Gyori Lab for Computational Biomedicine

gilda

Grounding of biomedical named entities with contextual disambiguation

pybiopax

PyBioPAX: A python implementation of the BioPAX object model

adeft

Tool for disambiguating acronyms and abbreviations in text for NLP applications

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.

emmaa

Ecosystem of Machine-maintained Models with Automated Analysis

mira

MIRA modeling framework

indra_cogex

INDRA Context Graph Extension

indra_world

INDRA World Modelers services

protmapper

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

gyorilab.github.io

Gyori Lab website

covid-19

Scripts and other utilities relevant to the CORD-19 dataset

depmap_analysis

panacea_indra

INDRA applications for the DARPA Panacea project

protmapper_paper

Code to generate results and figures relevant to the ProtMapper manuscript.

opaque

Outlier Prevalence Analysis for Quantification of Unknown Entities

adeft_indra

Build Adeft models with content from the INDRA Database

causal_precedence_training

Scripts for assembling datasets for causal precedence prediction

go_networks

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

indra_curation

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

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_network_search

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

indra_reading

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

indra_signor

Connecting INDRA to the SIGNOR database curation workflow

indra_spine

indralab-vue

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

neuroimmune_interactome

outbreak_kg

Knowledge graphs for disease outbreak scenarios

trialsynth

TrialSynth interprets and integrates clinical trials data from multiple registries in a computable form

ui_util

This repo creates general utilities for our user interfaces.