Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
Projects in Awesome Lists by cthoyt
A curated list of projects in awesome lists by cthoyt .
https://github.com/cthoyt/class-resolver
🔍 Lookup classes and instantiate them with style
Last synced: 01 Nov 2024
https://github.com/cthoyt/chembl-downloader
Write reproducible code for getting and processing ChEMBL
bioinformatics chembl cheminformatics chemogenomics chemometrics machine-learning pharmacology proteochemometrics python reproducible-research toxicology
Last synced: 27 Oct 2024
https://github.com/cthoyt/pystow
👜 Easily pick a place to store data for your Python code.
file-management file-manager filesystem pathlib python reproducibility reproducible-research reproducible-science
Last synced: 01 Nov 2024
https://github.com/cthoyt/drugbank-downloader
Don't worry about DrugBank licensing - write code that knows how to download it automatically
drugbank python reproducible-research
Last synced: 26 Oct 2024
https://github.com/cthoyt/cookiecutter-snekpack
🍪 A cookiecutter package for an enlightened python package
cookiecutter cookiecutter-python cookiecutter-python3 cookiecutter-snekpack cookiecutter-template python template
Last synced: 27 Oct 2024
https://github.com/cthoyt/umls_downloader
Don't worry about UMLS, RxNorm, SNOMED, or SemMedDB licensing - write code that knows how to download it automatically
python reproducibility reproducible-research rxnorm semmeddb snomed snomed-ct umls
Last synced: 27 Oct 2024
https://github.com/cthoyt/doctoral-thesis
📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology
biocuration biological-expression-language computational-biology curation data-integration knowledge-graph-embeddings knowledge-graphs networks-biology simulation systems-biology
Last synced: 13 Oct 2024
https://github.com/cthoyt/zenodo-client
A tool for automated uploading and version management of scientific data to Zenodo
Last synced: 26 Oct 2024
https://github.com/cthoyt/autoreviewer
👁️🗨️ Scientists often do the same bad stuff. Automate giving feedback during peer review.
metascience peer-review reproducibility
Last synced: 28 Oct 2024
https://github.com/cthoyt/pyrdle
Play Wordle in the CLI. Write an algorithm to play Wordle for you. Ruin all of the fun you've been having.
Last synced: 28 Oct 2024
https://github.com/cthoyt/ols-client
🎡 Unified access to OLS instances like from the EBI and TIB
ontologies ontology-lookup-services
Last synced: 28 Oct 2024
https://github.com/cthoyt/curies4j
🐸 Idiomatic conversion between URIs and compact URIs (CURIEs)
curies java obofoundry semantic-web uris
Last synced: 13 Oct 2024
https://github.com/cthoyt/pybacting
A Python wrapper around Bacting (https://github.com/egonw/bacting)
Last synced: 28 Oct 2024
https://github.com/cthoyt/quickstatements_client
A data model and client for QuickStatements (for Wikidata)
bibliometrics python quickstatements wikidata
Last synced: 28 Oct 2024
https://github.com/cthoyt/pydeogram
Generate Ideograms using ideogram.js in Python
Last synced: 13 Oct 2024
https://github.com/cthoyt/rhea-fingerprints
Automatically generate differential reaction fingerprints on reactions in Rhea
differential-reaction-fingerprints rhea
Last synced: 13 Oct 2024
https://github.com/cthoyt/geometric-graphs
Generate knowledge graphs with interesting geometries, like lattices
Last synced: 13 Oct 2024
https://github.com/cthoyt/more_click
Extra stuff for click I use in basically every repo
Last synced: 13 Oct 2024
https://github.com/cthoyt/orcid_downloader
Get ORCID in bulk and free it from XML
Last synced: 28 Oct 2024
https://github.com/cthoyt/authorship
🚢 Generate publication-ready authorship lists via Google Sheets and more
academia automation bibliometrics publishing scientometrics writing
Last synced: 13 Oct 2024
https://github.com/cthoyt/nrl
Network Representation Learning in Python with igraph
Last synced: 13 Oct 2024
https://github.com/cthoyt/ontoportal-client
🎡 Unified access to OntoPortal instances like BioPortal, AgroPortal, and EcoPortal
agroportal bioportal cookiecutter-snekpack ecoportal obo obofoundry ontologies ontoportal python
Last synced: 13 Oct 2024
https://github.com/cthoyt/semantic-pydantic
Annotate data models in Pydantic and APIs in FastAPI with the Bioregistry to make them more FAIR
Last synced: 20 Oct 2024
https://github.com/cthoyt/cthoyt.github.io
My personal website, served at https://cthoyt.com
artificial-intelligence biocuration bioinformatics biological-expression-language cheminformatics deep-learning drug-discovery drug-repurposing drug-synergy knowledge-graph-embeddings knowledge-graphs machine-learning obofoundry ontologies proteochemometrics target-prioritization target-validation toxicology utterances wikidata
Last synced: 13 Oct 2024
https://github.com/cthoyt/unittest-templates
Write less unittest boilerplate
Last synced: 13 Oct 2024
https://github.com/cthoyt/flask-celery-docker-demo
A short demo on how to process files with Flask and Celery inside Docker
Last synced: 13 Oct 2024
https://github.com/cthoyt/rorio
Convert the Research Organization Registry (ROR) into an OWL instance ontology
bibliometrics ror scientometrics
Last synced: 13 Oct 2024
https://github.com/cthoyt/citation-url
Parse URLs for DOIs, PubMed identifiers, PMC identifiers, arXiv identifiers, etc.
Last synced: 13 Oct 2024
https://github.com/cthoyt/chemrxiv-summarize
Summarize usage of ChemRxiv by using Figshare's API endpoint
Last synced: 13 Oct 2024
https://github.com/cthoyt/orcidio
🐨 Make a subset of ORCID available as an OWL ontology
Last synced: 13 Oct 2024
https://github.com/cthoyt/twin-identifier-analysis
How many local unique identifiers overlap between each biomedical vocabulary in the Bioregistry?
Last synced: 13 Oct 2024
https://github.com/cthoyt/obo-community-health
🫀 Check the OBO Foundry repositories to see what's going on
Last synced: 28 Oct 2024
https://github.com/cthoyt/depmap_downloader
Reproducibly download the latest version of various DepMap datasets
Last synced: 13 Oct 2024
https://github.com/cthoyt/schoolwork
✎ Code I've written for classes in school
Last synced: 13 Oct 2024
https://github.com/cthoyt/embeddingdb
A database for storing and comparing entity embeddings
database network-representation-learning representation-learning
Last synced: 13 Oct 2024
https://github.com/cthoyt/apicuron-client
A python client for interacting with the APICURON curation metadatabase's RESTful API
Last synced: 13 Oct 2024
https://github.com/cthoyt/biomodels-metadata-analysis
Generate a summary of metadata annotations in the BioModels database
biomodels fair-data modeling reproducibility-crisis sbml systems-biology
Last synced: 13 Oct 2024
https://github.com/cthoyt/vsmo
Revival of the Vector Surveillance and Management Ontology
Last synced: 13 Oct 2024
https://github.com/cthoyt/translational-toys
Knowledge graphs representing geometric shapes matched to knowledge graph embedding models to learn them
Last synced: 13 Oct 2024
https://github.com/cthoyt/pykeen-playtime
A place for one-off experiments with PyKEEN that can be re-run anytime
Last synced: 13 Oct 2024
https://github.com/cthoyt/obo-foundry-graph
Demonstrate combining all OBO Foundry ontologies via Bioregistry, Bioontologies, and ROBOT
Last synced: 13 Oct 2024
https://github.com/cthoyt/n2t-ark-resolver
Re-implement N2T's ARK resolver using curies (https://github.com/cthoyt/curies/)
Last synced: 13 Oct 2024
https://github.com/cthoyt/chendi
Chemical Entities of Neurodegenerative Disease Interest
Last synced: 13 Oct 2024
https://github.com/cthoyt/biocuration-diversity-search
Find biocurators that aren't from Australia, Canada, USA, or western Europe
Last synced: 13 Oct 2024
https://github.com/cthoyt/methodalyze
Evaluate the reproducibility of scientific protocols.
Last synced: 13 Oct 2024
https://github.com/cthoyt/protein-embedding-review
A list of papers and information on whether they are useful
Last synced: 13 Oct 2024
https://github.com/cthoyt/orkg-dataset
Preprocessing of the Open Research Knowledge Graph for use in KGEMs
Last synced: 13 Oct 2024
https://github.com/cthoyt/rdb2rdf2web
Maps RDB to RDF and exposes SPARQL API
Last synced: 13 Oct 2024
https://github.com/cthoyt/ols-standardization-analysis
Analysis of public OLS instances for conformity to Bioregistry standards
Last synced: 13 Oct 2024
https://github.com/cthoyt/resume
The résumé of Charles Tapley Hoyt
bioinformatics cheminformatics resume software-development
Last synced: 13 Oct 2024
https://github.com/cthoyt/nx2d3
Display NetworkX graphs inline in Jupyter notebooks
Last synced: 13 Oct 2024
https://github.com/cthoyt/table-validator
Use tables with validation schemata to validate other tables.
Last synced: 13 Oct 2024
https://github.com/cthoyt/biogrid-embeddings
Learned embeddings for proteins using physical interactions in BioGRID
Last synced: 13 Oct 2024
https://github.com/cthoyt/mirbase
miRBase seeminly deleted its data after version 22.1, this is a re-posting of it
Last synced: 13 Oct 2024
https://github.com/cthoyt/masters-thesis
LaTeX source for my master's thesis
biological-expression-language pybel
Last synced: 13 Oct 2024
https://github.com/cthoyt/omega_implementation
Final Project Repository for Causal ML class
Last synced: 13 Oct 2024
https://github.com/cthoyt/spdx-obo
Converts the @spdx license list to OBO using @pyobo
Last synced: 13 Oct 2024
https://github.com/cthoyt/flask-security-testing-demo
A short demo how to test with logged-in users in Flask-Security
Last synced: 13 Oct 2024
https://github.com/cthoyt/hypothesis-ebnf
A Hypothesis strategy for generating sentences from an EBNF grammar
Last synced: 13 Oct 2024
https://github.com/cthoyt/gha-together
Use @lvermue's model for explicit GHA requests while also allowing pull requests
Last synced: 13 Oct 2024
https://github.com/cthoyt/multisplitby
Split an iterable into multiple using arbitrary predicates.
Last synced: 13 Oct 2024
https://github.com/cthoyt/family
Visualization and Exploration of the Hoyt and Grave Family Trees
Last synced: 13 Oct 2024
https://github.com/cthoyt/indra-machines
Several configuration files for biomedical relation extraction with INDRA
Last synced: 13 Oct 2024
https://github.com/cthoyt/hetnetana
Integration of heterogeneous networks and topological footprint calculation
Last synced: 13 Oct 2024
https://github.com/cthoyt/chemtools
⚗Cool stuff for undergraduate chemistry classes
Last synced: 13 Oct 2024
https://github.com/cthoyt/fairsharing-client
A client to the FAIRsharing API
Last synced: 13 Oct 2024
https://github.com/cthoyt/docdata
Add structured information to the end of your python docstrings
Last synced: 13 Oct 2024
https://github.com/cthoyt/cx-rdf
A Python utility for converting CX to RDF
cx cytoscape ndex ndex-python-client rdf semantic-web
Last synced: 13 Oct 2024
https://github.com/cthoyt/snekpack-demo
Demonstrates using the cookecutter-snekpack template.
Last synced: 13 Oct 2024
https://github.com/cthoyt/umlsst
An ad-hoc site to show information about UMLS Semantic Types
Last synced: 13 Oct 2024
https://github.com/cthoyt/selventa-knowledge
Updated versions of the Selventa Small and Large Corpus
Last synced: 13 Oct 2024
https://github.com/cthoyt/python-devops-bootcamp-2019
Do she get the booty?
Last synced: 13 Oct 2024
https://github.com/cthoyt/ro-summary
Scripts for generating summaries of the Relation Ontology
Last synced: 13 Oct 2024