emergent-behaviors-in-biology Goto Github PK

community-simulator

Simulate microbial community batch culture experiments.

covid19

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"

geometry-of-coexistence

Repository of interactive visualizations for "Geometry of ecological coexistence and niche differentiation"

immune-svm

Using a machine-learning algorithm to understand adaptive immune system dynamics

lung-primordium

Analysis and plotting scripts used in Ikonomou et al., "The Genetic Program of Primordial Lung Progenitors."

mepp

Scripts and data to accompany arXiv:1901.09673

metabolic-homology

Predict community composition in novel environments using metabolic homology

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)

mlreview_notebooks

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

multi-trophic-ecosystem

This is repository associated with Feng et. al mansucript.

ness-topology

This contains notebook associated with paper "Thermodynamic origins of topological protection in nonequilibrium stochastic systems" by Mehta and Rocks.

proj_push_pull

random-qp

Code and data to accompany Mehta, Cui, Wang and Marsland, "Constrained optimization as ecological dynamics with applications to random quadratic programming in high dimensions," arXiv:1809.04221 (2019).

sctop

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

sctop-manuscript

Code and LaTeX files for "scTOP: physics-inspired order parameters for cellular identification and visualization"

sctop-pancanatlas

scTOP analysis of Pan-Cancer Atlas

sctop-r

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

species-packing-bound

Cavity method with linear resource dynamics

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).