HAL
@HybridAutomata
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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
It’s been a long time coming but HAL is finally published in @PLOSCompBiol check out our software paper https://t.co/BdUzIUJJxd and our website https://t.co/5fHNBbJ0og for more details on how to get started with our quick prototyping agent based platform! #AndersonLab
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Exciting News! Lenia-in-HAL! 🚨 We released Lenia in the Hybrid Automata Library (@HybridAutomata) and everyone can implement Lenia using this link https://t.co/6c9JjmsyaA
github.com
Repository for Lenia framework, implemented in Hybrid Automata Library (HAL) - MathOnco/Lenia-in-HAL
"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
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It's so cool to use @HybridAutomata to run the same simulation, but color-code and visualize many different ways:
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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:
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A thread on our #metaphenotypes paper: https://t.co/66z12ci0Ar 🧵🧵🧵
frontiersin.org
IntroductionMetabolism plays a complex role in the evolution of cancerous tumors, including inducing a multifaceted effect on the immune system to aid immune...
Excited to share the #AndersonLab 1st #Metaphenotype paper: https://t.co/Mdo90P2ZMH 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:
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"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
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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. https://t.co/DgxWGEyU07
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Re-sharing this old blog post on combining @HybridAutomata with #EvoFreq: https://t.co/wiTQfl968p even though i wrote it, i still refer to it myself when building models 😅
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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
Metabolism plays a complex role in the evolution of cancerous tumors, including inducing a multifaceted effect on the immune system to aid immune escape. Immune escape is, by definition, a collective...
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. https://t.co/eBk0s89ACr
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Moffitt Researchers Use Computer Modeling to Understand How Self-Renewal Processes Impact Skin Cell Evolution #AndersonLab @mathonco @MoffittNews
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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 https://t.co/QdexxWOR4L
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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/🧵
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Check out the landing page for @CommsMedicine
https://t.co/OQpTAVnFB7 highlighting @StroblMAR latest paper https://t.co/VdUkqgfNBL we see a gorgeous multi panel set of simulations using @HybridAutomata
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Another neat example of modeling using @HybridAutomata , this time in SARS-CoV-2 applications: https://t.co/hwuMXatdhB nice work @gergely_rost & @S_Marzban et al 💯
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Pleased to share a new collaboration with @cmaley on @EvolTherapy led by Daniel Thomas: In Silico Investigations of Multi-Drug Adaptive Therapy Protocols https://t.co/yPJ3B2Lf3r Another great application of @HybridAutomata!
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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:
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The code and data for the model and for all analyses presented in this paper is publicly available at
github.com
This repository contains the code and data for our publication Strobl et al (2022). Spatial structure impacts adaptive therapy by shaping intra-tumoral competition. Commun Med 2, 46, available at: ...
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Check out the landing page for @CommsMedicine
https://t.co/OQpTAVnFB7 highlighting @StroblMAR latest paper https://t.co/VdUkqgfNBL we see a gorgeous multi panel set of simulations using @HybridAutomata
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#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 ( https://t.co/hhM5lEOIZl) in the morning news of Hungarian national televison: https://t.co/HWae1FVVkx
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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! https://t.co/lLZntrg5fY
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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): https://t.co/eQqn0o61cM (the C.A. rules are in the next tweet)
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