Computational Biology @Pacific Northwest National Laboratory (PNNL-CompBio)

Computational Biology @Pacific Northwest National Laboratory

PNNL-CompBio

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This site is for repositories for computational biology work performed at the Pacific Northwest National Laboratory, a Department of Energy National Laboratory.

Location:Richland, WA

Home Page:https://www.pnnl.gov/computational-biology

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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.

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Snekmer

Pipeline to apply encoded Kmer analysis to protein sequences

Language:PythonLicense:BSD-3-ClauseStargazers:12Issues:5Issues:78

coderdata

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

Language:Jupyter NotebookLicense:NOASSERTIONStargazers:11Issues:4Issues:134
Language:Jupyter NotebookLicense:BSD-2-ClauseStargazers:10Issues:5Issues:1

BeatAMLproteomics

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

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spammR

Spatial Analysis of Multiomics Measurement in R

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srpAnalytics

This repository contains the code necessary to process any new data for the Superfund Research Program Analytics Portal.

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CONCERTO

Continuous integration and validation for genome-scale metabolic model consortia

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emll

some code for linlog model simulation

Language:Jupyter NotebookLicense:GPL-2.0Stargazers:3Issues:0Issues:7

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.

Language:Jupyter NotebookLicense:BSD-2-ClauseStargazers:3Issues:4Issues:0

CLEAN-Contact

PyTorch Implementation of CLEAN-Contact: Contrastive Learning-enabled Enzyme Functional Annotation Prediction with Structural Inference

Language:PythonLicense:NOASSERTIONStargazers:2Issues:4Issues:8

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.

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cytokineDrugResistance

Studying the impacts of cytokines on drug resistance in AML

Language:HTMLLicense:MITStargazers:1Issues:2Issues:5

ion-mob-ms

Workflow for analyzing ion mobility ms-ms data

Language:PythonLicense:BSD-2-ClauseStargazers:1Issues:4Issues:34

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

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AVine-GEM

azotobacter_vinelandii_dj

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CLEAN

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

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CLEAN_ESM2

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

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foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

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HomeownershipDisparity_2015_2019

Code associated with work presented in Race-Specific Risk Factors for Homeownership Disparity in the Continental United States

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Language:Jupyter NotebookLicense:GPL-2.0Stargazers:0Issues:0Issues:0

SERGIO

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

Language:HTMLLicense:GPL-3.0Stargazers:0Issues:1Issues:13

spatial-proteomics-mapping

Here we are evaluating the ability to measure spatially resolved proteomics

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