Julian's Polymath Explorations

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Visualization of Graph Databases Using Cytoscape.js

(UPDATED SEP. 2025) I have ample evidence from multiple sources that there are strong unmet needs in the area of visualization of graph databases. And whenever there's a vacuum, there's danger of having to deal with vendors circling like vultures - with incomplete, non-customizable, and at times ridiculously expensive, closed-box proprietary solutions. Fortunately, coming to the rescue is the awesome open-source cytoscape.js library , an offshoot of the "Cytoscape" project of the Institute for Systems Biology , a project with a long history that goes back to 2002. One can do amazing custom solutions, relatively easily, when one combines this Cytoscape library with: 1) a front-end framework such as Vue.js 2) backend libraries (for example in python) to prepare and serve the data For example, a while back I created a visualizer for networks of chemical reactions, for another open-source project I lead ( life123.science ) This ...

Graph Database Series - Beginners to Advanced, Full-Stack (Neo4j focus)

A growing, ongoing series on Graph Databases and Neo4j. The series has grown so large that I'm "factoring out" their Table of Contents as a separate entry, here! A series on Graph Databases and Neo4j part 0 (alternate version of part 1 for a general, non-technical audience) : What are Graph Databases - and Why Should I Care?? : "Graph Databases for Poets" part 1 : Intro to Graph Databases (Neo4j) - a revolution in modeling the real world! part 2 : Neo4j Sandbox Tutorial : try Neo4j and learn Cypher the free and easy way part 3 : Neo4j & Cypher Tutorial : Getting Started with a Graph Database and its Query Language part 4 : Using Neo4j with Python : the Open-Source Library NeoAccess part 5 : Using Schema in Graph Databases such as Neo4j part 6 : Putting it All Together - a Technology Stack on Top of a Graph Database SPECIAL TOPICS *...

Graph Database Data Modeling - ORDERED Sequences

Using graph databases, you may have a need for ORDERED SEQUENCES of data records... For example: ordered sequences of adverse events in clinical trials ordered sequences of text messages ordered sequences of chemical production steps ordered sequences of "content items" for a content management system Good news : an open-source library exists for conveniently managing this data model in a Neo4j graph database (and in principle could be ported to other graph databases.) This concept of ordered sequences of data nodes: 1) is hugely general : I gave them the name "(Ordered) Collections " 2) can be tricky to implement fully (for example, to deal with multiple insertions in the middle) 3) fortunately, all is handled by this open-source library! 😁 => Here's the documentation => Here's the source code This article is part of a growing, ongoing series on Graph Databases and Neo4j A Simple Example The attached image is a simple example of ...

What are Graph Databases - and Why Should I Care?? : "Graph Databases for Poets"

This is a very gentle introduction to the subject. The subtitle is inspired by university courses such as "Physics for Poets"! (if you're technically inclined, there's an alternate article for you.) It has been said that "The language of physics (or of God) is math". On a similar note, it could be said that: The language of the biological world - or of any subject or endeavor involving complexity - is networks ('meshes') What is a network? Think of it as the familiar 'friends of friends' diagram from social media. Everywhere one turns in biology, there's a network – at the cellular level, tissue level, organ level, ecosystem level. The weather and other earth systems are networks. Human societal organization is a network. Electrical circuits, the Internet, our own brains... Networks are everywhere! What can we do with networks, to better understand the world around us, or to create something that we need? Broadly ...