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adeft

Tool for disambiguating acronyms and abbreviations in text for NLP applications

bioagents

Biological reasoning agents

bioregistry

📮 An integrative registry of biological databases, ontologies, and nomenclatures.

causalityagent

classymixer

This is a project to create a commandline (for now) tool for creating playlists of classical music, such that multi-movement (and hence multi-track) pieces are kept together. This currently works only with google play, but will soon be expanded to work for local file systems.

cwc_integ_service

doyen

A tool for finding experts using publicly available data sources such as pubmed.

emmaa

Ecosystem of Machine-maintained Models with Automated Analysis

flask-jwt-extended

An open source Flask extension that provides JWT support (with batteries included)!

fp-vs-oop-demo

A demo of functional programming vs. object oriented programming approaches, using a grocery list generator as an example.

gilda

Grounding of biomedical named entities with contextual disambiguation

git-novice

Version Control with Git

grip

Graph Integration Platform

indra

Integrated Network and Dynamical Reasoning Assembler

indra_apps

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.

indra_deps_docker

Docker image to build latest REACH and Kappa.

indra_docker

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

indra_reading

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

indra_sparser_docker

A docker for AWS using sparser with indra.

indrabot

indralab-vue

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

ising-py

Implementation of the metropolis algorithm in c with a python interface.

kaggle_zillow_comp

This is the code I am using in the Kaggle Zillow competition.

kasim

Tool suite for kappa models. Documentation and binaries can be found in the release section. Try it online at

minerva-author

Tool to create images and configuration files for Minerva-Story

minerva-author-ui

Minerva Author is an authoring tool used to create Minerva narrated stories via selection of specific channel groupings and image views.

minerva-browser

minerva-cloud

Minerva Cloud is a novel cloud-native (AWS) platform for high-dimensional microscopy image storage, management, and visualization.