Repositories list

• worm_lifespan

  Public
  Studying genes affecting lifespan in C. elegans using knowledge assembly and networks

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Feb 17, 2025Feb 17, 2025

• indra_cogex

  Public
  INDRA Context Graph Extension

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •12•10•17•6•Updated Feb 13, 2025Feb 13, 2025

• indra_metascience

  Public
  Analyzing scientific trends based on INDRA-assembled knowledge

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

• indra_curation

  Public
  A utility build around the HTML assembler to enable easy curation of custom sets of INDRA Statements.

  JavaScript

  •4•0•1•1•Updated Feb 12, 2025Feb 12, 2025

• mira

  Public
  MIRA: machine-assisted modeling of dynamical systems

  modelingsystems-biologyepidemiology+ 4differential-equationsontologiesmodeling-and-simulationknowledge-graphs

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •7•12•15•4•Updated Feb 11, 2025Feb 11, 2025

• indra_gpt

  Public
  Jupyter Notebook

  •1•0•0•1•Updated Feb 10, 2025Feb 10, 2025

• mapnet

  Public
  Algorithms for semantic mapping between different ontologies

  Python

  •

  BSD 2-Clause "Simplified" License

  •1•0•0•0•Updated Jan 31, 2025Jan 31, 2025

• ui_util

  Public
  This repo creates general utilities for our user interfaces.

  Python

  •4•0•0•1•Updated Jan 30, 2025Jan 30, 2025

• indra_db

  Public
  A Database-based knowledge back-end built on and for INDRA. The INDRA Database is a service that can be set up by any user with their own content and knowledge access. Our implementation of the database is the back-end to many of our projects, providing a vast and detailed knowledge base derived from many resources.

  sqlalchemydatabasesystems-biology+ 3postgresqlindramachine-reading

  Python

  •

  GNU General Public License v3.0

  •10•16•8•5•Updated Jan 29, 2025Jan 29, 2025

• gyorilab.github.io

  Public
  Gyori Lab website

  HTML

  •

  Other

  •3•3•0•0•Updated Jan 25, 2025Jan 25, 2025

• covid-19

  Public
  Scripts and other utilities relevant to the CORD-19 dataset

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •5•2•0•2•Updated Jan 7, 2025Jan 7, 2025

• panacea_indra

  Public
  INDRA applications for the DARPA Panacea project

  HTML

  •2•1•0•1•Updated Jan 7, 2025Jan 7, 2025

• outbreak_kg

  Public
  Knowledge graphs for disease outbreak scenarios

  Python

  •

  BSD 2-Clause "Simplified" License

  •2•0•0•0•Updated Dec 13, 2024Dec 13, 2024

• indra_spine

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Oct 30, 2024Oct 30, 2024

• gilda

  Public
  Grounding of biomedical named entities with contextual disambiguation

  Python

  •

  BSD 2-Clause "Simplified" License

  •13•41•8•5•Updated Oct 29, 2024Oct 29, 2024

• emmaa

  Public
  Ecosystem of Machine-maintained Models with Automated Analysis

  cancerbiologymodeling+ 3systems-biologysystems-biology-simulationindra

  Python

  •

  BSD 2-Clause "Simplified" License

  •11•10•2•3•Updated Oct 21, 2024Oct 21, 2024

• indra_db_lite

  Public
  Work with content from indra_db in a local sqlite database.

  Python

  •

  BSD 2-Clause "Simplified" License

  •3•0•0•0•Updated Oct 18, 2024Oct 18, 2024

• indra_network_search

  Public
  REST API for querying the network of biochemical mechanisms in the INDRA DB.

  Python

  •

  BSD 2-Clause "Simplified" License

  •2•0•13•0•Updated Oct 17, 2024Oct 17, 2024

• protmapper_paper

  Public
  Code to generate results and figures relevant to the ProtMapper manuscript.

  Python

  •1•1•0•0•Updated Oct 10, 2024Oct 10, 2024

• trialsynth

  Public
  TrialSynth interprets and integrates clinical trials data from multiple registries in a computable form

  Python

  •

  BSD 2-Clause "Simplified" License

  •1•0•0•0•Updated Oct 1, 2024Oct 1, 2024

• depmap_analysis

  Public
  Jupyter Notebook

  •7•1•0•0•Updated Aug 16, 2024Aug 16, 2024

• indra_may_institute

  Public
  Jupyter Notebook

  •1•1•1•0•Updated Aug 16, 2024Aug 16, 2024

• indra_docker

  Public
  Docker build for INDRA, REACH, PySB, and related dependencies.

  Dockerfile

  •5•0•0•0•Updated Jul 30, 2024Jul 30, 2024

• indra_signor

  Public
  Connecting INDRA to the SIGNOR database curation workflow

  Python

  •0•0•0•0•Updated Jul 26, 2024Jul 26, 2024

• indra_world

  Public
  INDRA World Modelers services

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •5•7•0•0•Updated Jul 2, 2024Jul 2, 2024

• protmapper

  Public
  Map amino acid sites of post-translational modifications from models or data to reference positions.

  Python

  •

  BSD 2-Clause "Simplified" License

  •7•6•0•0•Updated Jun 26, 2024Jun 26, 2024

• selventa-knowledge

  Public
  Updated versions of the Selventa Small and Large Corpus

  Python

  •

  MIT License

  •3•0•0•0•Updated Jun 15, 2024Jun 15, 2024

• adeft

  Public
  Tool for disambiguating acronyms and abbreviations in text for NLP applications

  acronym-disambiguation

  Python

  •

  BSD 2-Clause "Simplified" License

  •10•21•1•0•Updated Jun 12, 2024Jun 12, 2024

• neuroimmune_interactome

  Public
  HTML

  •0•3•2•0•Updated May 13, 2024May 13, 2024

• pybiopax

  Public
  PyBioPAX: A python implementation of the BioPAX object model

  biologysystems-biologybiopax+ 1python

  Python

  •

  BSD 2-Clause "Simplified" License

  •6•24•1•0•Updated May 10, 2024May 10, 2024