Pinned Repositories
annot2pathologic
awesome-causality
Resources related to causality
crop
Consistent Reproduction of Phenotype
djinnomes-planets
ECemble
Enzyme class prediction using ensemble machine learning
MaxMass
Optimal protein reclamation with MaxMass
mentos
Maximum Entropy production Of the Stoichiometric matrix
PeakPhases
rxneqn
This is code to support the computation of stoichiometric equations for the Thermodynamic Electon Equivalents Model (TEEM) developed by Rittman and McCarty.
djinnome's Repositories
djinnome/apeg_pnnlcyc
djinnome/apegcyc
JGI A.pseudoterreus annotation
djinnome/AspergillusQ4Milestone
djinnome/ategcyc
Aspergillus terreus (Broad)
djinnome/bigraph
a python implementation of Robin Milner's bigraph formalism
djinnome/cameo
cameo - computer aided metabolic engineering & optimization
djinnome/cid-latex
Latex package for drawing (causal) influence diagrams (CIDs) and labeling incentives, maintained by the Causal Incentives Working Group
djinnome/DiffEqDocs.jl
Documentation for the DiffEq differential equations and scientific machine learning (SciML) ecosystem
djinnome/emll
some code for linlog model simulation
djinnome/experiments
small experiments and prototypes
djinnome/FluxObservabilityAnalysis
Based on Crown & Antoniewicz, 2012
djinnome/kappa-counterfactuals
Counterfactual reasoning in Kappa
djinnome/mecha
djinnome/mira
MIRA modeling framework
djinnome/nc12cyc
NeurosporaCyc Pathway/Genome Database
djinnome/normalization-by-evaluation
Normalization-by-evaluation in miniKanren
djinnome/posteriordb
Database with posteriors of interest for Bayesian inference
djinnome/Prompt-Engineering-Guide
🐙 Guides, papers, lecture, notebooks and resources for prompt engineering
djinnome/psst
PSST - Power System Simulation Toolbox
djinnome/putidacyc
PGDB for Pseudomonas putida KT2440
djinnome/py-acsets
A Catlab-compatible implementation of acsets in python.
djinnome/pyro
Deep universal probabilistic programming with Python and PyTorch
djinnome/rhtocyc
Full RHTO Cyc for IFO0880_4
djinnome/SARS-CoV-2-variants-of-concern-in-Ontario
Code for this paper: https://www.nature.com/articles/s41598-022-06159-x
djinnome/strepvcyc
PGDB for Streptomyces venezuelae
djinnome/Y0-blog
Reflections of a computational biologist navigating a causal universe
djinnome/Yarrowia_lipolytica_W29-GEM
Genome-scale model of Yarrowia lipolytica
djinnome/yarrowiacyc
djinnome/yeastcyc
Saccharomyces cerevisae Pathway/Genome database updated with links to Yarrowia
djinnome/z3_tutorial
Jupyter notebooks for tutorial on the Z3 SMT solver