Repositories list

• 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

  •11•17•7•3•Updated Oct 16, 2025Oct 16, 2025

• mira

  Public
  MIRA: machine-assisted modeling of dynamical systems

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

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •8•13•18•4•Updated Oct 16, 2025Oct 16, 2025

• indra

  Public
  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.

  nlpbioinformaticsbiology+ 6modelingsystems-biologycomputational-biologypysbindrasbml

  Python

  •

  BSD 2-Clause "Simplified" License

  •71•199•34•10•Updated Oct 16, 2025Oct 16, 2025

• indra_cogex

  Public
  INDRA Context Graph Extension

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •13•12•20•9•Updated Oct 15, 2025Oct 15, 2025

• gyorilab.github.io

  Public
  Gyori Lab website

  HTML

  •

  Other

  •3•4•0•0•Updated Oct 13, 2025Oct 13, 2025

• biomappings-curation-app

  Public
  Python

  •0•1•0•0•Updated Oct 9, 2025Oct 9, 2025

• 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•19•1•Updated Oct 1, 2025Oct 1, 2025

• depmap_analysis

  Public
  Jupyter Notebook

  •8•1•0•1•Updated Sep 30, 2025Sep 30, 2025

• trialsynth

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

  Python

  •

  BSD 2-Clause "Simplified" License

  •2•0•0•0•Updated Sep 24, 2025Sep 24, 2025

• indra_variants

  Public
  Causal networks for variant effect mechanisms and prediction

  Python

  •

  BSD 2-Clause "Simplified" License

  •2•0•1•0•Updated Sep 11, 2025Sep 11, 2025

• indra_gpt

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Sep 4, 2025Sep 4, 2025

• indra_signor

  Public
  Connecting INDRA to the SIGNOR database curation workflow

  Python

  •0•0•0•0•Updated Jul 29, 2025Jul 29, 2025

• gilda

  Public
  Grounding of biomedical named entities with contextual disambiguation

  Python

  •

  BSD 2-Clause "Simplified" License

  •14•44•8•8•Updated Jul 23, 2025Jul 23, 2025

• outbreak_kg

  Public
  Knowledge graphs for disease outbreak scenarios

  Python

  •

  BSD 2-Clause "Simplified" License

  •3•1•0•0•Updated Jul 21, 2025Jul 21, 2025

• ner_annotator

  Public
  HTML

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Jul 18, 2025Jul 18, 2025

• indra_perturbseq

  Public
  Using INDRA to explain Perturb-seq data

  BSD 2-Clause "Simplified" License

  •1•0•0•0•Updated Jul 11, 2025Jul 11, 2025

• mapnet

  Public
  Algorithms for semantic mapping between different ontologies

  Python

  •

  BSD 2-Clause "Simplified" License

  •1•0•0•0•Updated Jun 18, 2025Jun 18, 2025

• worm_lifespan

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

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•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

  •4•0•1•0•Updated May 20, 2025May 20, 2025

• emmaa

  Public
  Ecosystem of Machine-maintained Models with Automated Analysis

  cancerbiologymodeling+ 3systems-biologyindrasystems-biology-simulation

  Python

  •

  BSD 2-Clause "Simplified" License

  •11•11•2•4•Updated May 16, 2025May 16, 2025

• indra_may_institute

  Public
  Jupyter Notebook

  •1•1•1•0•Updated May 9, 2025May 9, 2025

• nexus

  Public
  Python

  •0•0•0•0•Updated May 4, 2025May 4, 2025

• indra_reading

  Public
  Tools used for large scale reading, mostly using AWS Batch.

  Python

  •6•0•0•1•Updated Apr 28, 2025Apr 28, 2025

• ui_util

  Public
  This repo creates general utilities for our user interfaces.

  Python

  •4•0•0•1•Updated Mar 21, 2025Mar 21, 2025

• indra_metascience

  Public
  Analyzing scientific trends based on INDRA-assembled knowledge

  Python

  •

  BSD 2-Clause "Simplified" License

  •1•0•0•0•Updated Feb 26, 2025Feb 26, 2025

• covid-19

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

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •4•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

• indra_spine

  Public
  Jupyter Notebook

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

• protmapper_paper

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

  Python

  •1•2•0•0•Updated Oct 10, 2024Oct 10, 2024