David Bass

matplotlib's `wheat` color is a 10/10

`|=` is a valid operator in Python for replacing a list with its union with another list, e.g. `x |= y` !!!!

the #1 reason not to use inline suggestions from Copilot is to preserve the joy of typing `if __name__ == "__main__":`

no other choice is a great movie and contains a lot of really fun camera tricks with phone/tablet screens

i've been unknowingly abbreviating "alignment" as both "alnmt" and "almnt" and it has finally caught up with me

figure from [Sibley et al. 2015](doi.org/10.1038/natu...) that shows how the brain dominates every other tissue's expression of long genes. each line is essentially a histogram, normalized w.r.t. the brain transcriptome's distribution. cool that neural complexity manifests in such a simple stat

nearly had a crisis of faith in Snakemake today

so much depends
upon

Cloudflare
service

even the
poetry-

foundation
dot org.

biblically accurate sequence logo (Hsiao et al. 2018, Genome Res., fig. 2G)

A figure panel showing a sketch of how, due to genetic linkage, SNPs are distinguished from RNA editing sites by sharing more mutual information.

interesting use of popgen in distinguishing SNVs from RNA edit sites: "a pair of SNPs within the mRNA ... possess perfect allelic linkage. In contrast ... RNA editing sites do not generally show significant allelic linkage with each other nor with SNPs" (L-GIREMI, Liu et al. 2023 Genome Biol.)

it's the kind of "prepping for union's Labor Day BBQ" morning that reminds a man just how heavy four watermelons can be

NYT Mini seems to be paywalled starting today :/

MBE - Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource

@jcbnunez.bsky.social et al. present an expanded release of the community-generated resource Drosophila Evolution over Space and Time (DEST 2.0), and showcase it by studying the species' demographic history and signatures of adaptation.

🔗 doi.org/10.1093/molbev/msaf132

#evobio #molbio #drosophila

accidentally applying `.set_xbound(0, 1)` instead of `.set_ybound(0, 1)` turns violin plots into KDE plots that cling to the walls

Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource Abstract. Large-scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population g

DEST 2.0 is now up on MBE! academic.oup.com/mbe/article/...

two of the three fake DOI URLs take me to an error page, while the third takes me to "Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines." sounds cool, but very much not what I research

beating the dead horse here, but I just tried my hand at asking GPT-4.1 (JHU gives us access to a bunch of premium LLMs for free) to help me look for a certain type of data, and it told me about four papers, precisely one of which actually exists. impressively wasteful

Panel of figure 2 of Choquet et al. 2023 "Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts" (Nat. Struct. Mol. Biol.) that uses zig-zagging lines of different thicknesses and (gray) colors to show frequencies of permutations of splicing order of four introns in a representative transcript.

fascinated by this plot for listing permutations (namely, the orders in which four introns can be spliced from a given RNA transcript) and denoting their frequencies with line thickness and shade. It avoids needing to enumerate all 4! permutations. from Choquet et al. 2023 (Nat. Struct. Mol. Biol.)

is there a pre-built/easy way to filter a BAM file to the reads that are aligned spliced over a given intron? The best that I can come up with is to do initial filtering with pysam's fetch function, then examine each read's alignment position and CIGAR string

Opinion | I’m a Genocide Scholar. I Know It When I See It.

My NYT op-ed this morning
I’m a Genocide Scholar. I Know It When I See It. www.nytimes.com/2025/07/15/o...

just learned that you can seamlessly concatenate sequences produced by brace expansion with explicit strings in Bash, e.g. `{1..22} X Y` to list all chromosome names. truly a language of many tricks and wiles

mmmm alignment to transcriptome :)

crush your enemies, see them driven before you, and hear the lamentations of their consultants

Picture from the Walters Museum of Art of their ~foot-tall bronze statue of the Celtic/Gallo-Roman deity Sucellus, standing in contraposto and holding up a mallet that has been lost to time. Floating behind him is a large mallet with five smaller mallets protruding from its head.

today is a good day because I saw the Sucellus statue at the Walters

I just finished Marilynne Robinson's Gilead. Incredible book about living on the edge of political violence and celebrating uncertainty. Makes me want to read the New Testament

the MD pride flowing through my veins today has got me like

Apparently not all my popgen advice is good.

Group photo of the Johns Hopkins University quizbowl team, shortly before round 1 of NAQT's 2025 Intercollegiate Championship Tournament. We are (mostly) wearing matching navy team sweaters. We sit in a large hotel convention space.

had a great time competing in @naqt.com's Intercollegiate Championship Tournament this weekend with my JHU teammates!

A promotional image of MacGyver, looking cool and carrying a missile, for the original '80s TV series.

how it feels to zoom out in order to see previous lines of output in a Linux screen after having your (foolish) attempt to scroll rewarded with a bunch of "^]]A"s

my Jupyter notebooks are vibrant ecosystems in which data analysis for my research and Balatro odds calculations coexist side-by-side (the expected xMult from five Bloodstone procs is 3.05)