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@gyorilab

Gyori Lab for Computational Biomedicine

Accelerating discovery in biomedicine using AI @ Northeastern University

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  1. indra 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…

    Python 203 72

  2. indra_cogex indra_cogex Public

    INDRA Context Graph Extension

    Jupyter Notebook 13 14

  3. emmaa emmaa Public

    Ecosystem of Machine-maintained Models with Automated Analysis

    Python 11 11

  4. indra_db 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 dat…

    Python 18 11

  5. gilda gilda Public

    Grounding of biomedical named entities with contextual disambiguation

    Python 47 15

  6. indra_world indra_world Public

    INDRA World Modelers services

    Jupyter Notebook 9 5

Repositories

Showing 10 of 62 repositories
  • indra_agent Public

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

    gyorilab/indra_agent’s past year of commit activity
    Python 0 BSD-2-Clause 2 0 0 Updated Jan 15, 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 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.

    gyorilab/indra_db’s past year of commit activity
    Python 18 GPL-3.0 11 7 2 Updated Jan 12, 2026
  • indra_cogex Public

    INDRA Context Graph Extension

    gyorilab/indra_cogex’s past year of commit activity
    Jupyter Notebook 13 BSD-2-Clause 14 19 8 Updated Jan 9, 2026
  • indralab-vue Public

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

    gyorilab/indralab-vue’s past year of commit activity
    Vue 0 4 0 23 Updated Jan 8, 2026
  • gilda Public

    Grounding of biomedical named entities with contextual disambiguation

    gyorilab/gilda’s past year of commit activity
    Python 47 BSD-2-Clause 15 8 6 Updated Jan 8, 2026
  • gyorilab.github.io Public

    Gyori Lab website

    gyorilab/gyorilab.github.io’s past year of commit activity
    HTML 4 3 0 0 Updated Dec 29, 2025
  • dglink Public

    Linking data portals to external knowledge

    gyorilab/dglink’s past year of commit activity
    Python 0 BSD-2-Clause 1 0 0 Updated Dec 23, 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.

    gyorilab/indra’s past year of commit activity
    Python 203 BSD-2-Clause 72 33 8 Updated Dec 19, 2025
  • adeft Public

    Tool for disambiguating acronyms and abbreviations in text for NLP applications

    gyorilab/adeft’s past year of commit activity
    Python 22 BSD-2-Clause 10 0 0 Updated Dec 18, 2025
  • openacme Public

    Implementing ACME decision tables on ICD-10 codes

    gyorilab/openacme’s past year of commit activity
    Python 0 BSD-2-Clause 1 0 0 Updated Dec 1, 2025
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