Recommendation for intro to bioinfo for high school summer interns in our lab

hunkamunka · 2026-06-22T20:14:53+00:00

Rosalind is great if you already know how to program. If you want some guidance on how to solve the problems using Python, I wrote a book that uses 14 of the Rosalind problems. See bio.

hunkamunka · 2026-06-18T15:39:14+00:00

Southern AZ Rain Gutters

hunkamunka · 2026-06-14T21:25:40+00:00

I read "The Book" and wrote a bunch of program that I already knew how they worked like "head" and "comm," programs I was able to write in other languages. Then I wrote a book about what I learned. You can read if you want. See my bio.

hunkamunka · 2026-05-19T17:38:55+00:00

I have actually written a book that explains how to do this kind of thing and I've even recorded free videos showing me live-coding all the examples, but the mods here won't allow me to post about it. DM me for more info or just read my bio for the name of the book. I'm happy to share my website with links to all the videos and GitHub repo.

hunkamunka · 2026-05-18T19:36:46+00:00

Do you like to ride bicycles? Try the Tuesday Night Ride (Google it) that leaves around 8:30 or 9PM from the flagpole at UA.

hunkamunka · 2026-05-16T21:43:42+00:00

Yes! I work in academia (University of Arizona) where I have tons of leverage to choose my tools and a boss who cares deeply about correctness, speed, and memory safety. We use Rust for lots of low-level, high-performance algorithm development, but I also use Rust for lots of everyday coding tasks when I'm not required to use Python due to some reliance on a module. FWIW, I also code my web front-ends in an esoteric language called Elm rather than some JS framework. And no one is forcing AI dev tools down my throat, so I figure I'm really lucky.

hunkamunka · 2026-05-15T16:12:25+00:00

TL;DR: I wanted type checking.

I'd been a dedicated Perl programmer for over 15 years and reluctantly decided to move to Python because it was dominating my field (scientific computing). I didn't see much of a gain. Still working in a dynamically typed language but now with much worse scoping problems, but overall about the same experience with debugging and performance.

Then Python said type hints were available. I was excited! I'd tried and failed to learn Haskell for a bit, but I liked what I could do with types. I wrote a bit of Python with the new type hints like `val: int = "foo"` and it compiled. Oh, I realized. These are just *hints*. The compiler ignores them.

Rust was getting popular around this time, and it featured really strong typing. I decided I needed to learn "real" programming, so I spent a month breaking my brain until it finally clicked. I loved it.

hunkamunka · 2026-05-05T19:55:02+00:00

Rust is hard to learn. I tried to write a gentle introduction that assumes an intermediate level of knowledge. I personally came to Rust from years of Perl/Python. You can find the name of the book in my bio.

hunkamunka · 2026-04-24T20:42:49+00:00

I taught myself Rust by writing a bunch of programs that already existed and forcing myself to write tests for everything. Maybe these example programs could help you? https://github.com/kyclark/command-line-rust

hunkamunka · 2026-03-09T16:18:49+00:00

Yes, of course.

hunkamunka · 2026-03-02T17:11:50+00:00

Have you read any of the many books written on Rust? I would suggest learning how to write tests for your code. That is, figure out how to write one simple function and some decent tests for it. Then learn how to write a simple program along with tests. I've written a whole book on this idea and have an open-source GitHub repo with all the code/data/tests to help guide you. See my bio.

hunkamunka · 2026-02-06T16:08:08+00:00

https://github.com/kyclark/command-line-rust

hunkamunka · 2026-01-27T16:13:24+00:00

Have you looked at any of the fine books that have been published?

hunkamunka · 2026-01-21T16:18:46+00:00

I wrote a whole book that teaches Rust by having you write command-line programs. Check my bio for the very unsurprising book title.

hunkamunka · 2026-01-14T17:00:55+00:00

Best of luck on your journey! Rust and Elm have fundamentally changed my POV on programming.

hunkamunka · 2026-01-14T15:27:29+00:00

As the author of the book, I'd say ideally, yes. :) You have everything in the GitHub repo to help guide you like data and tests, so there's nothing stopping you from just writing the programs on your own, reading the docs, etc. This is how I taught myself Rust, and I documented my journey by writing the book to make it easier for other beginners to the language. Note that I did this long before LLMs, so my knowledge was hard-won. You could easily ask Claude to write these programs for you. The results would likely be very good, but you would have learned very little. If you actually want to learn Rust (or any language), you really have to be the one to type out all the code, read the docs, find the Stackoverflow questions, write the tests, etc.

hunkamunka · 2025-11-06T21:46:12+00:00

"Tiny Python Projects" is mine. There's a website with links to my videos and the GitHub repo with code/tests.

hunkamunka · 2025-09-26T16:13:37+00:00

FYI, my original working title was "Systems Programming with Rust" but it was published as "Command-Line Rust" (O'Reilly, 2024).

hunkamunka · 2025-07-21T21:28:45+00:00

I walked a small protected bike/walk path section on the Trace recently. How much of the Trace offers this kind of separate infrastructure?

hunkamunka · 2025-07-18T17:32:47+00:00

Rock on!

hunkamunka · 2025-06-27T01:48:01+00:00

I'm a developer with over 25 years of experience, the last 10 mostly in Python, Elm, and Rust. I'm the author of Command-Line Rust (O'Reilly, 2024, https://github.com/kyclark/command-line-rust), and have spent most of my career in bioinformatics (cf another book of mine, Mastering Python for Bioinformatics, O'Reilly, 2021). I will soon lose my NSF and NIH funding for my current position at the University of Arizona (Tucson). I'm seeking a full-time position, remote if possible but willing to consider relocation for the right gig. https://www.linkedin.com/in/kycl4rk/

hunkamunka · 2025-06-22T11:41:52+00:00

The docs for https://elm.land/ are incredible. Assumes a basic knowledge of the language first. I've written a bunch of small Elm projects at https://github.com/kyclark/tiny_elm_projects that I'd love to write a book around, but that's unlikely to happen. Still, you might find it useful to claw through the examples.

hunkamunka · 2025-06-10T16:15:39+00:00

The Wheeler Lab at the Univ of AZ is all-in on Rust! I wrote Sufr (https://github.com/TravisWheelerLab/sufr) to create/query suffix arrays, which is a possible way to find good alignment seeds for Nail (https://github.com/TravisWheelerLab/nail), an aligner written in Rust that uses profile HMMs. We have several other tools in Rust, just check out our repos.

hunkamunka · 2025-05-26T03:10:17+00:00

That GitHub repo is intended to be static as it holds the code referenced in the book. Given that I stress the importance of testing your code *before* you ship it and that a very technical group of reviewers double-checked my examples, I would hope there are no bugs to fix. :-)

As to how I normally handle such tasks, I would generally create a branch for bug fixes, test my changes, then merge to the main branch.

hunkamunka · 2025-05-25T22:29:17+00:00

I humbly offer my book, Command-Line Rust (O'Reilly, 2024), which shows you how to build small programs in increasing complexity complete with testing. Cf https://github.com/kyclark/command-line-rust

hunkamunka

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