Will Fondrie
Head of Data Science & Engineering at Talus Bio. I post about data science, BioML, AI drug discovery, Python, mass spec, proteomics, and silly things my kids do.
I also blog sometimes: willfondrie.com/post
- I love that @obsidian.md requires you to type the key sequence to exit vim before enabling vim key bindings 😆
- How do you deal with missing values and "unique" proteins that were only identified in one condition in proteomics data? Mengchun Li, an amazing PhD student in my lab, developed this great Bayesian approach. Please try it and give feedback! www.biorxiv.org/content/10.6...
- Nice work! I’m curious how it compares to Triqler, which is conceptually similar 🤔
- This one is good read!
- How do you deal with missing values and "unique" proteins that were only identified in one condition in proteomics data? Mengchun Li, an amazing PhD student in my lab, developed this great Bayesian approach. Please try it and give feedback! www.biorxiv.org/content/10.6...
- Nerf guns + eye protection for the family (including us, the parents) were a huge hit. So many smiles and laughs have been shared in our epic battles for the basement today 😊
- Looking for an internship next summer? Join my team @talusbio.bsky.social! Apply 👇 by Jan 31 🤖🧬💻 www.applicantpro.com/openings/tal...
- Ha. Good to know I still get to code a bit 😀 git-wrapped.com
- Wednesday is typically one of my WFH deep work days 💻🧬🤖
- A nice write up of what we’ve been working on recently @talusbio.bsky.social by @afederation.bsky.social. Check it out to get a glimpse of our progress drugging AR and success from our lab-in-the-loop active learning cycles. And don’t forget to subscribe for more 👇 blog.talus.bio/p/progress-u...
- 😳 ... it was me. I'm part of the problem. Forgot about this PR github.com/lazear/sage/...
- Who in the training data used so many emojis in their code?
- Affinity has been my favorite design software for awhile now. Now that its free is even better!
- I'm a longtime fan of Affinity Designer as an affordable Illustrator-killer for figures, and... it's now free?! www.canva.com/newsroom/new... Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
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- Affinity has a cleaner UI and some tools that are missing in Inkscape. The suite also has a Photoshop and InDesign replacements - I’ve used the later for my scientific posters for awhile now
- Finally, the R package we needed, but don't deserve. I can already hear @benneely.com cackling from across the country. Thanks to @willfondrie.com for alerting me to this amazing repo.
- Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp.... genzplyr is dplyr, but bussin fr fr no cap.
- In case anyone, like me, needed a Python version: github.com/wfondrie/gen...
- I couldn't help it. Now for polars in #python 🐍🐻❄️ github.com/wfondrie/gen...
- Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp.... genzplyr is dplyr, but bussin fr fr no cap.
- Man; @typst.app is so good! That's all; that's the skeet.
- I agree! I’ve been writing more with it lately and it’s been nice. Need to get an NIH grant template together 🤔
- I’ve done a lot of math in my day… But none quite as confusing as early elementary Common Core.
- Me: Did you know that if something is a kilogram on earth, it’s still a kilogram on the moon? L: Kill a gram? That sounds dangerous
- I'm a huge fan of this proposal! If we can get vendor buy-in to an open, common format, it could bring more computational folks into the field. How can these folks be excited about #proteomics when its hard to even read the already complicated data? pubs.acs.org/doi/10.1021/...
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- I finally gave Marimo a try and it's pretty cool. I definitely recommend giving it a shot if you find yourself coding #Python in Jupyter notebooks with any frequency. marimo.io Clean UI, stored as a git-friendly plain python script, with reactivity for reproducibility. 🐍
- Oh and it plays nicely with uv, which I use for all the things 📦
- It was nice to get away to Mt Rainier 🏔️ for a long weekend camping trip. We even got to see some marmots!
- Definitely PhD level. No question 👏 But seriously, I thought other folks were joking 🙃
- I get this is likely due to tokenization, but come one - you can’t claim PhD level reasoning and not solve these kinds of problems.
- Just had an #AI agent (Gemini CLI) write data models to validate outputs of a pipeline and unit tests for the workflow. They need some work, but were pretty good. However, the best part is this was all while I was eating dinner and reading physical books with the kids. Pretty cool 😎
- Even with everything going on, happy Indepenence Day to my friend in the US. Here is a version of “Battle Hymn of the Republic” that I’ve been working on. 🪕 I’ll eventually learn to sing, but today is not that day 🙃
- Check out just a piece of the cool stuff we’ve been up to! 🧬
- Here we go, my first skeet-torial(?) on Bluesky for my first paper from @talusbio.bsky.social ! www.biorxiv.org/content/10.1... This preprint describes our scalable, mass spec-based method for measuring which (and how many of them) proteins are interacting with DNA. 1/?
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- 💯 agree bsky.app/profile/will...
- Stop by poster ThP 289 to… calmly discuss… metadata collection and management with Anastasiya 👏 #ASMS2025
- Looks like it was fun! I find folks tend to have very strong opinions about encoding metadata in filenames 🫠
- A nap and grilling fajitas on Father’s Day. What could be better than this? 🎵 Queue the Moana 2 soundtrack 🙃
- Our website @talusbio.bsky.social has a new look! 👀 talus.bio
- Nothing deflates a mood faster than a flat tire with no tube or patch 😔 🚲
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- Yep! Also I reposted this one to fix a typo. You’re too fast 😆
- Stop by poster ThP 289 to… calmly discuss… metadata collection and management with Anastasiya 👏 #ASMS2025
- It was a lot of fun participating in the Biomarker workshop panel at #ASMS2025. Thank you to all of you who were there! Also, they got some pictures:
- Cred to @lindsaykpino.com for the meme inspiration here 😆
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- Aww yay! I’m glad I could help 😊
- Come out - it’s going to be awesome! 👏 #ASMS2025
- Today @talusbio.bsky.social has @andreagut95.bsky.social in the #ASMS2025 Cancer Research session describing how we use our platform in drug discovery, using a neuroblastoma probe t to target MYCN as a vignette. Grab your coffee and join us at 9:10am!
- I’m at poster 510 today. Stop by and say hi! 👋
- That’s a wrap on our #ML for #MassSpec short course at #ASMS2025 🎉 Thanks to all of the participants who made it a joy to teach 👏
- Fueling up with a cortado at Ceremony again this morning Come see my poster #ASMS2025 on Tuesday about our recommender system method for predicting the retention times od undetected peptides… called Cortado 😉 #ASMSBmoreEats
- ☕️ ✅ #ASMS2025 #ASMSBmoreEats
- ☕️ ✅ #ASMS2025 #ASMSBmoreEats
- Going to #ASMS2025 and curious about what we've been up to @talusbio.bsky.social? Check out our posters, talk, and workshops! Check out all of our events here 👇 talusbio.github.io/talusbio-at-... Here are the events I'll be presenting at or helping with so far. Come by and say hi! 👋 🧵 (1/6)
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View full thread(5/6) Finally, I'll be participating in a "Meet the Developers" AMA in the Bioinformatics Hub on Thursday for Casanovo!
- (6/6) Again, check out this link for all of the events my colleagues and I from @talusbio.bsky.social are presenting or participating in at #ASMS2025! 👇 talusbio.github.io/talusbio-at-...
- (3/6) Then, I'll be at my poster talking about how to use a recommender system strategy for finding missing peptides in MS runs - and why you would want to! (TP 510)
- (4/6) I'll also be helping to lead the de novo sequencing workshop on Tuesday and be a panelist in the biomarker workshop on Wednesday.
- What, not brunch time at #ASMS2015?!? If you do find yourself needing a break, treat yourself to Spoons in Fed Hill. It’s tiny, quaint, and delicious 😋 www.spoonsbaltimore.com #ASMSBmoreEats
- Need another great coffee shop while at #ASMS2015? Try ceremonycoffee.com Ceremony is both delicious and has two nice locations: one that is an easy walk from the convention center and the other in Harbor East has a great view! #ASMSBmoreEats
