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adeft

Tool for disambiguating acronyms and abbreviations in text for NLP applications

adeft_app

simple flask app for grounding lists of terms

adeft_indra

Build Adeft models with content from the INDRA Database

aws_util

brain

Resources for assembling and analyzing information about brain research using INDRA.

causal_precedence_training

Scripts for assembling datasets for causal precedence prediction

covid-19

Scripts and other utilities relevant to the CORD-19 dataset

depmap_analysis

drug_similarity

Implement and combine multiple different methods of computing drug similarity.

emmaa

Ecosystem of Machine-maintained Models with Automated Analysis

foodome

Code related to the LSP - Barabasi Lab collaboration on understanding molecular mechanisms of food.

gilda

Grounding of biomedical named entities with contextual disambiguation

go_networks

INDRA-assembled networks of mechanisms between genes sets corresponding to GO terms

gyorilab.github.io

Gyori Lab website

idg_ion_channels

Repository for collaboration between the HMS INDRA and IDG Ion Channel teams.

indra_cogex

INDRA Context Graph Extension

indra_curation

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

indra_db

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.

indra_db_docker

Home to the docker file used on AWS for the indra_db tools.

indra_db_lite

Work with content from indra_db in a local sqlite database.

indra_db_paper

Scripts and Jupyter notebooks for the INDRA Database manuscript.

indra_deps_docker

Docker image to build latest REACH and Kappa.

indra_docker

Docker build for INDRA, REACH, PySB, and related dependencies.

indra_gpt

indra_may_institute

indra_network_search

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

indra_phospho

Tools for analyzing phosphoproteomic data using functional information assembled by INDRA.

indra_reading

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

indrabot

indralab-vue

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