Computational Biology @Pacific Northwest National Laboratory

decomprolute

A suite of scientific workflows to assess metrics to compare efficacy of protein-based tumor deconvolution algorithms.

Snekmer

Pipeline to apply encoded Kmer analysis to protein sequences

coderdata

Automation scripts and benchmark dataset package for cancer drug prediction deep learning models.

BeatAMLproteomics

Analysis of the 210 patient cohort processed by the OHSU/PNNL PTRC

ML_UVvisModels

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.

cNFOrganoidAnalysis

CONCERTO

Continuous integration and validation for genome-scale metabolic model consortia

emll

some code for linlog model simulation

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.

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

ProchlorococcusGEM

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

AVine-GEM

azotobacter_vinelandii_dj

CLEAN

CLEAN: a contrastive learning model for high-quality functional prediction of proteins

CLEAN-Contact

CLEAN_ESM2

CLEAN: a contrastive learning model for high-quality functional prediction of proteins (using ESM2)

ConsortiumModels

EinsumNetworks

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

ontogpt

GPT-based ontological extraction tools, including SPIRES

RToru-GEM

SElon7942-GEM

SERGIO

A simulator for single-cell expression data guided by gene regulatory networks

spatial-proteomics-mapping

Here we are evaluating the ability to measure spatially resolved proteomics