iiinova — where your digital self keeps evolving

BY FAR the most time was spent tweaking the UI. It is still not great at that, though surprisingly I found that providing screenshots does seem to help. We'll see how this (or any AI code) holds up as I have to maintain it. Feel free to leave issues/ideas on the repo. github.com/gwct/PhyloLens

GitHub - gwct/PhyloLens: Simple phylogenetic tree viewer extension for VSCode

Simple phylogenetic tree viewer extension for VSCode - gwct/PhyloLens

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At times I would ask for suggestions, which the chatbot of course would provide. A surprising number were useful, leading to feature creep in what was supposed to be a very simple app. Though in the end I'm happy where it ended up. Now working on updates for better performance for huge trees.

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But I started with a very simple design: an extension to VIEW phylogenies. It accomplished this almost immediately, but I was also able to see the potential for more (editing, conversion, image export) once I had that in place.

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I hope the extension will be useful, and it already has been for me, but it does leave me with thoughts on agentic coding. I'd guess overall time spent was about 6-8 hours of actual "work" chatting with the agent, which is not a lot of time for full project development.

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The interface provides status badges for the tree to tell you whether its rooted, binary, ultrametric, and allows for some minor editing and conversion between text formats as well as image export, though I don't see this as being useful for pretty tree pictures.

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marketplace.visualstudio.com

Blizzard outside, so I'll post about my first foray into fully agentic AI coding. I picked something I'd been wanting to do for a while, but had no experience with prior: a VSCode extension to view phylogenies in the editor. The result is PhyloLens. marketplace.visualstudio.com/items?itemNa...

PhyloLens - Visual Studio Marketplace

Extension for Visual Studio Code - View phylogenetic trees in VS Code (Newick, NEXUS, PhyloXML, NeXML).

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Reposted by Gregg Thomas

Fábio K. Mendes @fabiology.bsky.social · 12/07/2025

📣 The Mendes Lab is recruiting PhD students in statistical phylogenetics! Interested, or know someone who might be? Details here 👉 tinyurl.com/542wyfb9 — please share!

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Gregg Thomas @gwct.bio · 05/06/2025

Relatedly, but for a narrower audience, I also adapted the Snakemake SLURM executor plugin to perform automatic partition selection on the Harvard Cannon cluster. I was surprised by the amount of flexibility the plugins allowed, which may have finally won me over to them. github.com/harvardinfor...

GitHub - harvardinformatics/snakemake-executor-plugin-cannon: A Snakemake executor plugin for submitting jobs to the Harvard Cannon cluster

A Snakemake executor plugin for submitting jobs to the Harvard Cannon cluster - harvardinformatics/snakemake-executor-plugin-cannon

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Gregg Thomas @gwct.bio · 05/06/2025

Each task has an associated tutorial on our group's website: informatics.fas.harvard.edu/resources/#t... Feel free to reach out if you want to use any of these workflows and need help getting started or run into any issues!

informatics.fas.harvard.edu

Resources - Harvard FAS Informatics Group

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Gregg Thomas @gwct.bio · 05/06/2025

Recently I developed several Snakemake workflows for tasks related to Cactus and HAL files, including whole genome alignment and pangenome inference. The goal was to perform these tasks efficiently on SLURM-based (or possibly other) clusters. I hope they are useful! github.com/harvardinfor...

GitHub - harvardinformatics/cactus-snakemake: Snakemake workflows for performing whole genome alignment with Cactus efficiently on SLURM clusters

Snakemake workflows for performing whole genome alignment with Cactus efficiently on SLURM clusters - harvardinformatics/cactus-snakemake

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Reposted by Gregg Thomas

Matthew Hahn @3rdreviewer.bsky.social · 10/02/2025

New paper led by @glom.bsky.social! "Unprecedented female female bias in the aye-aye, a highly unusual lemur from Madagascar" 1/ journals.plos.org/plosbiology/...

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Reposted by Gregg Thomas

James Pease @jamesbpease.bsky.social · 10/01/2025

The Pease Lab in the Dept of Evolution, Ecology, and Organismal Biology at The Ohio State University is looking for a Postdoc interested in genotype-phenotype-environment evolution in plant and animal genomes. Details at osu.wd1.myworkdayjobs.com/en-US/OSUCar... and more info at www.peaselab.org

Aronoff Lab at The Ohio State University

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Reposted by Gregg Thomas

Emily Moore @ecmoore.bsky.social · 09/01/2025

If you know anyone who might be interested in working as a technician before a PhD, I'm looking for someone to work with me to generate some amazing data to understand the genetics of behavior, sex differences, and reproduction in an evolutionary context. Bonus? Amazing and supportive department!

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Reposted by Gregg Thomas

Emily Kopania @ekopania.bsky.social · 07/01/2025

Our paper on the evolution of male reproduction in murine rodents was selected as the editor's choice article in the January issue of Evolution!

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Hmm, yea that could work. I wonder if there is any mouse data that could work for this? @jeffreygood.bsky.social Although, I'm not sure how to map shortbreads. Maybe some batches with BWA-kery? :D

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Yea that would definitely help pinpoint which SNPs are being miscalled. I was also hoping to dig into why they are being miscalled - mis-mapped reads? unmapped reads? something else? Which I can't think of how to do without a truth set for the mappings themselves.

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A thorough look at what I think is an often overlooked problem in popgen and comparative genomics in general!

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We've (@jeffreygood.bsky.social) implemented this in pseudo-it (github.com/goodest-good...), though hard to quantify the effects without good simulations, which I've yet to find the right read simulation program for. Ideally want simulated bam and vcf to compare mapping and SNP calls. Ideas welcome!