Projects in Awesome Lists by gyorilab
A curated list of projects in awesome lists by gyorilab .
https://github.com/gyorilab/gilda
Grounding of biomedical named entities with contextual disambiguation
Last synced: 11 May 2025
https://github.com/gyorilab/pybiopax
PyBioPAX: A python implementation of the BioPAX object model
biology biopax python systems-biology
Last synced: 30 Apr 2025
https://github.com/gyorilab/adeft
Tool for disambiguating acronyms and abbreviations in text for NLP applications
Last synced: 30 Apr 2025
https://github.com/gyorilab/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.
database indra machine-reading postgresql sqlalchemy systems-biology
Last synced: 30 Apr 2025
https://github.com/gyorilab/mira
MIRA: machine-assisted modeling of dynamical systems
differential-equations epidemiology knowledge-graphs modeling modeling-and-simulation ontologies systems-biology
Last synced: 30 Apr 2025
https://github.com/gyorilab/emmaa
Ecosystem of Machine-maintained Models with Automated Analysis
biology cancer indra modeling systems-biology systems-biology-simulation
Last synced: 30 Apr 2025
https://github.com/gyorilab/protmapper
Map amino acid sites of post-translational modifications from models or data to reference positions.
Last synced: 23 Apr 2025
https://github.com/gyorilab/covid-19
Scripts and other utilities relevant to the CORD-19 dataset
Last synced: 30 Apr 2025
https://github.com/gyorilab/protmapper_paper
Code to generate results and figures relevant to the ProtMapper manuscript.
Last synced: 30 Apr 2025
https://github.com/gyorilab/panacea_indra
INDRA applications for the DARPA Panacea project
Last synced: 11 Mar 2025
https://github.com/gyorilab/indra_deps_docker
Docker image to build latest REACH and Kappa.
Last synced: 11 Mar 2025
https://github.com/gyorilab/adeft_indra
Build Adeft models with content from the INDRA Database
Last synced: 11 Mar 2025
https://github.com/gyorilab/foodome
Code related to the LSP - Barabasi Lab collaboration on understanding molecular mechanisms of food.
Last synced: 11 Mar 2025
https://github.com/gyorilab/drug_similarity
Implement and combine multiple different methods of computing drug similarity.
Last synced: 11 Mar 2025
https://github.com/gyorilab/indra_docker
Docker build for INDRA, REACH, PySB, and related dependencies.
Last synced: 11 Mar 2025
https://github.com/gyorilab/indra_phospho
Tools for analyzing phosphoproteomic data using functional information assembled by INDRA.
Last synced: 11 Mar 2025
https://github.com/gyorilab/adeft_app
simple flask app for grounding lists of terms
Last synced: 11 Mar 2025
https://github.com/gyorilab/opaque
Outlier Prevalence Analysis for Quantification of Unknown Entities
Last synced: 11 Mar 2025
https://github.com/gyorilab/go_networks
INDRA-assembled networks of mechanisms between genes sets corresponding to GO terms
Last synced: 11 Mar 2025
https://github.com/gyorilab/idg_ion_channels
Repository for collaboration between the HMS INDRA and IDG Ion Channel teams.
Last synced: 11 Mar 2025
https://github.com/gyorilab/nf_model
Resources for an EMMAA model focusing on molecular mechanisms of neurofibromatosis.
Last synced: 11 Mar 2025
https://github.com/gyorilab/causal_precedence_training
Scripts for assembling datasets for causal precedence prediction
Last synced: 11 Mar 2025
https://github.com/gyorilab/indra_db_paper
Scripts and Jupyter notebooks for the INDRA Database manuscript.
Last synced: 11 Mar 2025
https://github.com/gyorilab/indra_reading
Tools used for large scale reading, mostly using AWS Batch.
Last synced: 30 Apr 2025
https://github.com/gyorilab/ui_util
This repo creates general utilities for our user interfaces.
Last synced: 30 Apr 2025
https://github.com/gyorilab/outbreak_kg
Knowledge graphs for disease outbreak scenarios
Last synced: 30 Apr 2025
https://github.com/gyorilab/indra_network_search
REST API for querying the network of biochemical mechanisms in the INDRA DB.
Last synced: 30 Apr 2025
https://github.com/gyorilab/trialsynth
TrialSynth interprets and integrates clinical trials data from multiple registries in a computable form
Last synced: 11 Mar 2025
https://github.com/gyorilab/worm_lifespan
Studying genes affecting lifespan in C. elegans using knowledge assembly and networks
Last synced: 25 Feb 2025
https://github.com/gyorilab/mapnet
Algorithms for semantic mapping between different ontologies
Last synced: 11 Mar 2025
https://github.com/gyorilab/panacea_rnaseq
RNAseq data analysis pipelines for the Panacea project
Last synced: 11 Mar 2025
https://github.com/gyorilab/indra_db_lite
Work with content from indra_db in a local sqlite database.
Last synced: 18 Jan 2025
https://github.com/gyorilab/indra_signor
Connecting INDRA to the SIGNOR database curation workflow
Last synced: 11 Mar 2025
https://github.com/gyorilab/indra_db_docker
Home to the docker file used on AWS for the indra_db tools.
Last synced: 11 Mar 2025
https://github.com/gyorilab/brain
Resources for assembling and analyzing information about brain research using INDRA.
Last synced: 11 Mar 2025
https://github.com/gyorilab/indra_metascience
Analyzing scientific trends based on INDRA-assembled knowledge
Last synced: 15 May 2025
https://github.com/gyorilab/indra_curation
A utility build around the HTML assembler to enable easy curation of custom sets of INDRA Statements.
Last synced: 30 Apr 2025
https://github.com/gyorilab/indralab-vue
A package of Vue Components for use in Indralab web services.
Last synced: 11 Mar 2025
https://github.com/gyorilab/rest_tools
Tools used by multiple indralab REST APIs.
Last synced: 11 Mar 2025
https://github.com/gyorilab/parcdl-nl
Natural language implementation of the Mechanistic Pan-Cancer Model from the Birtwistle Lab: https://github.com/birtwistlelab/Mechanistic_Pan-Cancer_Model
Last synced: 11 Mar 2025