daily inspo: Push an API key to GitHub! You can do it!
05.03.2026 16:13
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daily inspo: Push an API key to GitHub! You can do it!
A plot showing the flow of metagenetic material in patients receiving fecal microbiota transplantation. Thick, colorful bands connect a column of donor patients on the left to a column of recipient patients on the right.
apparently this variant of the Sankey diagram is called an "alluvial plot" (fig. from Behling et al. 2024, doi.org/10.1186/s401...)
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
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
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!
