Pinned Repositories
cobrapy
COBRApy is a package for constraint-based modeling of biological networks
DeepEnzyme
fastgraphGEM
R package for building and visualising GEM graphs automatically with aid of cellDesigner 4.4
hongPy
hongR
It is a R package to collect some easy codes for handy use
machine-learning-books
this is a fork of collection of books for machine learning.
Tutorial_for_Yeastspot3D
Tutorial for Yeastspot3D
Unified_Yeast_GEMs_Database
vivarium
a multi-scale simulation platform for whole-cell modeling
yeast-model-update
Data and code for yeast-GEM update
hongzhonglu's Repositories
hongzhonglu/DeepEnzyme
hongzhonglu/Unified_Yeast_GEMs_Database
hongzhonglu/yeast-GEM
The consensus GEM for Saccharomyces cerevisiae
hongzhonglu/hongPy
hongzhonglu/awesome-deep-learning-single-cell-papers
hongzhonglu/biopandas
Working with molecular structures in pandas DataFrames
hongzhonglu/CellFactory-ecYeastGEM
Code and data for in silico strain design for enhanced production of +100 typical bio-products with yeast as a cell-factory. Predictions are based on the ecYeastGEM model avaiable at ecModels.
hongzhonglu/chemprop
Message Passing Neural Networks for Molecule Property Prediction
hongzhonglu/ColabFold
Making Protein folding accessible to all via Google Colab!
hongzhonglu/cosmis
COSMIS is a framework for quantifying the mutational constraint on amino acid sites in 3D spatial neighborhoods. The framework currently maps the landscape of 3D mutational constraint on 6.1 amino acid sites covering >80% (16,533) of human proteins.
hongzhonglu/ecFactory
A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism
hongzhonglu/essential-gene-detection
Detection of essential genes with Graph Neural Networks on protein-protein interaction networks
hongzhonglu/FALCONET_tutorial
hongzhonglu/GDGA_Shortcourse
Files for the Genome Design/Genome Analytics Short-course organized by the SBRG
hongzhonglu/geckopy
Enzyme-constrained genome-scale models in python
hongzhonglu/GraphGym
Platform for designing and evaluating Graph Neural Networks (GNN)
hongzhonglu/gvp-pytorch
Geometric Vector Perceptrons --- a rotation-equivariant GNN for learning from biomolecular structure
hongzhonglu/HGTfinder
hongzhonglu/low-N-protein-engineering
Code and data to reproduce analyses in Biswas et al. (2020) "Low-N protein engineering with data-efficient deep learning".
hongzhonglu/nn4dms
Neural networks for deep mutational scanning data
hongzhonglu/PhyloFisher
PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of protein sequences.
hongzhonglu/provis
Official code repository of "BERTology Meets Biology: Interpreting Attention in Protein Language Models."
hongzhonglu/pytorch-deep-learning
Materials for the Learn PyTorch for Deep Learning: Zero to Mastery course.
hongzhonglu/R_code_for_graph_in_evolution
hongzhonglu/scFEA
single cell Flux Estimation Analysis (scFEA) Try the below web server!
hongzhonglu/stat453-deep-learning-ss21
STAT 453: Intro to Deep Learning @ UW-Madison (Spring 2021)
hongzhonglu/straindesign
StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
hongzhonglu/Yeast-Species-GEMs
A universal metabolic model knowledge database (pan-GEM) for current existing yeast species with genome sequence, based on which we will build the GEMs of high quality for each yeast species.
hongzhonglu/yeast_GEM_multi_omics_analysis
This repo will be used to store all the related codes, datasets and results for multi-omics analysis under different nitrogen sources
hongzhonglu/Yli_GEMs