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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 206 74

  2. indra_cogex indra_cogex Public

    INDRA Context Graph Extension

    Jupyter Notebook 14 17

  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 49 17

  6. indra_world indra_world Public

    INDRA World Modelers services

    Jupyter Notebook 9 5

Repositories

Showing 10 of 63 repositories
  • gilda Public

    Grounding of biomedical named entities with contextual disambiguation

    gyorilab/gilda’s past year of commit activity
    Python 49 BSD-2-Clause 17 8 6 Updated Mar 30, 2026
  • 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 Mar 26, 2026
  • 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 1 BSD-2-Clause 3 0 1 Updated Mar 25, 2026
  • miradb Public

    An automatically extracted database of MIRA models

    gyorilab/miradb’s past year of commit activity
    Python 0 BSD-2-Clause 2 0 0 Updated Mar 25, 2026
  • mira Public

    MIRA: machine-assisted modeling of dynamical systems

    gyorilab/mira’s past year of commit activity
    Jupyter Notebook 13 BSD-2-Clause 9 18 5 Updated Mar 25, 2026
  • 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 206 BSD-2-Clause 74 34 13 Updated Mar 24, 2026
  • gyorilab.github.io Public

    Gyori Lab website

    gyorilab/gyorilab.github.io’s past year of commit activity
    HTML 4 3 0 0 Updated Mar 22, 2026
  • mapnet Public

    Algorithms for semantic mapping between different ontologies

    gyorilab/mapnet’s past year of commit activity
    Python 0 BSD-2-Clause 3 0 0 Updated Mar 11, 2026
  • openacme Public

    Implementing ACME decision tables on ICD-10 codes

    gyorilab/openacme’s past year of commit activity
    Python 0 BSD-2-Clause 2 0 1 Updated Mar 10, 2026
  • indra_cogex Public

    INDRA Context Graph Extension

    gyorilab/indra_cogex’s past year of commit activity
    Jupyter Notebook 14 BSD-2-Clause 17 19 9 Updated Mar 7, 2026
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