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Zucker, Jeremy [Pacific Northwest National Laboratory]

Publications and source records attributed to Zucker, Jeremy [Pacific Northwest National Laboratory].

18 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

ciemss/pyciemss

Causal and probabilistic reasoning with continuous time dynamical systems

Witty, Sam [Sorbus AI]↗
DOE OSTI2025

pnnl-predictive-phenomics/csc052cyc

Using the genome annotation as input, Pathway-tools generates a database containing all the information that can be inferred from the genome. The Pathway/Genome database (PGDB) can subsequently be curated manually Licensed under the CC-BY-4.0 license

Zucker, Jeremy [Pacific Northwest National Laborat↗
DOE OSTI2025

pnnl-predictive-phenomics/csc040cyc

Using the genome annotation as input, Pathway-tools generates a database containing all the information that can be inferred from the genome. The Pathway/Genome database (PGDB) can subsequently be curated manually

Zucker, Jeremy [Pacific Northwest National Laborat↗
DOE OSTI2025

pnnl-predictive-phenomics/csc031cyc

Organism-specific Pathway/Genome databases enable the analysis, visualization and interrogation of metabolism, regulation, and genetics. Licensed under the CC-BY-4.0 license

Zucker, Jeremy [Pacific Northwest National Laborat↗
DOE OSTI2025

pnnl-predictive-phenomics/csc009cyc

Using the genome annotation as input, Pathway-tools generates a database containing all the information that can be inferred from the genome. The Pathway/Genome database (PGDB) can subsequently be curated manually. Licensed under the CC-BY-4.0 license

Zucker, Jeremy [Pacific Northwest National Laborat↗
DOE OSTI2025

pnnl-predictive-phenomics/csc043cyc

Organism-specific Pathway/Genome databases enable the analysis, visualization and interrogation of metabolism, regulation, and genetics. Licensed under the CC-BY-4.0 license

Zucker, Jeremy [Pacific Northwest National Laborat↗
DOE OSTI2025

CRISPR-CARB/nocap

Network Optimization and Causal Analysis of Perturb-seq (NOCAP) is a software package for causal inference of gene regulation networks using data from perturb-seq.

George, August↗
DOE OSTI2025

pnnl-predictive-phenomics/SElon-GEM

The software was developed to solve the problem of continuous validation for genome-scale model of S. elongatus. The origin of the work was due to the difficulty of curating genome-scale metabolic models, and memote was invented to solve this problem.

Pino, James [Pacific Northwest National Laboratory↗
DOE OSTI2025

pnnl-predictive-phenomics/emll

This codebase was designed to tackle the problem of how to directly utilize experimental omics measurements with a genome scale metabolic model of the organism of the study. Most models only loosely utilize known experimental quantities to constrain model simulation.

John, Peter St. [@NVIDIA]↗
DOE OSTI2024

pnnl-predictive-phenomics/csc052-gem

Genome-Scale Metabolic Model Continuous Validation with Memote for CarbStor Community Member Bacillus These repositories contain the continuous validation environment for an organism-specific genome-scale metabolic model (GEM) using Memote. Memote is a software tool that provides a suite of tests to ensure the quality and consistency of metabolic models. By integrating Memote into a continuous integration (CI) workflow, we can automatically validate updates to the GEM, ensuring that model modifications improve or maintain the model's integrity.

Torres, Victor E.↗
DOE OSTI2024

pnnl-predictive-phenomics/csc031-gem

Genome-Scale Metabolic Model of CarbStor Community member Microbacterium (csc031) Continuous Validation with Memote These repositories contain the continuous validation environment for an organism-specific genome-scale metabolic model (GEM) using Memote. Memote is a software tool that provides a suite of tests to ensure the quality and consistency of metabolic models. By integrating Memote into a continuous integration (CI) workflow, we can automatically validate updates to the GEM, ensuring that model modifications improve or maintain the model's integrity

McNaughton, Andrew [@PNNL]↗
DOE OSTI2024

pnnl-predictive-phenomics/csc009-gem

Genome-Scale Metabolic Model of CarbStore Community member Curtobacterium (csc009) Continuous Validation with Memote These repositories contain the continuous validation environment for an organism-specific genome-scale metabolic model (GEM) using Memote. Memote is a software tool that provides a suite of tests to ensure the quality and consistency of metabolic models. By integrating Memote into a continuous integration (CI) workflow, we can automatically validate updates to the GEM, ensuring that model modifications improve or maintain the model's integrity

Lin, Tesia↗
DOE OSTI2024

pnnl-predictive-phenomics/csc040-gem

Genome-Scale Metabolic Model Continuous Validation with Memote for CarbStor Community Member Rhodococcus These repositories contain the continuous validation environment for an organism-specific genome-scale metabolic model (GEM) using Memote. Memote is a software tool that provides a suite of tests to ensure the quality and consistency of metabolic models. By integrating Memote into a continuous integration (CI) workflow, we can automatically validate updates to the GEM, ensuring that model modifications improve or maintain the model's integrity.

McNaughton, Andrew [@PNNL]↗
DOE OSTI2024

pnnl-predictive-phenomics/csc043-gem

Genome-Scale Metabolic Model Continuous Validation with Memote for CarbStor Community Member Paenibacillus These repositories contain the continuous validation environment for an organism-specific genome-scale metabolic model (GEM) using Memote. Memote is a software tool that provides a suite of tests to ensure the quality and consistency of metabolic models. By integrating Memote into a continuous integration (CI) workflow, we can automatically validate updates to the GEM, ensuring that model modifications improve or maintain the model's integrity.

Zucker, Jeremy [Pacific Northwest National Laborat↗