Computational Biology @Pacific Northwest National Laboratory
This site is for repositories for computational biology work performed at the Pacific Northwest National Laboratory, a Department of Energy National Laboratory.
Richland, WA
Pinned Repositories
3D_Scaffold
BeatAMLproteomics
Analysis of the 210 patient cohort processed by the OHSU/PNNL PTRC
CLEAN-Contact
PyTorch Implementation of CLEAN-Contact: Contrastive Learning-enabled Enzyme Functional Annotation Prediction with Structural Inference
coderdata
Dataset package for facile training and testing of machine learning/AI algorithms that predict drug response in cancer model systems.
decomprolute
A suite of scientific workflows to assess metrics to compare efficacy of protein-based tumor deconvolution algorithms.
ML_UVvisModels
perseq
:cake: Per sequence functional classification and taxonomic assignments
pf-gnn_pli
Snekmer
Pipeline to apply encoded Kmer analysis to protein sequences
spammR
Spatial Analysis of Multiomics Measurement in R
Computational Biology @Pacific Northwest National Laboratory's Repositories
PNNL-CompBio/3D_Scaffold
PNNL-CompBio/pf-gnn_pli
PNNL-CompBio/CME-QM
PNNL-CompBio/amlDrugCombos
Experiments in AML cell lines where we assess proteomics of single and double drug treatments.
PNNL-CompBio/amlresistancenetworks
PNNL-CompBio/bayesian-inference
PNNL-CompBio/beatAMLpilotProteomics
Analysis of BEAT AML patient proteomics data
PNNL-CompBio/earlyLateAMLresistance
Investigations into differences between early and late resistance in AML patients
PNNL-CompBio/microPots-pancreas
Analysis of spatial proteomics data from pancrea
PNNL-CompBio/NEATO
PNNL-CompBio/AlphaFold
Open source code for AlphaFold.
PNNL-CompBio/AMECovDock
PNNL-CompBio/BayesianOptimization
A Python implementation of global optimization with gaussian processes.
PNNL-CompBio/bigscience
Central place for the engineering/scaling WG: documentation, SLURM scripts and logs, compute environment and data.
PNNL-CompBio/bioservices
Access to Biological Web Services from Python.
PNNL-CompBio/BoolODE
Git Repo for simulating Boolean Models
PNNL-CompBio/bsf-jaccard-core
C++ library of Blazing Signature Filter
PNNL-CompBio/bsf-jaccard-py
Python wrapper for Blazing Signature Filter
PNNL-CompBio/CLEAN
CLEAN: a contrastive learning model for high-quality functional prediction of proteins
PNNL-CompBio/DLKcat
Deep learning and Bayesian approach applied to enzyme turnover number for the improvement of enzyme-constrained genome-scale metabolic models (ecGEMs) reconstruction
PNNL-CompBio/EColi-GEM
Ecoli models to be used for memote testing standards. iML1515
PNNL-CompBio/esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
PNNL-CompBio/foldseek
Foldseek enables fast and sensitive comparisons of large structure sets.
PNNL-CompBio/google-research
Google Research
PNNL-CompBio/iRhto_memote
Memote-created repository for Rhodosporidium toruloides model iRhto
PNNL-CompBio/ontogpt
GPT-based ontological extraction tools, including SPIRES
PNNL-CompBio/optuna
A hyperparameter optimization framework
PNNL-CompBio/RToru-GEM
PNNL-CompBio/SecondarySnekmer
The files necessary to run the Porter 5 and Snekmer Docker container
PNNL-CompBio/spack
A flexible package manager that supports multiple versions, configurations, platforms, and compilers.