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@LMSE Laboratory for Metabolic Systems Engineering

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    49 repositories

    • CHE222

      Public
      Python Tutorials
      Jupyter Notebook
      •0•0•0•0•Updated Dec 17, 2025Dec 17, 2025

    • comMCS

      Public
      Code for implementing comMCS
      MATLAB
      •
      MIT License
      •0•0•0•0•Updated Nov 28, 2025Nov 28, 2025

    • ai-for-research

      Public
      A curated guide to AI tools that enhance research productivity
      HTML
      •
      MIT License
      •1•0•0•0•Updated Jun 12, 2025Jun 12, 2025

    • Dehalobacter_modelling

      Public
      Python
      •1•0•0•0•Updated Jun 6, 2025Jun 6, 2025

    • Quorum_sensingCrispri

      Public
      Jupyter Notebook
      •1•0•0•0•Updated May 15, 2025May 15, 2025

    • Seq_to_Func_Pred_Model

      Public
      Sequence-to-Function Learning Predictive Model
      Jupyter Notebook
      •0•1•0•0•Updated Aug 21, 2024Aug 21, 2024

    • Seq-to-Func-Learning-Marjan

      Public
      Seq-to-Func-Learning-Marjan
      Jupyter Notebook
      •0•0•0•0•Updated May 9, 2024May 9, 2024

    • community_engineering

      Public
      Increasing evenness and stability in synthetic microbial consortia
      Python
      •0•0•0•0•Updated Mar 26, 2024Mar 26, 2024

    • FOCUS_v1

      Public
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 25, 2024Mar 25, 2024

    • ocFBA

      Public
      This is the main repository for the paper Understanding bacterial adaptation to osmotic stress through the lenses of thermodynamics
      Python
      •0•0•0•0•Updated Mar 22, 2024Mar 22, 2024

    • CoCulture_KnockOut_Protocol_2023

      Public
      Bhanu's 2023 summer project.
      MATLAB
      •1•0•0•0•Updated Sep 6, 2023Sep 6, 2023

    • SprintGapFiller

      Public
      For fast gap filling in microbial communities
      MATLAB
      •
      MIT License
      •0•1•0•0•Updated Aug 18, 2023Aug 18, 2023

    • Generative_Protein_Design_Datasets

      Public
      A repository highlighting and linking existing resources and datasets for generative protein modeling.
      2•1•0•0•Updated Jul 11, 2023Jul 11, 2023

    • Anneal-Path

      Public
      Simulated Annealing-based branched novel biochemical pathway prediction tool
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Apr 29, 2023Apr 29, 2023

    • PathwayLenPred

      Public
      Machine Learning-based biochemical pathway length prediction
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Mar 13, 2023Mar 13, 2023

    • DC_dFBA

      Public
      Nonlinear programming reformulation of dynamic flux balance analysis models
      Julia
      •1•2•0•0•Updated Feb 1, 2023Feb 1, 2023

    • Compound_Protein_Interac_Pred

      Public
      Enzyme Activity Prediction of Sequence Variants onNovel Substrates using Improved Substrate Encodings and Convolutional Pooling
      Python
      •
      MIT License
      •5•18•0•0•Updated Nov 28, 2022Nov 28, 2022

    • genotheque

      Public
      Place of genomes. Extracting genomic protein sequences from genomic nucleotide sequences, and annotation with AYbRAH.
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 5, 2022Oct 5, 2022

    • fyrment

      Public
      Fungi pan-genome-scale network reconstruction
      Python
      •
      GNU General Public License v3.0
      •1•4•10•0•Updated Oct 5, 2022Oct 5, 2022

    • aybrah

      Public
      Analyzing Yeasts by Reconstructing Ancestry of Homologs
      HTML
      •1•4•14•0•Updated Oct 5, 2022Oct 5, 2022

    • KinMod

      Public
      The hierarchical ontology of the KinMod database allows flexible exploration of data attributes and investigation of metabolic relationships within- and cross-s…
      2•1•0•0•Updated Aug 9, 2022Aug 9, 2022

    • enhanced_bistable_switches

      Public
      Code to generate modeling results and parse experimental data for the research article titled "Model guided design of enhanced bi-stable controllers to effecti…
      Jupyter Notebook
      •0•0•0•0•Updated Jul 11, 2022Jul 11, 2022

    • Molecule-Graph-Attributes-For-GNN

      Public
      Obtain Molecule Graph Attributes For GNN
      Python
      •1•0•0•0•Updated May 16, 2022May 16, 2022

    • CPI_WebAPP

      Public
      Python
      •1•0•0•0•Updated May 10, 2022May 10, 2022

    • REVOLVER-protein-purifier

      Public
      Repository for building and operating REVOLVER: An automatic protein purification system for gravity columns. Developed at the University of Toronto.
      arduino3d-printingopen-source-hardwareprotein-purification
      C++
      •
      BSD 2-Clause "Simplified" License
      •1•3•0•0•Updated Apr 10, 2022Apr 10, 2022

    • Kinetic_Interactions

      Public
      this repository analyzes collected kinetic regulation in the in-house database and apply ML algorithms to estimate missing values.
      Python
      •
      Apache License 2.0
      •1•0•0•0•Updated Apr 8, 2022Apr 8, 2022

    • SMRN

      Public
      Reconstruction and analysis of the E coli small-molecule regulatory network.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 9, 2021Aug 9, 2021

    • Community_Gap-Filling

      Public
      Source code and input files for reproducing the results presented in "A gap-filling algorithm for prediction of metabolic interactions in microbial communities"…
      MATLAB
      •1•4•0•0•Updated Jul 30, 2021Jul 30, 2021

    • flux_sensing

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jun 25, 2021Jun 25, 2021

    • impact

      Public
      The impact framework is designed to help scientists extract insight from experimental data in a transparent and reproducible fashion.
      Python
      •
      GNU General Public License v3.0
      •5•4•0•1•Updated May 12, 2021May 12, 2021