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@gyorilab Gyori Lab for Computational Biomedicine

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    54 repositories

    • indra_cogex

      Public
      INDRA Context Graph Extension
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •13•10•20•8•Updated Apr 24, 2025Apr 24, 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-biologypostgresqlindramachine-reading
      Python
      •
      GNU General Public License v3.0
      •11•16•7•2•Updated Apr 24, 2025Apr 24, 2025

    • indra_variants

      Public
      INDRA-assembled pathways for variant effects
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•0•0•0•Updated Apr 23, 2025Apr 23, 2025

    • biomappings-curation-app

      Public
      Python
      •0•0•0•0•Updated Apr 23, 2025Apr 23, 2025

    • depmap_analysis

      Public
      Jupyter Notebook
      •7•1•0•1•Updated Apr 15, 2025Apr 15, 2025

    • gyorilab.github.io

      Public
      Gyori Lab website
      HTML
      •
      Other
      •3•3•0•0•Updated Apr 5, 2025Apr 5, 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 Apr 3, 2025Apr 3, 2025

    • indra_gpt

      Public
      Jupyter Notebook
      •1•0•0•1•Updated Apr 1, 2025Apr 1, 2025

    • ui_util

      Public
      This repo creates general utilities for our user interfaces.
      Python
      •4•0•0•1•Updated Mar 21, 2025Mar 21, 2025

    • gilda

      Public
      Grounding of biomedical named entities with contextual disambiguation
      Python
      •
      BSD 2-Clause "Simplified" License
      •13•43•8•5•Updated Mar 20, 2025Mar 20, 2025

    • mira

      Public
      MIRA: machine-assisted modeling of dynamical systems
      modelingsystems-biologyepidemiologydifferential-equationsontologiesmodeling-and-simulationknowledge-graphs
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •7•12•19•4•Updated Mar 12, 2025Mar 12, 2025

    • indra_reading

      Public
      Tools used for large scale reading, mostly using AWS Batch.
      Python
      •6•0•0•2•Updated Mar 4, 2025Mar 4, 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•15•1•Updated Mar 3, 2025Mar 3, 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

    • 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

    • mapnet

      Public
      Algorithms for semantic mapping between different ontologies
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•0•0•1•Updated Jan 31, 2025Jan 31, 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

    • emmaa

      Public
      Ecosystem of Machine-maintained Models with Automated Analysis
      cancerbiologymodelingsystems-biologysystems-biology-simulationindra
      Python
      •
      BSD 2-Clause "Simplified" License
      •11•11•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

    • 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

    • 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•7•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