[HN Gopher] Show HN: Phage Explorer
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Show HN: Phage Explorer
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
Author : eigenvalue
Score : 113 points
Date : 2026-01-31 05:22 UTC (17 hours ago)
(HTM) web link (phage-explorer.org)
(TXT) w3m dump (phage-explorer.org)
| jadengeller wrote:
| 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!
| bboydart91 wrote:
| 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!
| mentalgear wrote:
| 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).
| jurgenaut23 wrote:
| 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.
| tgv wrote:
| 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.
| noduerme wrote:
| Errors are just nonsense that shows up in the console until
| you spend more tokens to make them go bye bye, right? I think
| you're talking more about the idea of true and false
| information, which is such a human bias. Will it really
| matter to anyone in 5 years whether this accurately depicts
| phages? By then AI will have solved everything. /s
| jurgenaut23 wrote:
| 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.
| stavros wrote:
| 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 wrote:
| 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?
| stavros wrote:
| That's an entirely different argument, though. Let's not
| move the goalposts.
| jurgenaut23 wrote:
| 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.
| stavros wrote:
| Eh, my goal is to make something, personally.
| eigenvalue wrote:
| Look at the commit history. I've been working on this
| essentially every single day for over a month.
| Tiberium wrote:
| 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 wrote:
| >> 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.
| noduerme wrote:
| It's rather nice looking, but it would have been so much nicer if
| you'd done it yourself.
| stavros wrote:
| 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.
| eigenvalue wrote:
| 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 wrote:
| > This would be a full time job for 3 years to research and
| build this. For 10 people.
|
| No it wouldn't.
| makerofthings wrote:
| 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.
| jryb wrote:
| 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.
| gtsnexp wrote:
| 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.
| codingminds wrote:
| 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.
| kasperset wrote:
| 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/
| wefzyn wrote:
| 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.
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