Discover RamanLab/comm-synleth-virgo Open Source project

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RamanLab

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

ReactionMiner

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

C++

FastSL

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

iCOMIC

nbfpeg

PIVOT

minMicrobiome

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

MATLAB

MinReact

MATLAB

CAMP

MATLAB

fbc_curation_matlab

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

MATLAB

SysBioBook-codes

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

MATLAB

co-FSEOF

MATLAB

minRerouting

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

Jupyter Notebook

ramanlab.github.io

CSS

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'

MATLAB

picCASO

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

MATLAB

FastSL-py

Python implementation of FastSL

Python

ComPass

A tool to predict sub-networks from metabolic networks

Python

cTaG

Python

DiseaseModuleIdentification

Python

NBDriver

Codes required to reproduce the results from the NBDriver manuscript

Python

RamanLab/comm-synleth-virgo

RamanLab

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