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.
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.
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.
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)
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!
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.
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.
Show HN: I built a biological network visualization tool
(nodes.bio)39 points by jmg421 25 July 2025 | 28 comments
Comments
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
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.
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.