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
srpAnalytics
This repository contains the code necessary to process any new data for the Superfund Research Program Analytics Portal.
Computational Biology @Pacific Northwest National Laboratory's Repositories
PNNL-CompBio/coderdata
Dataset package for facile training and testing of machine learning/AI algorithms that predict drug response in cancer model systems.
PNNL-CompBio/decomprolute
A suite of scientific workflows to assess metrics to compare efficacy of protein-based tumor deconvolution algorithms.
PNNL-CompBio/Snekmer
Pipeline to apply encoded Kmer analysis to protein sequences
PNNL-CompBio/ML_UVvisModels
PNNL-CompBio/CLEAN-Contact
PyTorch Implementation of CLEAN-Contact: Contrastive Learning-enabled Enzyme Functional Annotation Prediction with Structural Inference
PNNL-CompBio/BeatAMLproteomics
Analysis of the 210 patient cohort processed by the OHSU/PNNL PTRC
PNNL-CompBio/srpAnalytics
This repository contains the code necessary to process any new data for the Superfund Research Program Analytics Portal.
PNNL-CompBio/spammR
Spatial Analysis of Multiomics Measurement in R
PNNL-CompBio/cNFOrganoidAnalysis
PNNL-CompBio/amlresistancenetworks
PNNL-CompBio/bmdrc
Python library for the calculation of benchmark dose response curves
PNNL-CompBio/CONCERTO
Continuous integration and validation for genome-scale metabolic model consortia
PNNL-CompBio/emll
some code for linlog model simulation
PNNL-CompBio/panCancerModelSystems
This project will explore the differences between model systems to identify systemic biases across tumors and models toward mapping from one to the other.
PNNL-CompBio/BoltzmannMFX
BoltzmannMFX is a biological simulation code that solves chemical reaction networks using maximum entropy methods. It uses modules from MFiX-Exa and is based on the AMReX framework for massively parallel block-structured adaptive mesh applications.
PNNL-CompBio/cdrp
PNNL-CompBio/cNFDrugScreening
This repository manages the code to analyze the results of drug screens in cNF organoids together with omics measurements of the tumor data.
PNNL-CompBio/EinsumNetworks
PNNL-CompBio/ProchlorococcusGEM
PNNL-CompBio/proteomics-drug-response
This repository will serve as the primary base to develop tools to assess and predict drug response from proteomics measurements in cancer model systems.
PNNL-CompBio/MPNST_Chr8
PNNL-CompBio/panSEA
Multi-omic Set Enrichment Analysis
PNNL-CompBio/AdvancedProbabilisticCircuits.jl
Probabilistic Circuits in Julia
PNNL-CompBio/AML_sorted_proteomics
PNNL-CompBio/CLEAN_ESM2
CLEAN: a contrastive learning model for high-quality functional prediction of proteins (using ESM2)
PNNL-CompBio/HomeownershipDisparity_2015_2019
Code associated with work presented in Race-Specific Risk Factors for Homeownership Disparity in the Continental United States
PNNL-CompBio/PythonCyc
PNNL-CompBio/SElon7942-GEM
PNNL-CompBio/SERGIO
A simulator for single-cell expression data guided by gene regulatory networks
PNNL-CompBio/spatial-proteomics-mapping
Here we are evaluating the ability to measure spatially resolved proteomics