Computational Biology @Pacific Northwest National Laboratory's repositories
decomprolute
A suite of scientific workflows to assess metrics to compare efficacy of protein-based tumor deconvolution algorithms.
BeatAMLproteomics
Analysis of the 210 patient cohort processed by the OHSU/PNNL PTRC
srpAnalytics
This repository contains the code necessary to process any new data for the Superfund Research Program Analytics Portal.
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.
CLEAN-Contact
PyTorch Implementation of CLEAN-Contact: Contrastive Learning-enabled Enzyme Functional Annotation Prediction with Structural Inference
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.
cytokineDrugResistance
Studying the impacts of cytokines on drug resistance in AML
ion-mob-ms
Workflow for analyzing ion mobility ms-ms data
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.
AdvancedProbabilisticCircuits.jl
Probabilistic Circuits in Julia
CLEAN
CLEAN: a contrastive learning model for high-quality functional prediction of proteins
CLEAN_ESM2
CLEAN: a contrastive learning model for high-quality functional prediction of proteins (using ESM2)
foldseek
Foldseek enables fast and sensitive comparisons of large structure sets.
HomeownershipDisparity_2015_2019
Code associated with work presented in Race-Specific Risk Factors for Homeownership Disparity in the Continental United States
spatial-proteomics-mapping
Here we are evaluating the ability to measure spatially resolved proteomics