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
coderdata
Automation scripts and benchmark dataset package for cancer drug prediction deep learning models.
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
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/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/coderdata
Automation scripts and benchmark dataset package for cancer drug prediction deep learning models.
PNNL-CompBio/BeatAMLproteomics
Analysis of the 210 patient cohort processed by the OHSU/PNNL PTRC
PNNL-CompBio/ML_UVvisModels
PNNL-CompBio/spammR
Spatial Analysis of Multiomics Measurement in R
PNNL-CompBio/srpAnalytics
This repository contains the code necessary to process any new data for the Superfund Research Program Analytics Portal.
PNNL-CompBio/cNFOrganoidAnalysis
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/cytokineDrugResistance
Studying the impacts of cytokines on drug resistance in AML
PNNL-CompBio/ion-mob-ms
Workflow for analyzing ion mobility ms-ms data
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/AdvancedProbabilisticCircuits.jl
Probabilistic Circuits in Julia
PNNL-CompBio/AVine-GEM
azotobacter_vinelandii_dj
PNNL-CompBio/CLEAN
CLEAN: a contrastive learning model for high-quality functional prediction of proteins
PNNL-CompBio/CLEAN-Contact
PNNL-CompBio/CLEAN_ESM2
CLEAN: a contrastive learning model for high-quality functional prediction of proteins (using ESM2)
PNNL-CompBio/ConsortiumModels
PNNL-CompBio/EinsumNetworks
PNNL-CompBio/foldseek
Foldseek enables fast and sensitive comparisons of large structure sets.
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/ontogpt
GPT-based ontological extraction tools, including SPIRES
PNNL-CompBio/RToru-GEM
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