Pinned Repositories
aybrah
Analyzing Yeasts by Reconstructing Ancestry of Homologs
Community_Gap-Filling
Source code and input files for reproducing the results presented in "A gap-filling algorithm for prediction of metabolic interactions in microbial communities".
Compound_Protein_Interac_Pred
Enzyme Activity Prediction of Sequence Variants onNovel Substrates using Improved Substrate Encodings and Convolutional Pooling
DC_dFBA
Nonlinear programming reformulation of dynamic flux balance analysis models
fyrment
Fungi pan-genome-scale network reconstruction
HH-PBPK-Ethanol
impact
The impact framework is designed to help scientists extract insight from experimental data in a transparent and reproducible fashion.
KinMod
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 metabolic regulation network encourages the development of novel machine learning techniques for predicting missing kinetic parameters and promotes accurate kinetic model construction of cells metabolism by providing a comprehensive list of available kinetic measurements. To define a thorough depiction of KinMod data, we develop six analyses to visualize associations between data classes belonging to separate sections of the metabolism. Through these analyses, we demonstrate that the KinMod database provides a unique framework for biologists and engineers to retrieve, evaluate and compare the functional metabolism of species, including the regulatory network, and discover the extent of available and missing experimental values of the metabolic regulation.
move
MoVE is a tool that identifies metabolic valves to switch from a growth to a production stage.
REVOLVER-protein-purifier
Repository for building and operating REVOLVER: An automatic protein purification system for gravity columns. Developed at the University of Toronto.
Laboratory for Metabolic Systems Engineering's Repositories
LMSE/Compound_Protein_Interac_Pred
Enzyme Activity Prediction of Sequence Variants onNovel Substrates using Improved Substrate Encodings and Convolutional Pooling
LMSE/aybrah
Analyzing Yeasts by Reconstructing Ancestry of Homologs
LMSE/fyrment
Fungi pan-genome-scale network reconstruction
LMSE/impact
The impact framework is designed to help scientists extract insight from experimental data in a transparent and reproducible fashion.
LMSE/Community_Gap-Filling
Source code and input files for reproducing the results presented in "A gap-filling algorithm for prediction of metabolic interactions in microbial communities".
LMSE/REVOLVER-protein-purifier
Repository for building and operating REVOLVER: An automatic protein purification system for gravity columns. Developed at the University of Toronto.
LMSE/DC_dFBA
Nonlinear programming reformulation of dynamic flux balance analysis models
LMSE/Generative_Protein_Design_Datasets
A repository highlighting and linking existing resources and datasets for generative protein modeling.
LMSE/HH-PBPK-Ethanol
LMSE/KinMod
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 metabolic regulation network encourages the development of novel machine learning techniques for predicting missing kinetic parameters and promotes accurate kinetic model construction of cells metabolism by providing a comprehensive list of available kinetic measurements. To define a thorough depiction of KinMod data, we develop six analyses to visualize associations between data classes belonging to separate sections of the metabolism. Through these analyses, we demonstrate that the KinMod database provides a unique framework for biologists and engineers to retrieve, evaluate and compare the functional metabolism of species, including the regulatory network, and discover the extent of available and missing experimental values of the metabolic regulation.
LMSE/Seq_to_Func_Pred_Model
Sequence-to-Function Learning Predictive Model
LMSE/SprintGapFiller
For fast gap filling in microbial communities
LMSE/Anneal-Path
Simulated Annealing-based branched novel biochemical pathway prediction tool
LMSE/automated_scaledown
LMSE/deepmind-research
This repository contains implementations and illustrative code to accompany DeepMind publications
LMSE/Molecule-Graph-Attributes-For-GNN
Obtain Molecule Graph Attributes For GNN
LMSE/ocFBA
This is the main repository for the paper Understanding bacterial adaptation to osmotic stress through the lenses of thermodynamics
LMSE/PathwayLenPred
Machine Learning-based biochemical pathway length prediction
LMSE/CoCulture_KnockOut_Protocol_2023
Bhanu's 2023 summer project.
LMSE/community_engineering
Increasing evenness and stability in synthetic microbial consortia
LMSE/COVID_19_Mutations
Identifying mutations on the COVID-19 sequences gathered from https://www.gisaid.org/ database.
LMSE/CPI_WebAPP
LMSE/enhanced_bistable_switches
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)
LMSE/EthyleneGlycol-to-Glycolate
Code for modeling and computational analyses for EG-to-Glycolate conversion in E. coli
LMSE/flux_sensing
LMSE/FOCUS_v1
LMSE/genotheque
Place of genomes. Extracting genomic protein sequences from genomic nucleotide sequences, and annotation with AYbRAH.
LMSE/Kinetic_Interactions
this repository analyzes collected kinetic regulation in the in-house database and apply ML algorithms to estimate missing values.
LMSE/Seq-to-Func-Learning-Marjan
Seq-to-Func-Learning-Marjan
LMSE/SMRN
Reconstruction and analysis of the E coli small-molecule regulatory network.