Computational Biology @Pacific Northwest National Laboratory's repositories
amlDrugCombos
Experiments in AML cell lines where we assess proteomics of single and double drug treatments.
beatAMLpilotProteomics
Analysis of BEAT AML patient proteomics data
earlyLateAMLresistance
Investigations into differences between early and late resistance in AML patients
AlphaEnzyme
Open source code for AlphaFold.
BayesianOptimization
A Python implementation of global optimization with gaussian processes.
bigscience
Central place for the engineering/scaling WG: documentation, SLURM scripts and logs, compute environment and data.
bioservices
Access to Biological Web Services from Python.
BoolODE
Git Repo for simulating Boolean Models
CompositeReactionFreeEnergies
Computational Notebooks comparing the Alberty chemical potentials and reaction free energies to traditional textbook approaches.
deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
DLKcat
Deep learning and Bayesian approach applied to enzyme turnover number for the improvement of enzyme-constrained genome-scale metabolic models (ecGEMs) reconstruction
google-research
Google Research
gpt-2
Code for the paper "Language Models are Unsupervised Multitask Learners"
ident
Perform identifiability analysis in small kinetic models for experimental design using steady state fluxes and concentrations.
iRhto_memote
Memote-created repository for Rhodosporidium toruloides model iRhto
mongochemdeploy
Scripts to install/deploy the MongoChem server/web client
openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.