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Graph Databases to Build Plugin-Driven Web Apps, such as Multimedia Content Management Systems

Eleven years ago, the 2015 origins of the open-source project BrainAnnex.org was as a Multimedia Content Management System .   Fast-forward to 2021 : the project had a radical makeover with v. 5, and is now a much more general, modular, full-stack technology solution to effectively utilize graph databases. For example, you can opt to install just the python library, if that's all you need.  But if you elect to install the entire repo (python library, web API and web app), you will have a UI that includes:  a control panel - including search and visualization a plugin-driven web app that you can customize relatively easily The plugin-driven web app is the focus of this entry.  More specifically, the existing plugins that come with the standard release, and provide a Multimedia Content Management System This article is part of a growing,  ongoing series  on Graph Databases and Neo4j Plugin-Driven Architecture A "plugin", i...
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Life123 : An OPEN-SOURCE Platform for Quantitative Interactomics

NOTE:  this entry was inspired by talks I gave at the "Bio-IT World 2025" conference in Boston, and at the "Aging & Gerontology 2025" conference in San Francisco.   A VIDEO VERSION also exists    (slightly shorter and outdated to Apr. 2025)    Life123 is an open-source platform for quantitative interactomics, aiming towards simulations of virtual biological cells or parts thereof – among other things. And it has a slogan:  AI and Big Data aren't enough! We also need Dynamical modeling. What does it mean to say "engine for quantitative reactomics"?  It means that we perform dynamical modeling of biological systems. And the initial focus is towards eventually creating whole-cell simulations. The platform consists of python libraries, which allow us to do in-silico experiments. Early this year, this project left the beta stage, after a few years of development. Motivation There's a practical motiva...
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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 ...
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