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@RamanLab Raman Lab, IIT Madras

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    49 repositories

    • FastSL

      Public
      A MATLAB toolbox to rapidly evaluate synthetic lethal sets in organisms using the genome-scale metabolic models
      MATLAB
      •7•7•0•0•Updated Feb 8, 2025Feb 8, 2025

    • COSMOS

      Public
      Compares monocultures and cocultres in an identical environment to identify the optimal microbial system
      MATLAB
      •0•0•0•0•Updated Feb 8, 2025Feb 8, 2025

    • metquest

      Public
      Enumerating biosynthetic pathways in metabolic networks
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •11•12•0•0•Updated Feb 5, 2025Feb 5, 2025

    • TNBC-single-cell-markers

      Public
      Reproducible code for identifying TIL-based markers from single-cell RNA-seq data of TNBC patients
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 2, 2025Feb 2, 2025

    • Neobacillus

      Public
      Neobacillus driksii sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in Neobacillus
      0•0•0•0•Updated Jan 25, 2025Jan 25, 2025

    • BenchmCommDetection

      Public
      Contains the python module to implement community detection algos along with the final results obtained from benchmark analysis
      Jupyter Notebook
      •0•0•0•0•Updated Jan 3, 2025Jan 3, 2025

    • CAMP

      Public
      MATLAB
      •0•2•0•0•Updated Dec 3, 2024Dec 3, 2024

    • fbc_curation_matlab

      Public
      fbc_curation contains MATLAB/COBRA helpers for reproducibility of fbc models.
      MATLAB
      •
      GNU Lesser General Public License v3.0
      •2•2•1•0•Updated Aug 29, 2024Aug 29, 2024

    • phoenix-novel-species

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Aug 21, 2024Aug 21, 2024

    • NonLinearAdaptation

      Public
      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
      •0•1•0•0•Updated May 29, 2024May 29, 2024

    • ISS_Enterobacter

      Public
      Python
      •0•0•0•0•Updated May 16, 2024May 16, 2024

    • Panera

      Public
      MATLAB repository to construct pan-genus metabolic models (PGMM)
      MATLAB
      •0•0•0•0•Updated May 7, 2024May 7, 2024

    • DNA-Computing-for-the-Subset-Sum-Problem

      Public
      This repository contains the code I wrote for my undergraduate research project on 'DNA-based computing for the Subset Product Problem', done at IIT Madras.
      Jupyter Notebook
      •1•0•0•0•Updated May 6, 2024May 6, 2024

    • minRerouting

      Public
      Package to understand the compensatory mechanisms performing similar metabolic functions through analysis of Synthetic Lethals
      Jupyter Notebook
      •1•2•7•0•Updated Mar 19, 2024Mar 19, 2024

    • minMicrobiome

      Public
      Code for generation of Minimal Microbiomes using a constraint-based approach
      MATLAB
      •
      MIT License
      •1•4•1•0•Updated Dec 12, 2023Dec 12, 2023

    • metquest2

      Public
      Enumerating biosynthetic pathways in metabolic networks
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •11•8•0•1•Updated Sep 6, 2023Sep 6, 2023

    • SysBioBook

      Public
      HTML
      •0•0•4•0•Updated Jul 6, 2023Jul 6, 2023

    • structure-based-drug-design

      Public
      Structure based Drug Design using Distance prediction with Graph Neural Networks - Dual Degree Project
      Jupyter Notebook
      •1•0•0•0•Updated Jun 3, 2023Jun 3, 2023

    • CASTLE

      Public
      HTML
      •0•0•0•0•Updated Jun 2, 2023Jun 2, 2023

    • FastSL-py

      Public
      Python implementation of FastSL
      linear-programmingcomputational-biologyflux-balance-analysissynthetic-lethality-analysis
      Python
      •
      GNU General Public License v3.0
      •1•0•0•2•Updated May 22, 2023May 22, 2023

    • Robust-Adaptation

      Public
      MATLAB
      •0•0•0•0•Updated Feb 20, 2023Feb 20, 2023

    • co-FSEOF

      Public
      MATLAB
      •1•2•1•0•Updated Jan 23, 2023Jan 23, 2023

    • cobratoolbox

      Public
      The COnstraint-Based Reconstruction and Analysis Toolbox
      MATLAB
      •
      Other
      •321•0•0•0•Updated Jul 9, 2022Jul 9, 2022

    • COWAVE

      Public
      COVID-19 Wave dataset, based on WHO dataset and labelled as waves based on a new definition.
      machine-learningxgboostclassificationcovid-19dataset
      Jupyter Notebook
      •0•0•0•0•Updated Jul 4, 2022Jul 4, 2022

    • iCOMIC_doc

      Public
      iCOMIC is an open source genomic data analysis tool characterized by a user friendly GUI. It integrates many independent core workflows for Whole Genome/Exome Sequencing and RNA-Seq data analysis.
      Creative Commons Zero v1.0 Universal
      •3•0•0•0•Updated Jun 17, 2022Jun 17, 2022

    • iCOMIC

      Public
      Perl
      •
      Apache License 2.0
      •5•5•0•0•Updated Jun 14, 2022Jun 14, 2022

    • PIVOT

      Public
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •1•3•0•0•Updated May 10, 2022May 10, 2022

    • Metabolic-Modelling-of-the-ISS-Microbiome

      Public
      Created on 2020-11-04 to maintain versions of the project from this time point onwards.
      Python
      •0•0•0•0•Updated Mar 5, 2022Mar 5, 2022

    • SystemsTheoryAdaptation

      Public
      MATLAB
      •
      MIT License
      •1•0•0•0•Updated Nov 13, 2021Nov 13, 2021

    • NBDriver

      Public
      Codes required to reproduce the results from the NBDriver manuscript
      Python
      •1•1•0•0•Updated Sep 25, 2021Sep 25, 2021