Emergent Behaviors in Biology
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mlreview_notebooks
mlreview_notebooks PublicNotebooks for "A high bias low-variance introduction to Machine Learning for physicists."
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community-simulator
community-simulator PublicSimulate microbial community batch culture experiments.
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crossfeeding-transition
crossfeeding-transition PublicCode and data to accompany Marsland et al. (2018) "Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities"
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typical-random-ecosystems
typical-random-ecosystems PublicThis is the code accompanying the manuscript: Cui, Wenping, Robert Marsland III, and Pankaj Mehta. "Diverse communities behave like typical random ecosystems." arXiv:1904.02610 (2019).
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microbiome-patterns
microbiome-patterns PublicScripts and data to accompany Marsland, Cui and Mehta "A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns," bioRxiv 622829 (2019)
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These are notebooks for the Differentiable Gillespie Algorithm
Emergent-Behaviors-in-Biology/Differentiable-Gillespie-Algorithm’s past year of commit activity - syn-phospho-circuits Public
Code and accompanying data for the paper 'Engineering synthetic phosphorylation signaling networks in human cells' authored by X. Yang and colleagues. This repository provides code to reproduce the biophysical modeling analysis presented in the paper.
Emergent-Behaviors-in-Biology/syn-phospho-circuits’s past year of commit activity - scTOP-manuscript Public
Code and LaTeX files for "scTOP: physics-inspired order parameters for cellular identification and visualization"
Emergent-Behaviors-in-Biology/scTOP-manuscript’s past year of commit activity - Geometry-of-Coexistence Public
Repository of interactive visualizations for "Geometry of ecological coexistence and niche differentiation"
Emergent-Behaviors-in-Biology/Geometry-of-Coexistence’s past year of commit activity - proj_push_pull Public
Emergent-Behaviors-in-Biology/proj_push_pull’s past year of commit activity
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