Repositories list

• gyorilab.github.io

  Public
  Gyori Lab website

  HTML

  •

  Other

  •33 forks•44 stars•00 issues•00 pull requests•Updated May 1, 2026May 1, 2026

• indra_agent

  Public
  An MCP server around INDRA CoGEx enabling AI agent interaction with the knowledge graph

  Python

  •

  BSD 2-Clause "Simplified" License

  •33 forks•22 stars•00 issues•11 pull request•Updated Apr 28, 2026Apr 28, 2026

• indra

  Public
  INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowled…

  nlpbioinformaticsbiology+ 6

  nlpbioinformaticsbiologymodelingsystems-biologycomputational-biologypysbindrasbml

  Python

  •

  BSD 2-Clause "Simplified" License

  •7777 forks•209209 stars•3434 issues•1414 pull requests•Updated Apr 17, 2026Apr 17, 2026

• trialsynth

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

  Python

  •

  BSD 2-Clause "Simplified" License

  •33 forks•00 stars•00 issues•11 pull request•Updated Apr 8, 2026Apr 8, 2026

• mira

  Public
  MIRA: machine-assisted modeling of dynamical systems

  modelingsystems-biologyepidemiology+ 4

  modelingsystems-biologyepidemiologydifferential-equationsontologiesmodeling-and-simulationknowledge-graphs

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •99 forks•1313 stars•1818 issues•55 pull requests•Updated Apr 6, 2026Apr 6, 2026

• gilda

  Public
  Grounding of biomedical named entities with contextual disambiguation

  bdf-toolbox

  bdf-toolbox

  Python

  •

  BSD 2-Clause "Simplified" License

  •1616 forks•5151 stars•88 issues•66 pull requests•Updated Mar 30, 2026Mar 30, 2026

• adeft

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

  acronym-disambiguation

  acronym-disambiguation

  Python

  •

  BSD 2-Clause "Simplified" License

  •1010 forks•2222 stars•00 issues•00 pull requests•Updated Mar 26, 2026Mar 26, 2026

• miradb

  Public
  An automatically extracted database of MIRA models

  Python

  •

  BSD 2-Clause "Simplified" License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Mar 25, 2026Mar 25, 2026

• mapnet

  Public
  Algorithms for semantic mapping between different ontologies

  Python

  •

  BSD 2-Clause "Simplified" License

  •33 forks•00 stars•00 issues•11 pull request•Updated Mar 11, 2026Mar 11, 2026

• openacme

  Public
  Implementing ACME decision tables on ICD-10 codes

  Python

  •

  BSD 2-Clause "Simplified" License

  •22 forks•00 stars•00 issues•11 pull request•Updated Mar 10, 2026Mar 10, 2026

• indra_cogex

  Public
  INDRA Context Graph Extension

  bdf-toolbox

  bdf-toolbox

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •1818 forks•1414 stars•1919 issues•1111 pull requests•Updated Mar 7, 2026Mar 7, 2026

• 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 …

  sqlalchemydatabasesystems-biology+ 3

  sqlalchemydatabasesystems-biologypostgresqlindramachine-reading

  Python

  •

  GNU General Public License v3.0

  •1111 forks•1919 stars•77 issues•44 pull requests•Updated Mar 2, 2026Mar 2, 2026

• dglink

  Public
  Linking data portals to external knowledge

  Python

  •

  BSD 2-Clause "Simplified" License

  •11 fork•00 stars•00 issues•11 pull request•Updated Feb 3, 2026Feb 3, 2026

• indralab-vue

  Public
  A package of Vue Components for use in Indralab web services.

  Vue

  •44 forks•00 stars•00 issues•2323 pull requests•Updated Jan 23, 2026Jan 23, 2026

• indra_bert

  Public
  Python

  •

  BSD 2-Clause "Simplified" License

  •00 forks•00 stars•00 issues•11 pull request•Updated Jan 21, 2026Jan 21, 2026

• protmapper

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

  Python

  •

  BSD 2-Clause "Simplified" License

  •77 forks•77 stars•00 issues•00 pull requests•Updated Nov 22, 2025Nov 22, 2025

• indra_network_search

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

  Python

  •

  BSD 2-Clause "Simplified" License

  •22 forks•00 stars•1818 issues•00 pull requests•Updated Oct 21, 2025Oct 21, 2025

• depmap_analysis

  Public
  Jupyter Notebook

  •99 forks•11 star•00 issues•11 pull request•Updated Oct 20, 2025Oct 20, 2025

• biomappings-curation-app

  Public
  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Oct 9, 2025Oct 9, 2025

• indra_variants

  Public
  Causal networks for variant effect mechanisms and prediction

  Python

  •

  BSD 2-Clause "Simplified" License

  •22 forks•00 stars•11 issue•00 pull requests•Updated Sep 11, 2025Sep 11, 2025

• indra_gpt

  Public
  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Sep 4, 2025Sep 4, 2025

• indra_signor

  Public
  Connecting INDRA to the SIGNOR database curation workflow

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 29, 2025Jul 29, 2025

• outbreak_kg

  Public
  Knowledge graphs for disease outbreak scenarios

  Python

  •

  BSD 2-Clause "Simplified" License

  •33 forks•11 star•00 issues•00 pull requests•Updated Jul 21, 2025Jul 21, 2025

• ner_annotator

  Public
  HTML

  •

  BSD 2-Clause "Simplified" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 18, 2025Jul 18, 2025

• indra_perturbseq

  Public
  Using INDRA to explain Perturb-seq data

  BSD 2-Clause "Simplified" License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 11, 2025Jul 11, 2025

• worm_lifespan

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

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 30, 2025May 30, 2025

• indra_curation

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

  JavaScript

  •

  BSD 2-Clause "Simplified" License

  •44 forks•00 stars•11 issue•00 pull requests•Updated May 20, 2025May 20, 2025

• emmaa

  Public
  Ecosystem of Machine-maintained Models with Automated Analysis

  cancerbiologymodeling+ 3

  cancerbiologymodelingsystems-biologyindrasystems-biology-simulation

  Python

  •

  BSD 2-Clause "Simplified" License

  •1111 forks•1111 stars•22 issues•44 pull requests•Updated May 16, 2025May 16, 2025

• indra_may_institute

  Public
  Jupyter Notebook

  •11 fork•11 star•11 issue•00 pull requests•Updated May 9, 2025May 9, 2025

• nexus

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 4, 2025May 4, 2025