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@Emergent-Behaviors-in-Biology

Emergent Behaviors in Biology

Research group of Pankaj Mehta and collaborators.

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  1. mlreview_notebooks mlreview_notebooks Public

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

    Jupyter Notebook 67 55

  2. community-simulator community-simulator Public

    Simulate microbial community batch culture experiments.

    Jupyter Notebook 42 13

  3. scTOP scTOP Public

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

    Jupyter Notebook 4 2

  4. crossfeeding-transition crossfeeding-transition Public

    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 2 1

  5. typical-random-ecosystems typical-random-ecosystems Public

    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).

    Mathematica 2 1

  6. microbiome-patterns microbiome-patterns Public

    Scripts and data to accompany Marsland, Cui and Mehta "A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns," bioRxiv 622829 (2019)

    Jupyter Notebook 1 5

Repositories

Showing 10 of 22 repositories
  • community-simulator Public

    Simulate microbial community batch culture experiments.

    Emergent-Behaviors-in-Biology/community-simulator’s past year of commit activity
    Jupyter Notebook 42 MIT 13 5 1 Updated Oct 31, 2024
  • Differentiable-Gillespie-Algorithm Public

    These are notebooks for the Differentiable Gillespie Algorithm

    Emergent-Behaviors-in-Biology/Differentiable-Gillespie-Algorithm’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Jul 5, 2024
  • 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
    Jupyter Notebook 0 MIT 0 0 0 Updated May 7, 2024
  • Multi-trophic-ecosystem Public

    This is repository associated with Feng et. al mansucript.

    Emergent-Behaviors-in-Biology/Multi-trophic-ecosystem’s past year of commit activity
    Mathematica 0 MIT 0 0 0 Updated Mar 18, 2024
  • scTOP Public

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

    Emergent-Behaviors-in-Biology/scTOP’s past year of commit activity
    Jupyter Notebook 4 GPL-3.0 2 0 0 Updated Nov 27, 2023
  • 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
    Jupyter Notebook 0 0 0 0 Updated Jul 21, 2023
  • scTOP-PanCanAtlas Public

    scTOP analysis of Pan-Cancer Atlas

    Emergent-Behaviors-in-Biology/scTOP-PanCanAtlas’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated May 16, 2023
  • 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
    Mathematica 0 0 0 0 Updated Apr 2, 2023
  • scTOP-R Public

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

    Emergent-Behaviors-in-Biology/scTOP-R’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Dec 15, 2022
  • Emergent-Behaviors-in-Biology/proj_push_pull’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Sep 16, 2022

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