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    22 repositories

    • community-simulator

      Public
      Simulate microbial community batch culture experiments.
      Jupyter Notebook
      •
      MIT License
      •13•42•5•1•Updated Oct 31, 2024Oct 31, 2024

    • Differentiable-Gillespie-Algorithm

      Public
      These are notebooks for the Differentiable Gillespie Algorithm
      Jupyter Notebook
      •0•0•0•0•Updated Jul 5, 2024Jul 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.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 7, 2024May 7, 2024

    • Multi-trophic-ecosystem

      Public
      This is repository associated with Feng et. al mansucript.
      Mathematica
      •
      MIT License
      •0•0•0•0•Updated Mar 18, 2024Mar 18, 2024

    • scTOP

      Public
      A package for identifying cell phenotype from single-cell RNA-sequencing data.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •2•4•0•0•Updated Nov 27, 2023Nov 27, 2023

    • scTOP-manuscript

      Public
      Code and LaTeX files for "scTOP: physics-inspired order parameters for cellular identification and visualization"
      Jupyter Notebook
      •0•0•0•0•Updated Jul 21, 2023Jul 21, 2023

    • scTOP-PanCanAtlas

      Public
      scTOP analysis of Pan-Cancer Atlas
      Jupyter Notebook
      •0•0•0•0•Updated May 16, 2023May 16, 2023

    • Geometry-of-Coexistence

      Public
      Repository of interactive visualizations for "Geometry of ecological coexistence and niche differentiation"
      Mathematica
      •0•0•0•0•Updated Apr 2, 2023Apr 2, 2023

    • scTOP-R

      Public
      An R package for identifying cell phenotype from single-cell RNA-sequencing data.
      Jupyter Notebook
      •0•0•0•0•Updated Dec 15, 2022Dec 15, 2022

    • proj_push_pull

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Sep 16, 2022Sep 16, 2022

    • NESS-Topology

      Public
      This contains notebook associated with paper "Thermodynamic origins of topological protection in nonequilibrium stochastic systems" by Mehta and Rocks.
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Jun 15, 2022Jun 15, 2022

    • immune-svm

      Public
      Using a machine-learning algorithm to understand adaptive immune system dynamics
      Jupyter Notebook
      •
      MIT License
      •2•1•0•0•Updated Aug 20, 2020Aug 20, 2020

    • 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
      •1•2•0•0•Updated Jul 6, 2020Jul 6, 2020

    • covid19

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Apr 29, 2020Apr 29, 2020

    • 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
      •5•1•0•0•Updated Feb 24, 2020Feb 24, 2020

    • lung-primordium

      Public
      Analysis and plotting scripts used in Ikonomou et al., "The Genetic Program of Primordial Lung Progenitors."
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 5, 2020Feb 5, 2020

    • mepp

      Public
      Scripts and data to accompany arXiv:1901.09673
      Jupyter Notebook
      •1•0•0•0•Updated Dec 23, 2019Dec 23, 2019

    • 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
      •
      MIT License
      •1•2•1•0•Updated Dec 16, 2019Dec 16, 2019

    • species-packing-bound

      Public
      Cavity method with linear resource dynamics
      Jupyter Notebook
      •1•1•0•0•Updated Nov 6, 2019Nov 6, 2019

    • mlreview_notebooks

      Public
      Notebooks for "A high bias low-variance introduction to Machine Learning for physicists."
      machine-learningphysics
      Jupyter Notebook
      •54•67•1•0•Updated Oct 15, 2019Oct 15, 2019

    • metabolic-homology

      Public
      Predict community composition in novel environments using metabolic homology
      Python
      •
      MIT License
      •2•1•0•0•Updated Sep 18, 2019Sep 18, 2019

    • random-qp

      Public
      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).
      Mathematica
      •1•0•0•0•Updated May 1, 2019May 1, 2019