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Jeremy Zucker (djinnome)

djinnome

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Company:Pacific Northwest National Laboratory

Twitter:@djinnome

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PNNL-CompBio

Jeremy Zucker's repositories

apeg_pnnlcyc

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apegcyc

JGI A.pseudoterreus annotation

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AspergillusQ4Milestone

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ategcyc

Aspergillus terreus (Broad)

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bigraph

a python implementation of Robin Milner's bigraph formalism

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cameo

cameo - computer aided metabolic engineering & optimization

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cid-latex

Latex package for drawing (causal) influence diagrams (CIDs) and labeling incentives, maintained by the Causal Incentives Working Group

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DiffEqDocs.jl

Documentation for the DiffEq differential equations and scientific machine learning (SciML) ecosystem

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emll

some code for linlog model simulation

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experiments

small experiments and prototypes

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FluxObservabilityAnalysis

Based on Crown & Antoniewicz, 2012

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kappa-counterfactuals

Counterfactual reasoning in Kappa

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mecha

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mira

MIRA modeling framework

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nc12cyc

NeurosporaCyc Pathway/Genome Database

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normalization-by-evaluation

Normalization-by-evaluation in miniKanren

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posteriordb

Database with posteriors of interest for Bayesian inference

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Prompt-Engineering-Guide

🐙 Guides, papers, lecture, notebooks and resources for prompt engineering

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psst

PSST - Power System Simulation Toolbox

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putidacyc

PGDB for Pseudomonas putida KT2440

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py-acsets

A Catlab-compatible implementation of acsets in python.

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pyro

Deep universal probabilistic programming with Python and PyTorch

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rhtocyc

Full RHTO Cyc for IFO0880_4

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SARS-CoV-2-variants-of-concern-in-Ontario

Code for this paper: https://www.nature.com/articles/s41598-022-06159-x

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strepvcyc

PGDB for Streptomyces venezuelae

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Y0-blog

Reflections of a computational biologist navigating a causal universe

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Yarrowia_lipolytica_W29-GEM

Genome-scale model of Yarrowia lipolytica

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yarrowiacyc

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yeastcyc

Saccharomyces cerevisae Pathway/Genome database updated with links to Yarrowia

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z3_tutorial

Jupyter notebooks for tutorial on the Z3 SMT solver

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