RamanLab/minMicrobiome

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MATLAB
License
MIT License
Created over 2 years ago
Updated 12 months ago

RamanLab/minMicrobiome

RamanLab

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Code for generation of Minimal Microbiomes using a constraint-based approach

ReactionMiner

Tool to predict (bio)chemical reactions using graph mining.

FastSL

A MATLAB toolbox to rapidly evaluate synthetic lethal sets in organisms using the genome-scale metabolic models

iCOMIC

nbfpeg

PIVOT

Jupyter Notebook

MinReact

CAMP

fbc_curation_matlab

fbc_curation contains MATLAB/COBRA helpers for reproducibility of fbc models.

SysBioBook-codes

This repository contains companion codes, developed for use with the CRC Press Book "An Introduction to Systems Biology" by Karthik Raman

co-FSEOF

minRerouting

Package to understand the compensatory mechanisms performing similar metabolic functions through analysis of Synthetic Lethals

Jupyter Notebook

ramanlab.github.io

ramanlab.github.io

NonLinearAdaptation

This repository contains the necessary MATLAB and SIMULINK files for the simulation studies done in the manuscript titled, 'Design Principles for Global, Perfect Adaptation]{Design Principles for Perfect Adaptation in Biological Networks with Nonlinear Dynamics'

picCASO

picCASO is a MATLAB package to simulate the dynamics of spatial patterning of a microbial consortium on a 2-dimensional surface.

FastSL-py

Python implementation of FastSL

ComPass

A tool to predict sub-networks from metabolic networks

cTaG

DiseaseModuleIdentification

NBDriver

Codes required to reproduce the results from the NBDriver manuscript

comm-synleth-virgo

Repository for running FastSL on the community models of Human gut microbes on the Virgo cluster at IIT Madras.