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

MELI-3D: A computational pipeline of enzyme
selection using enzyme-ligand interactions

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

WebCell is a web-based interface of integrated
simulation environment for cellular networks

BioSilico is a web-based database that facilitates the search and analysis of metabolic pathways

EcoProDB services integrated protein information,
localization, theoretical and experimental 2-D map

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