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)
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.
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.
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.
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.
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.
Hey @JayEquilibria — thanks again for your thoughtful comment!
I used to share some of your skepticism — a lot of network visualizations do feel like scientistic performance art. That started to shift for me after discovering NFX and reading The Cold Start Problem by Andrew Chen. I began thinking more seriously about network effects when I applied for my first U.S. patent after leaving JP Morgan Chase, where I spent 14 years in technology, leadership, and innovation. That experience led to the early ideas behind Nodes.bio.
I do rely on Cytoscape.js as a rendering engine — so I want to be transparent about that. But I’ve moved deliberately away from the legacy metaphors and plugin model of desktop Cytoscape. Nodes.bio is browser-native, install-free, and designed for speed, storytelling, and shareability. It's built for researchers, founders, investors, and even patients — not just PhD bioinformaticians.
I understand the “performance art” critique, but I’ve seen what happens when visualization actually delivers insight. One of my early users, Dr. Patrick Sewell, a clinical geneticist, has gone on record saying:
“Nodes.bio transformed my hand-drawn network into a publication-quality, interactive diagram in minutes—something I simply couldn't have achieved with any other tool.”
That kind of feedback reshaped how I think about the epistemic value of visualization. In a world increasingly shaped by LLMs, I believe pictures that are worth thousands of tokens are becoming essential — not ornamental.
And even from a utilitarian standpoint — forget truth claims, just ask: does this help people make better decisions, faster, with fewer errors? From what I’ve seen: yes. Visual structure helps surface non-obvious connections, prioritize experiments, flag off-target effects, and bridge gaps between data producers and decision makers. That’s reason enough to keep going.
As for scaling: I’m running on AWS ECR/EB, so infrastructure is solid. The real challenge is cognitive scaling — how to keep massive biological networks legible and meaningful. That’s where I’m focusing next.
I’ll also be publishing the Nodes.bio APIs in the near future — because the value here isn’t just in pretty diagrams, it’s in enabling others to build, extend, and integrate with their own data pipelines, dashboards, or discovery workflows.
Appreciate the challenge. If you do decide to build in this space, I’d love to trade notes!
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.
TODO: Swagger documentation on the API
Here's the API!
https://api.nodes.bio/docs/index.html
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)
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.
Looks potentially cool but your mobile version needs work, currently looks like its broken
Thanks for the feedback... this is one of the top items I'm working on!
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.
Check out https://nodes.bio/mobile/
thanks for the feedback. I'm working on this right now.
Thats a terrible ontology (the relations) - needs to be much lower level to understand anything important.
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.
hey you made it to the front page but looks like its down
It's back up, thanks for checking it out!
Hi, I'm interested in the tool but I get this error, 502 Bad Gateway.
Not sure what happened, it should be back up momentarily. Thanks for having a look at it!
I’m getting 502 on mobile
It should be back up momentarily- I think I had a deployment issue while I was working on the mobile experience.
It’s working. I’m checking it out now.
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.
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.
@JayEquilibria- This is a great comment, thanks so much, it helps tremendously. I will reply separately in a more comprehensive way :-).
Hey @JayEquilibria — thanks again for your thoughtful comment!
I used to share some of your skepticism — a lot of network visualizations do feel like scientistic performance art. That started to shift for me after discovering NFX and reading The Cold Start Problem by Andrew Chen. I began thinking more seriously about network effects when I applied for my first U.S. patent after leaving JP Morgan Chase, where I spent 14 years in technology, leadership, and innovation. That experience led to the early ideas behind Nodes.bio.
I do rely on Cytoscape.js as a rendering engine — so I want to be transparent about that. But I’ve moved deliberately away from the legacy metaphors and plugin model of desktop Cytoscape. Nodes.bio is browser-native, install-free, and designed for speed, storytelling, and shareability. It's built for researchers, founders, investors, and even patients — not just PhD bioinformaticians.
I understand the “performance art” critique, but I’ve seen what happens when visualization actually delivers insight. One of my early users, Dr. Patrick Sewell, a clinical geneticist, has gone on record saying:
That kind of feedback reshaped how I think about the epistemic value of visualization. In a world increasingly shaped by LLMs, I believe pictures that are worth thousands of tokens are becoming essential — not ornamental.And even from a utilitarian standpoint — forget truth claims, just ask: does this help people make better decisions, faster, with fewer errors? From what I’ve seen: yes. Visual structure helps surface non-obvious connections, prioritize experiments, flag off-target effects, and bridge gaps between data producers and decision makers. That’s reason enough to keep going.
As for scaling: I’m running on AWS ECR/EB, so infrastructure is solid. The real challenge is cognitive scaling — how to keep massive biological networks legible and meaningful. That’s where I’m focusing next.
I’ll also be publishing the Nodes.bio APIs in the near future — because the value here isn’t just in pretty diagrams, it’s in enabling others to build, extend, and integrate with their own data pipelines, dashboards, or discovery workflows.
Appreciate the challenge. If you do decide to build in this space, I’d love to trade notes!
I'm getting a 502 error on laptop
It's back up, thanks for checking it out!