pagreene
Senior Software Engineer, Full Stack. I have a background in Physics and years of experience developing full-stack solutions for bio-research.
Sail BiomedicineGreater Boston Area
Pinned Repositories
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
emmaa
Ecosystem of Machine-maintained Models with Automated Analysis
indra
Integrated Network and Dynamical Reasoning Assembler
indra_db
A Database-based knowledge back-end built on and for INDRA.
ising-py
Implementation of the metropolis algorithm in c with a python interface.
nose-notify
This is a simple script that can be used to execute nose-tests and send the results to slack or email upon failure.
py_ggcm
A sophisticated python interface to OpenGGCM (deprecated)
pagreene's Repositories
pagreene/indra
Integrated Network and Dynamical Reasoning Assembler
pagreene/bioagents
Biological reasoning agents
pagreene/bioregistry
📮 An integrative registry of biological databases, ontologies, and nomenclatures.
pagreene/emmaa
Ecosystem of Machine-maintained Models with Automated Analysis
pagreene/indra_db
A Database-based knowledge back-end built on and for INDRA.
pagreene/doyen
A tool for finding experts using publicly available data sources such as pubmed.
pagreene/fp-vs-oop-demo
A demo of functional programming vs. object oriented programming approaches, using a grocery list generator as an example.
pagreene/gilda
Grounding of biomedical named entities with contextual disambiguation
pagreene/git-novice
Version Control with Git
pagreene/indra_curation
A utility build around the HTML assembler to enable easy curation of custom sets of INDRA Statements.
pagreene/indra_deps_docker
Docker image to build latest REACH and Kappa.
pagreene/indra_docker
Docker build for INDRA, REACH, PySB, and related dependencies.
pagreene/indra_reading
Tools used for large scale reading, mostly using AWS Batch.
pagreene/indralab-vue
A package of Vue Components for use in Indralab web services.
pagreene/minerva-author
Tool to create images and configuration files for Minerva-Story
pagreene/minerva-author-ui
Minerva Author is an authoring tool used to create Minerva narrated stories via selection of specific channel groupings and image views.
pagreene/minerva-browser
pagreene/minerva-cloud
Minerva Cloud is a novel cloud-native (AWS) platform for high-dimensional microscopy image storage, management, and visualization.
pagreene/minerva-cloud-ui
Minerva Cloud is a novel cloud-based (AWS) software for high-dimensional image management, storage and visualization.
pagreene/minerva-lib-python
Minerva Python Library
pagreene/minerva-story
Minerva Story is an image viewer that is designed specifically to make it easy for non-expert users to interact with complex tissue images.
pagreene/moto
A library that allows you to easily mock out tests based on AWS infrastructure.
pagreene/music-matching
Use ML/DS techniques to match a sample of music to another performance of that same piece of music (primarily for Western Classical music).
pagreene/protmapper
Map amino acid sites of post-translational modifications from models or data to reference positions.
pagreene/pubmed_parser
:clipboard: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset
pagreene/python-novice-gapminder
Plotting and Programming in Python
pagreene/sat-stat
A final project for HES CSCI E88: model satellite orbits, and analyze the data from those orbits using Akka.
pagreene/ui_util
This repo creates general utilities for our user interfaces.
pagreene/ytmusicapi
Unofficial API for YouTube Music
pagreene/Zappa
Serverless Python Web Services