Show HN: I built a biological network visualization tool

30•jmg421•1d ago

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?

Comments

gibsonf1•12h ago

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

jmg421•11h ago

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.

bloqs•5h ago

hey you made it to the front page but looks like its down

jmg421•1h ago

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

puppycodes•12h ago

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

jmg421•1h ago

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

throwaway127482•11h ago

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•11h ago

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.

jmg421•11h ago

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.

kvthweatt•9h ago

I’m getting 502 on mobile

jmg421•1h ago

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

cbracketdash•7h ago

I'm getting a 502 error on laptop

jmg421•1h ago

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

8mobile•7h ago

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

jmg421•1h ago

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

jmg421•1h ago

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•48m ago

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•42m ago

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

jmg421•19m ago

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

jmg421•17m ago

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.

Rust on Every GPU

Bringing a decade old bicycle navigator back to life with open source software

Do not download the app, use the website

Breaking the WASM/JS communication performance barrier

Open Sauce is a confoundingly brilliant Bay Area event

It's time for modern CSS to kill the SPA

The append-and-review note

Simon Tatham's Portable Puzzle Collection

CCTV footage captures the first-ever video of an earthquake fault in motion

Yes, the Book of PF, Fourth Edition Is Coming Soon

The rise and fall of the Hanseatic League

Keep Pydantic out of your Domain Layer

It's a DE9, not a DB9 (but we know what you mean)

Never write your own date parsing library

Why I do programming

I am a SOTA 0-shot classifier of your slop

Why MIT switched from Scheme to Python (2009)

Efficient Computer's Electron E1 CPU – 100x more efficient than Arm?

The natural diamond industry is getting rocked. Thank the lab-grown variety

The future is not self-hosted

Animated Cursors

Experimental surgery performed by AI-driven surgical robot

Vanilla JavaScript support for Tailwind Plus

Steam, Itch.io are pulling ‘porn’ games. Critics say it's a slippery slope

Developing our position on AI

Users claim Discord's age verification can be tricked with video game characters

CO2 Battery

Programming vehicles in games

What is X-Forwarded-For and when can you trust it? (2024)

Women dating safety app 'Tea' breached, users' IDs posted to 4chan

Show HN: I built a biological network visualization tool

Comments

Rust on Every GPU

Bringing a decade old bicycle navigator back to life with open source software

Do not download the app, use the website

Breaking the WASM/JS communication performance barrier

Open Sauce is a confoundingly brilliant Bay Area event

It's time for modern CSS to kill the SPA

The append-and-review note

Simon Tatham's Portable Puzzle Collection

CCTV footage captures the first-ever video of an earthquake fault in motion

Yes, the Book of PF, Fourth Edition Is Coming Soon

The rise and fall of the Hanseatic League

Keep Pydantic out of your Domain Layer

It's a DE9, not a DB9 (but we know what you mean)

Never write your own date parsing library

Why I do programming

I am a SOTA 0-shot classifier of your slop

Why MIT switched from Scheme to Python (2009)

Efficient Computer's Electron E1 CPU – 100x more efficient than Arm?

The natural diamond industry is getting rocked. Thank the lab-grown variety

The future is not self-hosted

Animated Cursors

Experimental surgery performed by AI-driven surgical robot

Vanilla JavaScript support for Tailwind Plus

Steam, Itch.io are pulling ‘porn’ games. Critics say it's a slippery slope

Developing our position on AI

Users claim Discord's age verification can be tricked with video game characters

CO2 Battery

Programming vehicles in games

What is X-Forwarded-For and when can you trust it? (2024)

Women dating safety app 'Tea' breached, users' IDs posted to 4chan