Jeremy Zucker's repositories
bbh
Bidirectional Best Hits using exonerate
BioContainers.github.io
Docker for Bioinformatics
cobrame
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
deepmetabolism
DeepMetabolism is a deep learning algorithm to predict phenotype from genome sequencing
dynamicme
Dynamic ME simulations (separate module)
ecol316435-wgscyc
E. coli Nissle
enzynet
EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation
gnina
gnina is not smina/vina
gnina-models
Trained caffe models
MOMA
Multi-Omics Modeling and Analytics
NeurosporaGlucoseCompensation
Based on the Hong et al model, we explore the effect of the clock on metabolism and metabolism on the clock
PADME
This is the repository containing the source code for my Master's thesis research, about predicting drug-target interaction using deep learning.
pflu216595cyc
Pseudomonas fluorescens SBW25 PFLU216595
Probabilistic-Programming-and-Bayesian-Methods-for-Hackers
aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)
pyefm
A collection of routines for calculating elementary flux modes and minimum cut sets for cobra models
pyGRN
Python GRNs, GRN evolutionary algorithm, and a GRN Keras layer
rhotitchedcyc
Rhodococcus opacus PD630
rogain
Recurrent Geometric Network in Pytorch
sone211586cyc
Shewanella oneidensis MR-1 Pathway/Genome database
strain129cyc
P. kudriavzeveii
Tars
A deep generative model library in Theano and Lasagne
tensor2tensor
Library of deep learning models and datasets designed to make deep learning more accessible and accelerate ML research.
ypes214092cyc
Yersinia pestis CO92