Taxonomic Tree Visualizer

look still very great :smiling_face_with_three_hearts: … but i miss the svg export, which i prefer because it is loose less vector and not pixel like png :folded_hands: :wink:

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incredible. It looks like a phylogeny tree.

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It looks really cool! Would you consider open-sourcing your code? It would be good for people to build upon it and help to avoid security flaws (e.g. too many permissions, data leaking and such)

You say you are not a dev, so it is fair to assume this was vibe coded? Good vibe coding skills :slight_smile: I am also curious on the set up you used (models and such), because it seems quite efficient. Is it just repl.it default?

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Thanks. Yea I can post the github repo.

Yea literally all vibe-coded (we need a better word for using a LLM on a project for weeks/months at a time and thinking through the process.). So I’ve been learning the overall concepts, layouts, API, hosting, authentication (turns out not necessary), SQL, cloudflare workers, etc. but letting the AI write the actual code. I have a background in physics and math and I do GIS work professionally so I usually just spin up python scripts.

I started ‘way’ back in January with Claude 3.5 on replit I think. Now I use Cursor IDE and my chatgpt subscription. Set up a project in chatgpt, GPT-5 writes the code there, move it to cursor, push to git, sync with replit and deploy. I’m hot and cold on replit and i never use the AI on their platform anymore. It was just an easy way to host a site at first and it has a great UI until it spontaneously breaks. I’m thinking of moving this to github pages or the like now that I know a bit more of what I’m doing.

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Where did the idea / inspiration come from? I think i am quite excited somebody is setting up an app like this. I’ve always wanted a tree view for all of my observations or a single taxon, if you expanded it to the whole taxonomy of iNaturalist (i know would probably be extremely resource consuming), you would basically get a tree of all life.

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I stumbled onto markmap one day and decided if I can make a little visualization of my iNaturalist observations: https://markmap.js.org/repl And the project has ballooned from there :sweat_smile:

I just tried using ‘Life’ for a query for my records and I had quite a bad time :X (works better for lower groups like Insecta, or if you have less observed species of course). I’m sure there are other data viz graphs and such we could use too.

I kinda want to expand the map part so we can get a better tool for seeing what species are around you that you haven’t seen yet. iNaturalist has this checklist compare feature which kinda does what my checklist tab does but in a list. I’d like to include the default taxa images of the most commonly observed that you haven’t seen yet in a region too. eBird has a feature like this (Target Species).

I still have to populate the map’s observations in a smarter way (using another one of pisum’s suggestions!)

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i added an interactive html export, let me know if that is what you had in mind.

added a little favicon

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Essentially it is a phylogeny (according to iNat). It just doesn’t have any nodes that aren’t iNat taxonomic levels (or one could consider that effectively all such nodes are collapsed).

There are actually a lot of programs that already exist for manipulating and visualizing trees which use fairly standard formats, see: https://evomics.org/resources/tree-formats/ which are fairly simple.

@mmulqueen Not sure how possible it would be to implement (or if it is worth it!), but you could consider creating an export option for one of those formats (probably Newick) which could support their use in tree viewers/editors (and then publications, etc. or for people to just use existing programs to pretty up/display the trees however they’d like).

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That’s a really good idea actually. I’m looking into it. Newick format looks very simple, so definitely doable. But we could possibly embed more information using other formats though I’m not sure what would be valuable. Links, counts, dates, lat/long, etc.?

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May some metadata, annotations, fields, projects, may sorted by date, how ever this could get a huge thing.

i love it :heart_hands:

May some Obsidian.md (https://obsidian.md/) format or Mermaid ( https://www.mermaidchart.com/play )?

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Added a date filter for Explore/PvP tabs. Let me know if you find something that isn’t working right.

Also new export options, newick tree .nwk, .nhx, phyloxml (broken still i think), node and edge csv. Mermaid should be easy to add since we already have the generated markdown, gotta clean it up a bit

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