and our model is of a more generic ductal tumour: biorxiv.org/content/10.1101/… – at Tampa, FL
Proud to share our work showing how tumor acidity controls pancreatic cancer cell metabolism and tumor immune landscape. Tampering with tumor acidity elicits anti-tumor immune responses and overcomes resistance to immunotherapy in pancreatic cancer models.
nature.com/articles/s43018-0…
HAL retweeted
Moffitt Researchers Use Computer Modeling to Understand How Self-Renewal Processes Impact Skin Cell Evolution #AndersonLab @mathonco @MoffittNews moffitt.org/newsroom/press-r…
HAL retweeted
Please to announce our latest paper led by @research_junkie just out in @PNASNews on how, Homeostasis limits keratinocyte evolution. #AndersonLab Many years in the making with help from Eunjung Kim, Rafael Bravo, @mathoncbro @leedham_simon & Darryl Shibata pnas.org/doi/10.1073/pnas.20…
HAL retweeted
I’m excited to share our recently published manuscript in PNAS on clonal dynamics in the homeostatic epidermis. This paper took a winding course and was the first project that was incorporated into my DPhil. 1/🧵
HAL retweeted
Check out the landing page for @CommsMedicine nature.com/commsmed/ highlighting @StroblMAR latest paper nature.com/articles/s43856-0… we see a gorgeous multi panel set of simulations using @HybridAutomata
HAL retweeted
Another neat example of modeling using @HybridAutomata , this time in SARS-CoV-2 applications:
mdpi.com/1999-4915/14/5/1103
nice work @gergely_rost & @S_Marzban et al 💯
HAL retweeted
Pleased to share a new collaboration with @cmaley on @EvolTherapy led by Daniel Thomas: In Silico Investigations of Multi-Drug Adaptive Therapy Protocols mdpi.com/1655416 Another great application of @HybridAutomata!
HAL retweeted
My latest weekend project: implementing @BertChakovsky's Lenia project in @HybridAutomata.
It's an elegant and mathematically beautiful method to extend discrete cellular automata (e.g. Game of Life) to allow continuous states.
🧵 incoming thread of cool automata gifs:
Check out the landing page for @CommsMedicine nature.com/commsmed/ highlighting @StroblMAR latest paper nature.com/articles/s43856-0… we see a gorgeous multi panel set of simulations using @HybridAutomata
The code and data for the model and for all analyses presented in this paper is publicly available at github.com/MathOnco/strobl20…
#HAL showcased on Hungarian national tv! Thanks @gergely_rost for using our hybrid automata platform!
I had to get up very early to talk about our hybrid agent based - partial differential equation model for viral dynamics (royalsocietypublishing.org/d…) in the morning news of Hungarian national televison: facebook.com/mtva.hirado/vid…
HAL retweeted
Pleased to announce the release of #AndersonLab latest tool: GATTACA, for base pair resolution mutation tracking in agent-based models like @HybridAutomata. Developed by @research_junkie for our somatic evolution studies. Here’s a cool gif! biorxiv.org/content/10.1101/… – at Tampa, FL
HAL retweeted
Learned something new from @normonics' talk at #RWRI today -- Turing patterns can form in an *extremely simple* discrete cell automata:
Here's my code using Young's model (1984) created in @HybridAutomata):
github.com/JeffreyWest/HAL-e…
(the C.A. rules are in the next tweet)