Julian's Polymath Explorations

(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 ...

[UPDATED MAY 2022]  D3.js is a very powerful visualization tool, especially for specialized/custom needs...  On the flip side, it's rather hard to use - with a steep learning curve. Even worse if one also wants interactivity ! But why is D3 so hard/clunky to use?  And what can be done about it? Spoiler alert: Vue.js (or other modern front-end framework) to the rescue - if done right... All code in the examples is available in this GitHub repository . The Root of the Problem In a nutshell, what makes D3 awkward to use is that, for historical reasons, it tries to do too much : most painfully, it uses an old way to do direct DOM manipulation (i.e. restructuring the page layout) - an operation that nowadays is superbly handled in a far more friendly way by modern front-end frameworks, such as Vue.js Document Object Model ( DOM ) is a programming interface for web documents.  In simple terms, it's the structure of the elements on a web page (text, images, etc.) Let ...