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@gyorilab

Gyori Lab for Computational Biomedicine

Accelerating discovery in biomedicine using AI @ Northeastern University

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  1. emmaa Public

    Ecosystem of Machine-maintained Models with Automated Analysis

    Python 11 11

  2. 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 16 11

  3. gilda Public

    Grounding of biomedical named entities with contextual disambiguation

    Python 43 13

  4. protmapper Public

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

    Python 7 7

  5. indra_world Public

    INDRA World Modelers services

    Jupyter Notebook 7 5

  6. indra_cogex Public

    INDRA Context Graph Extension

    Jupyter Notebook 10 13

Repositories

Showing 10 of 52 repositories
  • indra_curation Public

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

    JavaScript 0 BSD-2-Clause 4 1 0 Updated Mar 27, 2025
  • gyorilab.github.io Public

    Gyori Lab website

    HTML 3 3 0 0 Updated Mar 27, 2025
  • indra_cogex Public

    INDRA Context Graph Extension

    Jupyter Notebook 10 BSD-2-Clause 13 18 5 Updated Mar 26, 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.

    Python 16 GPL-3.0 11 8 2 Updated Mar 21, 2025
  • ui_util Public

    This repo creates general utilities for our user interfaces.

    Python 0 4 0 1 Updated Mar 21, 2025
  • gilda Public

    Grounding of biomedical named entities with contextual disambiguation

    Python 43 BSD-2-Clause 13 8 5 Updated Mar 20, 2025
  • mira Public

    MIRA: machine-assisted modeling of dynamical systems

    Jupyter Notebook 12 BSD-2-Clause 7 19 4 Updated Mar 12, 2025
  • indra_reading Public

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

    Python 0 6 0 1 Updated Mar 4, 2025
  • indra_network_search Public

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

    Python 0 BSD-2-Clause 2 15 1 Updated Mar 3, 2025
  • indra_metascience Public

    Analyzing scientific trends based on INDRA-assembled knowledge

    Python 0 BSD-2-Clause 1 0 0 Updated Feb 26, 2025
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