Show HN: Phage Explorer

Show HN: Phage Explorer(phage-explorer.org)

127 points by eigenvalue 107 days ago | 35 comments

I got really interested in biology and genetics a few months ago, just for fun.

This was largely inspired by the work of Sydney Brenner, which became the basis of my brennerbot.org project.

In particular, I became very fascinated by phages, which are viruses that attack bacteria. They're the closest thing to the "fundamental particles" of biology: the minimal units of genetic code that do something useful that allows them to reproduce and spread.

They also have some incredible properties, like having a structure that somehow encodes an icosahedron.

I always wondered how the DNA of these things translated into geometry in the physical world. That mapping between the "digital" realm of ACGT, which in turn maps onto the 20 amino acids in groups of 3, and the world of 3D, analog shapes, still seems magical and mysterious to me.

I wanted to dig deeper into the subject, but not by reading a boring textbook. I wanted to get a sense for these phages in a tangible way. What are the different major types of phages? How do they compare to each other in terms of the length and structure of their genetic code? The physical structure they assume?

I decided to make a program to explore all this stuff in an interactive way.

And so I'm very pleased to present you with my open-source Phage Explorer:

phage-explorer.org

I probably went a bit overboard, because what I ended up with has taken a sickening number of tokens to generate, and resulted in ~150k lines of Typescript and Rust/Wasm.

It implements 23 analysis algorithms, over 40 visualizations, and has the complete genetic data and 3D structure of 24 different classes of phage.

It actually took a lot of engineering to make this work well in a browser; it's a surprising amount of data (this becomes obvious when you look at some of the 3D structure models).

It works fairly well on mobile, but if you want to get the full experience, I highly recommend opening it on a desktop browser in high resolution.

As far as I know, it's the most complete informational / educational software about phages available anywhere. Now, I am the first to admit that I'm NOT an expert, or even that knowledgeable, about, well, ANY of this stuff.

So if you’re a biology expert, please take a look and let me know what you think of what I've made! And if I've gotten anything wrong, please let me know in the GitHub Issues and I'll fix it:

https://github.com/Dicklesworthstone/phage_explorer

gtsnexp 106 days ago |

The premise behind this vibe-coded website is excellent. It would have been great if a bit more effort had been invested in the visualization side and, if instead of using "AI-rendered" images, you'd have fetched scientifically accurate representations from papers and open repositories.

Tiberium 107 days ago |

Sorry, but I really wouldn't trust a website that uses Gemini's image models for generating scientific diagrams. The website itself is also vibe-coded. That's not an issue by itself, but there are lots of layout issues visible, see https://i.imgur.com/SidB6pI.png

A bit offtopic: If anyone wants to check whether a specific image is generated by Google models without using Gemini, go to https://images.google.com/, upload the image, click the "About this image" section. It'll say "Made with Google AI" if it was generated with their models.

noduerme 107 days ago | |

>> what I ended up with has taken a sickening number of tokens to generate

I was a bit confused by this as to whether it related only to the graphics or to the UI as well.

makerofthings 107 days ago |

AI really loves that purple-blue style with rounded corners. I asked chatGPT to make a few sites to see how it worked and any time I said "make the site look nicer", it did that. I wonder why.

codingminds 106 days ago |

At least put a big warning in your introduction box that highlights that those data might be invalid because you are not an expert in this topic. Let the use acknowledge this before continuing.

jryb 107 days ago |

This is so riddled with inaccuracies that I can spot them immediately despite not being a phage biologist. For example, the PhiX image has a DNA with about 20 base pairs - wildly not to scale. M13 is also wildly scaled, and it clearly has a double stranded DNA which is labeled as single stranded.

What the hell is this amino acid view? This is not how genes work at all. This is biology 101 and it's completely wrong. Why did you buy a domain name to share disinformation that you don't even understand?

None of this is displayed in a way that would be useful to working biologists, and I don't see how this could be used as a teaching tool even if all the errors were corrected. This simply doesn't provide any insight into how phages work. Looking at a raw sequence is pointless (also that color scheme is incredibly garish) - you need annotations! The 3D structures don't have their domains labeled and you can't connect sequence features to structural elements.

Why wouldn't you just use all of the existing tools that already do all of this correctly? Look, I don't mean to gate keep, and it's great that you learned something (assuming you didn't vibe code this), but this is a lot of effort that could have been avoided if you had had a single conversation with a biologist of any background, or asked an LLM to critique your idea, or made a single reddit post asking if this would be useful.

Edit: This may come across as super harsh - but really, I love the enthusiasm and I hope you keep pursuing this. But the right place for this passion at this point in your life is a classroom or some kind of structured course.

jart 106 days ago | |

Yeah we're all quickly figuring out that LLMs shift the engineering work from computer science to bullshit detection. You basically have to become that guy on the Internet who's always trying to prove you wrong when working with Claude Code. Otherwise you're going to build yourself a false reality and get skewered if you try to share it. I mean I've done it myself, because we're so used to blindly trusting the things other people built, that we forget we're the ones building it. Nothing in life is free.

jryb 105 days ago | | |

LLMs may be enabling, but OP explicitly stated "I wanted to dig deeper into the subject, but not by reading a boring textbook", which, of course, would have eliminated the issues in this tool, or at least made it clear to them that they needed to dive deeper before publishing. I feel like there might be some analogy with blaming cars for drunk driving - by definition, not possible without cars, but you can drive responsibly if you choose to.

noduerme 107 days ago |

It's rather nice looking, but it would have been so much nicer if you'd done it yourself.

eigenvalue 107 days ago | |

I find this to be a bizarre sentiment. It’s an artifact that exists. The chances of me making this by hand are 0. This would be a full time job for 3 years to research and build this. For 10 people. And it would have to charge a ton of money to access in that case.

flexagoon 106 days ago | | |

> This would be a full time job for 3 years to research and build this. For 10 people.

No it wouldn't.

stavros 107 days ago | |

He did do it himself.

If you meant "without AI", then it would have never been done in the first place, so you can choose your preference there.

noduerme 106 days ago | | |

If he paid the same amount of money to an offshore worker to build it, would you say he'd done it himself?

jadengeller 107 days ago |

some quick feedback on the user interface:

- i pressed "Amino Acids", and nothing updated below the toolbar. can't figure out what it does

- the "Tools" buttons looks like a segmented picker, but both seem to actually initiate a modal presentation

this tool seems interesting, but it would be worth polishing some of these ui quirks because my first impression was that it seems a bit broken (or confused me)!

but seems like a cool project otherwise, love people building and sharing explainers as they learn stuff!

kasperset 106 days ago |

It looks nice but very "LLMsy". I liked that it specifically annotates "Lytic" vs "Lysogenic" categorization for phages. Important in terms of virome analysis. https://pmc.ncbi.nlm.nih.gov/articles/PMC11097211/

jurgenaut23 107 days ago |

What used to be a life time project that would inspire awe and respect and make OP an instant hire for most managers is now a fun 1-week stunt that makes you go “cool, how many tokens?” Of course, the result is cool and maybe even useful (I wouldn’t dare say _correct_, being ignorant of the topic), but I cannot help but think that this would have been tremendously better if done the old (proper?) way.

Also, I suspect that OP would have learned so much more on the topic.

stavros 107 days ago | |

Yeah but the choice isn't "do I spend two weeks on this, or do I spend a lifetime?". It's "I have two weeks, do I spend them making the whole thing with AI, or 5% of it without?".

codingminds 106 days ago | | |

If it's inaccurate it's worthless anyhow.

It's absolutely no issue to build all the technical and design stuff with AI, but science facts must be science facts and not just AI gibberish presented like facts.

What's the benefit of presenting not trustworthy data?

jurgenaut23 106 days ago | | |

It must be me getting old, but definitely 5% of it without, if your goal is to learn something. 5% of thinking about a hard problem is more valuable than 100% of letting it being done by someone else.

Especially when the value of the end result is close to zero, since it is now so easy to do and replicate.

tgv 107 days ago | |

I'm pretty much on the no-AI side (learning, art, decision making, etc.), but this is the kind of thing I can appreciate. I suppose OP didn't want to learn more about coding this kind of visualization, but rather learn from the visualization. Any tool that can help with that is acceptable, whether it produces code or not. That the tool produced code has the advantage that OP can share this with us. I only hope it doesn't contain fundamental errors, because that would make this project a negative contribution.

jurgenaut23 107 days ago | | |

Sure, I don’t discard the contribution altogether, but I am dubious that it is possible to properly draw the line between what to vibe code and what to do it “by hand” to make sure you get the benefits of building.

wefzyn 106 days ago |

Very good idea and very interesting. Great use of AI. The next step in this project, if you were funded, would be to have human experts double check the accuracy of the information and images.

Since this isn't funded, you could have a frontier model evaluate all the information for inaccuracies and fix them it can't find any. Then have another frontier model do the same. Then go back to the first model and see if it finds any inaccuracies.

Keep at it. You are doing a great job, but there is more work to be done before you can productionize it.

mentalgear 107 days ago |

Research into phages is paramount, as they represent one of our best hopes for combating the rapidly increasing problem of antibiotic resistance (largely driven by the overuse of antibiotics, even including last-resort antibiotics, in industrial animal agriculture so industrial farms can place more animals per sq/m without them dying from lack of space and cut-off body parts so they take even less space).

bboydart91 107 days ago |

I really resonate with your goal of creating a more intuitive tool than a boring textbook. Being able to visually see how complex genetic code translates into physical geometry (3D structures) would be incredibly helpful for students. Thank you for sharing such a wonderful educational tool!