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anneal-path

Simulated Annealing-based branched novel biochemical pathway prediction tool

automated_scaledown

aybrah

Analyzing Yeasts by Reconstructing Ancestry of Homologs

coculture_knockout_protocol_2023

Bhanu's 2023 summer project.

community_engineering

Increasing evenness and stability in synthetic microbial consortia

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

covid_19_mutations

Identifying mutations on the COVID-19 sequences gathered from https://www.gisaid.org/ database.

cpi_webapp

dc_dfba

Nonlinear programming reformulation of dynamic flux balance analysis models

deepmind-research

This repository contains implementations and illustrative code to accompany DeepMind publications

dsol_rv0.2

deep protein solubility prediction

emilio

Source code for EMILiO: A fast algorithm for genome-scale strain design.

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)

etfl

ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints

ethyleneglycol-to-glycolate

Code for modeling and computational analyses for EG-to-Glycolate conversion in E. coli

flux_sensing

focus_v1

fyrment

Fungi pan-genome-scale network reconstruction

generative_protein_design_datasets

A repository highlighting and linking existing resources and datasets for generative protein modeling.

geneva

Gene based modification of MoVE - a tool that identifies metabolic valves to switch from a growth to a production stage.

genotheque

Place of genomes. Extracting genomic protein sequences from genomic nucleotide sequences, and annotation with AYbRAH.

hh-pbpk-ethanol

ident

Perform identifiability analysis in small kinetic models for experimental design using steady state fluxes and concentrations.

impact

The impact framework is designed to help scientists extract insight from experimental data in a transparent and reproducible fashion.

kbistable

Code for Model-based Design of Bistable Cell Factories for Metabolic Engineering

kinetic_interactions

this repository analyzes collected kinetic regulation in the in-house database and apply ML algorithms to estimate missing values.

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.

malate_pyruvate_shuttle

Models associated with the research article - "An interspecies malate-pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community"

mcpecaso

A two stage optimization framework that finds optimal operating points to maximize desired process variables. First introduced in the article - "Novel two-stage processes for optimal chemical production in microbes"