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    61 repositories

    • llm-text-to-knowledge-graph

      Public
      A package and command-line interface for extracting knowledge graphs from text, with a special focus on supporting agents working with scientific hypotheses and experiment design
      Python
      •
      MIT License
      •0•1•6•0•Updated Dec 20, 2024Dec 20, 2024

    • ndex-rest

      Public
      NDEx Rest Server
      ndexndexbio
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •2•5•0•0•Updated Dec 13, 2024Dec 13, 2024

    • ndex2-client

      Public
      NDEx2 Client
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•6•7•0•Updated Dec 5, 2024Dec 5, 2024

    • iquery

      Public
      Frontend code for the Search Portal.
      JavaScript
      •4•7•2•12•Updated Nov 6, 2024Nov 6, 2024

    • ndex-object-model

      Public
      Java object model for the external data model for NDEx - can be used by applications accessing NDEx via API
      ndexbiondex
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •3•3•0•0•Updated Nov 4, 2024Nov 4, 2024

    • ndex-webapp

      Public
      This is WebApp code that was officially released with NDEx v.1.3 on March 17, 2016. Please do not commit to this branch.
      JavaScript
      •3•5•0•9•Updated Oct 18, 2024Oct 18, 2024

    • ndexsearch-rest

      Public
      Java
      •2•0•0•4•Updated Sep 19, 2024Sep 19, 2024

    • gsoc_llm

      Public
      GSOC 2024 LLM Project
      Jupyter Notebook
      •
      MIT License
      •0•0•6•0•Updated Sep 19, 2024Sep 19, 2024

    • ndex-java-client

      Public
      Java client library for accessing NDEx REST server
      ndexndexbio
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Sep 12, 2024Sep 12, 2024

    • ndex-enrichment-rest

      Public
      Java
      •4•1•0•4•Updated Aug 30, 2024Aug 30, 2024

    • ndex-neighborhood-query-java

      Public
      Neighobrhood and related query engine for individual cx network. This is one internal service in NDEx server
      Java
      •0•0•0•1•Updated Jul 31, 2024Jul 31, 2024

    • ndex-vagrant

      Public
      Vagrant configuration to test run NDEx distribution
      Shell
      •0•0•0•0•Updated May 8, 2024May 8, 2024

    • ndex-interactome-search

      Public
      Interactome search service for NDEx iQuery
      Java
      •3•1•0•2•Updated Dec 20, 2023Dec 20, 2023

    • ndex-enrichment-rest-client

      Public
      Java
      •2•0•0•4•Updated Dec 5, 2023Dec 5, 2023

    • ndex-jupyter-notebooks

      Public
      NDEx application code examples in Jupyter notebooks
      Jupyter Notebook
      •2•5•3•0•Updated Apr 17, 2023Apr 17, 2023

    • ndex-js-client

      Public
      JavaScript
      •
      MIT License
      •0•1•0•12•Updated Mar 2, 2023Mar 2, 2023

    • ndex_webapp_python_exporters

      Public
      Command line exporters written in Python used by the NDex REST service
      Python
      •0•0•6•2•Updated Dec 26, 2022Dec 26, 2022

    • ndexutils

      Public
      Python
      •2•2•1•0•Updated Oct 3, 2022Oct 3, 2022

    • ndex-layout

      Public
      *integrate with ndex-example-development* experiments in python-based layout algorithms that can be used with NDEx networks.
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Dec 28, 2021Dec 28, 2021

    • openapi-reader

      Public
      An OpenAPI reader application giving users the ability to view the NDEx rest api and interactively "try out" NDEx api requests.
      JavaScript
      •
      Apache License 2.0
      •9k•0•0•0•Updated Dec 17, 2020Dec 17, 2020

    • openapi-specification

      Public
      OpenAPI specification for the ndexbio.org rest server api and used by ndextools/openapi-reader. This repository is created by Mike Fidel and transferred to NDEx project in March 2018.
      openapi-specificationopenapi3ndexndex-serverndex-restndexbio
      MIT License
      •1•1•1•0•Updated Dec 17, 2020Dec 17, 2020

    • community-detection-app

      Public
      Cytoscape app to provide simple interface for community detection using the backend REST service
      0•0•0•0•Updated Jul 1, 2019Jul 1, 2019

    • community-detection-service

      Public
      Community detection service - fast, scalable service to be backend of a Cytoscape app
      0•0•0•0•Updated Jul 1, 2019Jul 1, 2019

    • load-content

      Public
      load content
      ndexndexbio
      Python
      •1•0•0•0•Updated Mar 4, 2019Mar 4, 2019

    • ndex-enrich

      Public
      Python-based enrichment module that uses NDEx. Implements worker code for CI-based NDEx enrichment service.
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Jan 26, 2019Jan 26, 2019

    • ndex-python

      Public
      NDEx Python Client v3.1 - Superseded by the NDEx2 Client v1.0
      ndexndex-python-clientaccess-ndexndex-server
      Python
      •6•2•7•0•Updated Jan 11, 2019Jan 11, 2019

    • ndex-example-development

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 28, 2018Nov 28, 2018

    • excel-neo4j-integration

      Public
      0•1•0•0•Updated Oct 15, 2018Oct 15, 2018

    • civic-loader

      Public
      TSV loader for the CIViC
      Python
      •0•0•0•0•Updated Oct 11, 2018Oct 11, 2018

    • indra_me

      Public
      INDRA interface scripts from 2018.
      Jupyter Notebook
      •1•0•0•1•Updated Sep 4, 2018Sep 4, 2018