Repositories list

• 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-species. Representing missing experimental values supports the rational experimental design to abridge kinetic parameter measurements. Linking multi-omics data and providing data on the me…

  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 effectively switch cellular states" - Raj et al (2022)

  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-hardware+ 1protein-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