GeTPRA is a framework that systematically predicts Gene-Transcript-Protein-Reaction Associations
in human metabolism and updates a human genome-scale metabolic model

Recon manager is a collection of scripts to generate Recon 2M and simulate Recon models

DeepEC: A deep learning-powered computational
framework

A framework that systematically predicts drug-drug
interactions (DDIs) and drug-food interactions (DFIs)

iBridge: A gene overexpression targeting method that considers both endogenous and heterologous genes

13C-MFA: A MATLAB-based simulator for flux
analysis using carbon 13

DeepTFactor: a deep learning-based tool for
the prediction of transcription factors

DeepRFC: a deep learning approach to evaluate
biochemical reaction feasibility

Retro-precursor-selection is a framework that
predicts precursors of target products using
retrobiosynthesis

DeepECtransformer: a deep learning model
which utilizes transformer layers as a neural network
architecture to predict EC numbers

A deep learning model that predicts the impact of
cultivation conditions on gene regulation in E. coli

The method of predicting metabolites and metabolic
pathways associated with specific gene mutations

MetaFluxNet is a program package for managing
information on the metabolic reaction network and for quantitatively analyzing metabolic fluxes in an
interactive and customized way

Interactive chemicals map is web-based interactive visual tool that allows the interactive visualization, exploration, and analysis of a complex network of biological and chemical reactions

Recon2M is a biochemically consistent and transcript-level data-compatible generic human GEM

Bacterial genome-scale models constructed by MBEL

antiSMASH allows the rapid genome-wide
identification, annotation and analysis of secondary metabolite biosynthesis gene clusters

The antiSMASH database contains pre-computed
antiSMASH results for bacterial genomes available in the NCBI GenBank repository

CRISPy-web is a user-friendly tool to design single
guide RNAs (sgRNAs) for the CRISPR/Cas9 system

Computational tools to facilitate synthetic biology of
secondary metabolite production