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