Show HN: I built a biological network visualization tool

[jmg421]

I've been working on nodes.bio - an interactive tool for visualizing biological networks and systems thinking. The tool features interactive network visualization powered by Cytoscape.js, with real-time graph editing and manipulation capabilities. It supports JSON import/export and provides a responsive design that works seamlessly on the desktop (mobile-friendly version coming later).

The tech stack combines modern frontend technologies with robust backend architecture. The frontend uses Next.js 14 with TypeScript and Cytoscape.js for the visualization engine. The backend is built with FastAPI and Python.

The featured demo showcases a Traumatic Brain Injury Nasal Spray mechanism of action visualization, demonstrating the tool's capability to handle complex biological pathway mapping.

You can explore the live demo at <https://nodes.bio> to see the TBI Nasal Spray visualization in action, along with other biological network examples.

I'd love feedback on the visualization capabilities or any suggestions for biological data integration. What do you think?

[jmg421]

I wanted to share why I built this - it's deeply personal. In 2020, my mother was diagnosed with glioblastoma. As I navigated her treatment, I found myself completely overwhelmed by the complexity of biological networks. The medical literature was fragmented across hundreds of papers, and I struggled to see how her specific genetic markers related to potential treatments.

[jmg421]

At its heart, the Nodes.bio API addresses a fundamental gap in biological data accessibility. While vast repositories of biological information exist, they often remain siloed and difficult to manipulate programmatically. Our API transforms static biological data into dynamic, interactive networks that can be built, modified, and analyzed in real-time.

The platform's biological network graph system (/api/v3/graph) allows users to create nodes representing proteins, genes, receptors, and enzymes, then define the complex relationships between these entities through edges that represent molecular interactions such as binding, activation, and inhibition. This isn't merely data visualization—it's a living, breathing representation of biological systems that responds to real-time updates and modifications.

TODO: Swagger documentation on the API

[jmg421]

Here's the API!

https://api.nodes.bio/docs/index.html

[jmg421]

UPDATE: I've added a quick demo page for mobile at https://nodes.bio/mobile/ . The mobile page now showcases three major network visualizations:

TBI Nasal Spray Mechanism - Shows molecular pathways and drug delivery mechanisms for traumatic brain injury treatment.

Biological Network Introduction - Demonstrates protein-protein interactions, signaling pathways, and cellular communication systems.

Innovation Pipeline Network - Visualizes the research-to-commercialization pipeline, mapping connections from scientific discoveries to market applications.

The full interactive experience is available on desktop for advanced features and larger networks.

Thanks everyone for the feedback about adding compelling demo screenshots - this gives mobile visitors a clear sense of what the tool can visualize across different biological domains.

[throwaway127482]

The website has a little card that says "Interactive Mobile Experience" but your post says "mobile-friendly version coming later," which is confusing. I tried it, and it doesn't seem to work on mobile at all (Chrome/Android)

[jmg421]

Thank you for the feedback! You're absolutely right about the mobile experience - I need to fix that "Interactive Mobile Experience" card. The mobile version is indeed broken right now, and I should have been clearer about that. Working on a proper mobile-responsive version.

[puppycodes]

Looks potentially cool but your mobile version needs work, currently looks like its broken

[jmg421]

Thanks for the feedback... this is one of the top items I'm working on!

[jmg421]

Update on the 502s- looks like it was a memory issue during an overnight deployment. I'm working on getting a proper staging environment running. Sorry for the inconvenience!

[rickcarlino]

Reading the threads, it sounds like mobile is a WIP. you should consider adding screenshots of a compelling demo use case to the mobile landing page in the interim.

[jmg421]

Check out https://nodes.bio/mobile/

[jmg421]

thanks for the feedback. I'm working on this right now.

[gibsonf1]

Thats a terrible ontology (the relations) - needs to be much lower level to understand anything important.

[jmg421]

The current demo shows a simplified view, but the tool can handle much more granular relationships. I have some glioblastoma and pancreatic cancer networks with protein-protein interactions, phosphorylation events, and pathway cross-talk that show the lower-level detail. The challenge is balancing accessibility with scientific rigor.

[8mobile]

Hi, I'm interested in the tool but I get this error, 502 Bad Gateway.

[jmg421]

Not sure what happened, it should be back up momentarily. Thanks for having a look at it!

[kvthweatt]

I’m getting 502 on mobile

[jmg421]

It should be back up momentarily- I think I had a deployment issue while I was working on the mobile experience.

[JayEquilibria]

Maybe I dream of building a competitor and Traumatic Brain Injury is deeply personal to me so I am super biased but it is super "meh" because of Cytoscape.

To me, Cytoscape is simply outdated and an arbitrary constraint on the software, a relic of network science history.

The deeper problem though is how valuable is network data visualization from an epistemological standpoint? Pretty useless from my experiments besides for a kind of scientism performance art. That is not to say scientistic performance art data viz can not be lucrative in a post modern scientism society.

Take this with a grain of salt because biological networks are never going to be my strong point. There is this huge node data viz scaling problem I don't think has been solved and I am kind of waiting for this to be solved with biological network so I can just rip off the idea.

[rowanxmas]

What about the Cytoscape Desktop metaphor do you not like? As one of the original folks on the project I wrote the early API, and we very specifically made it data-agnostic. So unless you don't want to use nodes and edges (in which case yeah... look elsewhere) I think it's pretty adaptable.

When I was doing grad school work while working on Cytoscape the rendering engine part was only for figure generation. Most of the "real" work was using the networks-subnetworks and doing interesting things with the graph model.

[jmg421]

@JayEquilibria- This is a great comment, thanks so much, it helps tremendously. I will reply separately in a more comprehensive way :-).

[cbracketdash]

I'm getting a 502 error on laptop

[jmg421]

It's back up, thanks for checking it out!