Repositories list

• sulab.org

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •8•0•0•1•Updated Sep 20, 2025Sep 20, 2025

• DBR-X

  Public
  DBR-X: Drug-Based Reasoning Explainer

  Jupyter Notebook

  •0•3•0•0•Updated Jul 30, 2025Jul 30, 2025

• TSRI-CBB

  Public
  This is the Github repository for The Scripps Research Institute Computational Biology and Bioinformatics (CBB) community and affiliated core track for graduate students.

  HTML

  •0•7•1•0•Updated Jun 6, 2025Jun 6, 2025

• DrugMechDB

  Public
  A database of paths that represent the mechanism of action from a drug to a disease in an indication.

  ncats-translator

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •18•65•7•2•Updated May 13, 2025May 13, 2025

• Applied-Bioinformatics-2025

  Public
  R

  •

  Apache License 2.0

  •0•0•0•0•Updated Mar 4, 2025Mar 4, 2025

• KnowledgeGraphEmbedding

  Public
  Jupyter Notebook

  •

  MIT License

  •268•1•0•0•Updated Aug 9, 2024Aug 9, 2024

• CBRonMRN

  Public
  Python

  •0•0•0•0•Updated Feb 21, 2024Feb 21, 2024

• WikidataIntegrator

  Public
  A Wikidata Python module integrating the MediaWiki API and the Wikidata SPARQL endpoint

  Python

  •

  MIT License

  •48•257•11•0•Updated Nov 14, 2023Nov 14, 2023

• DMDB_Analysis

  Public
  Jupyter Notebook

  •3•0•0•2•Updated Apr 20, 2023Apr 20, 2023

• DrugMechDB-1

  Public
  A database of paths that represent the mechanism of action from a drug to a disease in an indication.

  Jupyter Notebook

  •

  MIT License

  •18•0•0•0•Updated Apr 13, 2023Apr 13, 2023

• path_plots

  Public
  A simple repo to quickly plot paths in a newtorkx graph

  Python

  •3•0•0•0•Updated Mar 23, 2023Mar 23, 2023

• scheduled-bots

  Public
  GeneWiki Scheduled Bots

  Jupyter Notebook

  •

  MIT License

  •15•9•15•2•Updated Feb 17, 2023Feb 17, 2023

• GeneWikiCentral

  Public
  GeneWiki Organization

  JavaScript

  •

  MIT License

  •2•5•74•9•Updated Feb 2, 2023Feb 2, 2023

• mark2cure

  Public
  Mark2Cure allows anyone that can read English, regardless of background, to help in the process of biomedical discovery.

  Python

  •8•14•35•50•Updated Jan 11, 2023Jan 11, 2023

• Lit2Hybrid

  Public
  Vue

  •0•0•0•26•Updated Jan 6, 2023Jan 6, 2023

• genewikiworld

  Public
  Generate a network of all items we care about, and some we don't....

  Jupyter Notebook

  •

  Apache License 2.0

  •2•6•2•6•Updated Dec 8, 2022Dec 8, 2022

• Wikidata-phenomizer

  Public
  Incorporate wikidata statements into phenomizer

  Jupyter Notebook

  •

  MIT License

  •1•3•0•22•Updated Dec 8, 2022Dec 8, 2022

• wikidata-translate

  Public
  Python

  •2•0•0•6•Updated Dec 8, 2022Dec 8, 2022

• Krusty

  Public
  neo4j <-> wikibase import/export tool

  neo4jwikibaseimport-export

  Python

  •2•2•9•4•Updated Dec 8, 2022Dec 8, 2022

• garbanzo

  Public
  Wikidata Semantic Query API

  Python

  •6•2•1•7•Updated Dec 7, 2022Dec 7, 2022

• bioshovel

  Public
  Biological text mining tool.

  Python

  •1•3•0•1•Updated Oct 20, 2022Oct 20, 2022

• Applied-Bioinformatics

  Public
  Student course material for the Applied Bioinformatics course at Scripps Research

  Jupyter Notebook

  •32•38•2•0•Updated Oct 11, 2022Oct 11, 2022

• dataset-repository-selector

  Public
  A tool to help biologists make their datasets more findable, accessible, and schema.org-compliant

  R

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 21, 2022Sep 21, 2022

• Wikidata_Biomedical-Subgraph

  Public
  This is a follow-up effort from work done within Waagmeester et al 2020 eLife and Mayers et al 2022 Bioinformatics

  pythonjsonwikidata+ 2knowledge-graphdrug-repurposing

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •0•0•3•0•Updated Aug 26, 2022Aug 26, 2022

• sparql_to_pandas

  Public
  Example for accessing SPARQL endpoints in Python with Pandas

  Jupyter Notebook

  •9•13•0•7•Updated Aug 23, 2022Aug 23, 2022

• biogps_core

  Public
  JavaScript

  •

  GNU General Public License v3.0

  •0•0•50•3•Updated Jul 8, 2022Jul 8, 2022

• niaid-data-portal

  Public
  NIAID Dataset Portal

  Python

  •

  MIT License

  •2•0•0•0•Updated May 18, 2022May 18, 2022

• MechRepoNet

  Public
  Jupyter Notebook

  •1•5•0•0•Updated Apr 12, 2022Apr 12, 2022

• mercator_shiny

  Public
  A web application for visualization, exploration, and analysis of public bulk RNA-seq data.

  R

  •0•0•0•0•Updated Jun 18, 2021Jun 18, 2021

• biogps_dataset

  Public
  BioGPS.org dataset & dataset loading code repository

  CSS

  •2•0•17•3•Updated Jun 10, 2021Jun 10, 2021