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:
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.
I was a bit confused by this as to whether it related only to the graphics or to the UI as well.
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.
No it wouldn't.
If you meant "without AI", then it would have never been done in the first place, so you can choose your preference there.
Asking for something out of your head, whether you're requesting a custom sandwich at a drive-thru restaurant or you're the project manager of a software company, is not the same as making it yourself. If it were, then you wouldn't need to drive through the restaurant or be a mid-level managerial parasite to get what you envisioned.
We should still judge people's skills on the merits of what they can create themselves. I've never had much interest in people who just ordered things up from their underlings, and claimed they were the creators. That's stolen merit, if you ask me. Show me someone who can create a piece of code from scratch, and then we can evaluate how well they leveraged an AI or a team of people to do the next piece of code for them. Not every piece of code has to be written from scratch, but it needs to be understood. You seemed to assert that this project would've taken many people many years or it wouldn't otherwise have been written. That's not true. It could be written in a week by a competent human. The fact that it wasn't could be a clue that it doesn't add value to begin with, which in turn implies that its output may be unreliable (even if it were useful).
- 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!
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.
Also, I suspect that OP would have learned so much more on the topic.
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?
Especially when the value of the end result is close to zero, since it is now so easy to do and replicate.
