Emergent-Behaviors-in-Biology/metabolic-homology

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Python
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MIT License
Created over 5 years ago
Updated about 5 years ago

Emergent-Behaviors-in-Biology/metabolic-homology

Emergent-Behaviors-in-Biology

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Predict community composition in novel environments using metabolic homology

mlreview_notebooks

Notebooks for "A high bias low-variance introduction to Machine Learning for physicists."

Jupyter Notebook

community-simulator

Simulate microbial community batch culture experiments.

Jupyter Notebook

scTOP

A package for identifying cell phenotype from single-cell RNA-sequencing data.

Jupyter Notebook

typical-random-ecosystems

This 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).

crossfeeding-transition

Code and data to accompany Marsland et al. (2018) "Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities"

Jupyter Notebook

microbiome-patterns

Scripts 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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proj_push_pull

Jupyter Notebook

species-packing-bound

Cavity method with linear resource dynamics

Jupyter Notebook

covid19

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