Jeremy Zucker's repositories
awesome-causality
Resources related to causality
aracyc
Arabidopsis pathway/genome database v15.0
bel_specifications
BEL Specifications - functional specifications and associated tooling and language documentation
biohacker-1
debugging biological networks to reach coherence, completeness and consistency
caid01cyc
Genbank version of Ostreococcus tauri
causalML
A course on causal machine learning.
common
Common resources shared among all task repositories
cookiecutter-python-package
A cookiecutter package for an englightened python package
gpt-3
GPT-3: Language Models are Few-Shot Learners
humancyc
HumanCyc PGDB with small edits
indra
INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
MetaboliteProducibility
Metabolite producibility analysis as described in Imielinski 2005 and 2008
multiverse
MultiVerse: Probabilistic Programming Language for Causal Reasoning
nasbench
NASBench: A Neural Architecture Search Dataset and Benchmark
pgmpy
Python Library for Probabilistic Graphical Models
pybel
An ecosystem in Python for working with the Biological Expression Language (BEL)
pybel-notebooks
Notebooks demonstrating the usage of PyBEL and PyBEL Tools
python-novice-gapminder
Introduction to Python for non-programmers using gapminder data
python-package-best-practices
http://education.molssi.org/python-package-best-practices/
simpsons-paradox
Generating examples of Simpson's Paradox
WholeCellEcoliRelease
Release of the whole cell E. coli model.
workshop-template
Rendering of the workshop-template site
ySBGN
Translation between GraphML (yED) and SBGN-ML