RamanLab/NonLinearAdaptation

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RamanLab/NonLinearAdaptation

RamanLab

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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'

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

minMicrobiome

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

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

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.