Tempted to port some old R code over so we can have hmmmmm in crates.io

tää oli kunnon hv -haku, deadline välittömästi joululomien jälkeen ja hylsyt pari päivää ennen juhannusta. Tsemiä kaikille rannalle jääville.

why, yes, of course I want to buy 7000 kg of antibiotics

We also improved the precision of SNP and INDEL calling compared to other tools by using a specialized variant calling algorithm based on the suffix match lengths of both query vs. reference and reference vs. query.

In reference-based mapping, we are within 1-2% of using sequencing reads

(the preprint does not show Figure 3 and Figure 4 for some reason, here they are)

Solidaarisuutta 7.5. lakkoileville Tampereen yliopiston työntekijöille!

Liity kokoontumiseen Porthanian edessä 7.5. klo 16.30, jos yliopistot ei keskiviikkoon mennessä tarjoa reilua sopimusta työntekijöille.

lifecycle of a github issue

Haven't done much web stuff but pretty pleased with how this is coming along

This even runs on a phone, although with some hiccups if the `Detailed` box is checked.

Hope to enable analyses like in-browser AMR gene finding eventually! Still some ways to go though 😄:

editor of the year material whoever let the authors get away with this www.sciencedirect.com/science/arti...

it works!! Querying presence/absence of genes in a genome in the browser, in a few seconds, in rust/webassembly, built on top of the SBWT crate github.com/jnalanko/sbw...

We also compared genomes from Pakistan to carbapenem resistant E. coli from Norway. For ST38 this revealed a clade with high potential to transmit intercontinentally and to acquire carbapenem resistance in the right environment although these resistance genes were not detected in Pakistan 4/5

Most participants were colonised by >3 lineages but overall the cohort revealed two different survival strategies: Multiple E. coli that could be called endemic in Pakistan are able to colonise the same host at the same time, while lineages such as ST69 and ST131 survive by excluding others 3/5

ST10 was the only lineage that had staying power in paired samples taken 30 days apart. The rest were more random/transient, but antibiotics use selected for the more “Western“ lineages ST69 and ST131. Some lineages that are common in Europe, like ST95 and ST73, were nearly absent in Pakistan 2/5

Helsingin yliopiston työntekijät ulosmarssi vastalauseena Orpon hallituksen suunnitelmille heikentää työntekijöiden oikeuksia. Kuvat Tieteentekijöiden järjestäytymisestä Porthanian eteen ja marssilta Akavan yhteistapahtumaan Kolmen sepän patsaalle, leikkauslista SAK.