James Fellows Yates

Day 2 #30DayMapChallenge - Road Conditions in York

If you're travelling through York beware the condition of the roads!

#rstats #dataviz

Just getting back from two day teaching #Snakemake programming on #HPC clusters. And I have several observations:

- the education level everywhere else seems way better, than on my home cluster. It is still a good idea, to assume the worst.
- it is never a good idea to accept […]

This mastodon client came to me in a fever dream.
I had to waste the whole day, but now you too can bunnyhop through your fedi feed.
https://files.burning.homes/experimental/hall-of-toots/index.html

* webgl required
* mobile somewhat supported
* yes this html file is a whole client and the […]

During this #OAWeek, consider publishing your next archaeology paper in a diamond open access journal.

If you're unsure where to start, check out https://diamond.open-archaeo.info for a list of several dozen diamond open access archaeology journals and some additional information about OA and […]

I'm part of multiple teams/communities that use multiple messaging services, so at one time I need to have open a several of slacks, a couple of discord servers and two discourse forums; also whatsapp. I know there are several tools that try to integrate all of them into a single window (life […]

Profile HMMs and other Hidden Markov Models explained from we @weratedags.com at #bsky
#bioinformatics #generativemodels #probability #latentvariables #statistics

A serene, slightly foggy polder landscape, in the early morning. The ‘Wulptocht’ (a straight, calm canal) runs vertically through the center of the frame. The canal acts as a mirror, reflecting the blue sky, white clouds, sun glare, and the tall structures along its edge. The banks of the canal are lush with tall grasses and reeds in earthy tones of green, gold, and brown. To the right of the canal, a row of large, modern wind turbines stretches into the distance. The sun is bright and low on the left side of the horizon, casting a strong flare and long rays across the upper left of the image. The sky is a mix of bright blue and wispy white clouds, with prominent contrails from aircraft crossing high above.

Flevoland

#SilentSunday #Landscape #Photography

Preprint of my paper with Amanda Arranz-Otaegui, using ecological niche modelling to reconstruct the likely ranges of crop progenitors and wild plant resources in West Asia at the onset of agriculture:

https://doi.org/10.32942/X2DD27

#Archaeology #Prehistory #Ecology #Paleoecology […]

Tour promo image for Opeth, playing live at TK MAXX Presents Live, Piece Hall, Halifax

Words I never thought I'd see in the same sentence:

TK Maxx presents
Halifax
Opeth

Poster advertising an event Meta-*omics Nextflow Pipeline Community Exhibition Day Do you work with . Want to find out how to metagenomics, metaxaxonomics, make your analysis more metaproteomics, metatranscriptomics efficient, scalable, and datasets? reproducible? Meet developers for an introduction and practical hands-on demonstration of their meta-*omics Nextflow pipelines! When is it happening? December 10th 2025. Times pending Where is happening? Online! Platform pending What do you need? - Ability to navigate the UNIX command line Online - Be already familiar with basic theory/concepts pjatform pending of the analysis of your meta-*omics data - A computer, and an internet connection Interested? Register your interest and choose your pipeline(s) https://tally.so/r/31gJyQ Supported by NFDI4MIcrobiota and NextflowAmbassadors

Poster advertising event Featured pipelines nf-core/createtaxdb (nf-co.re/createtaxdb) nf-core/createtaxdb is a bioinformatics pipeline that constructs custom metagenomic classifier databases for multiple classifiers and profilers from the same input FASTA reference genome set in a highly automated and parallelised manner. Biobakery-nextflow (github.com/BonhamLab/biobakery-nextflow) Shotgun metagenomics community profiling (taxonomic and functional) of Illumina short read data using the Biobakery suite of tools and databases. epi2me-labs/wf-metagenomics (github.com/epi2me-labs/wf-metagenomics) Taxonomic classification of Nanopore sequenced metagenomic sequencing data and identification of antimicrobial resistance (AMR) or virulence genes. It includes an optional step to remove host sequences. It can also be run through the EPI2ME Desktop Application. nf-core/taxprofiler (nf-co.re/taxprofiler) nf-core/taxprofiler is a pipeline for taxonomic classification and profiling of shotgun short- and long-read metagenomic data. It performs in-parallel taxonomic identification of reads or taxonomic abundance estimation with multiple classification and profiling tools against multiple databases, with standardised output profiles. (and more! Please contact James Fellows Yates for the rest of the list - hitting Alt text limits now)

Join us on December 10th for an online ‘Meta-*omics #Nextflow #pipeline community exhibition day’, for an intro and hands-on tutorial of #metagenomics #metataxonomics #metaproteomics #metatranscriptomics pipelines directly from the developers!

Since the first […]

[Original post on genomic.social]

Nextpie: A web-based reporting tool and database for reproducible #Nextflow pipelines academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/bishwaG/Next...

Spicy take:

Normal people shouldn't self host.

From an energy use perspective, the users per watt are WAY higher in a data center.

People are already awful at running patches and doing security updates.

OMG are people awful at doing backups.

From an ewaste POV, consumer electronics just […]

Me standing in my back yard holding a large pot in front of me with both hands. It borrows its spherical form from Nigerian water vessels and has a short, flared neck. It is about 16” (40cm) in diameter and 14” (36cm) in height. The pot has been divided laterally into six parts and each section has been decorated with carved lines in alternating patterns: a symmetrical abstract leaf motif and a large double diamond pattern. The colors are dark brick red, olive green, dark purplish brown, dusky pink and aqua. The interior is glazed glossy aqua to reference the water this form would historically have contained. Behind me is dense foliage and small blue patch of sky. I am smiling and wearing a black and white top and red paints, only partially visible from behind the large pot.

Still warm from the kiln, covered in warm earth tones—I’m so relieved this piece came out successfully on the other side of firing. I worked on it over the course of a month and remembered to document moments of process which I think I’ll share in a thread […]

[Original post on mastodon.social]

It's International Research Software Engineering Day! Celebrate me!

No, but really, RSEs are a crucial and under-appreciated piece of modern science. Learn more about what an RSE is (you might be one or work with one!) here: https://us-rse.org/about/what-is-an-rse/

#rse #us_rse #rseng […]

Empty water reservoir with archs

Empty water reservoir with archs

Empty water reservoir with archs

Empty water reservoir with archs

every 3-4 years when they are cleaning it the authorities allow visitors into the #Lodz waterworks.
They are pretty fussy about security (I guess rightly so) but they do allow pictures.

#pictures #water

Poster advertising an event Meta-*omics Nextflow Pipeline Community Exhibition Day Do you work with . Want to find out how to metagenomics, metaxaxonomics, make your analysis more metaproteomics, metatranscriptomics efficient, scalable, and datasets? reproducible? Meet developers for an introduction and practical hands-on demonstration of their meta-*omics Nextflow pipelines! When is it happening? December 10th 2026. Times pending Where is happening? Online! Platform pending What do you need? - Ability to navigate the UNIX command line Online - Be already familiar with basic theory/concepts pjatform pending of the analysis of your meta-*omics data - A computer, and an internet connection Interested? Register your interest and choose your pipeline(s) https://tally.so/r/31gJyQ Supported by NFDI4MIcrobiota and NextflowAmbassadors

Poster advertising event Featured pipelines nf-core/createtaxdb (nf-co.re/createtaxdb) nf-core/createtaxdb is a bioinformatics pipeline that constructs custom metagenomic classifier databases for multiple classifiers and profilers from the same input FASTA reference genome set in a highly automated and parallelised manner. Biobakery-nextflow (github.com/BonhamLab/biobakery-nextflow) Shotgun metagenomics community profiling (taxonomic and functional) of Illumina short read data using the Biobakery suite of tools and databases. epi2me-labs/wf-metagenomics (github.com/epi2me-labs/wf-metagenomics) Taxonomic classification of Nanopore sequenced metagenomic sequencing data and identification of antimicrobial resistance (AMR) or virulence genes. It includes an optional step to remove host sequences. It can also be run through the EPI2ME Desktop Application. nf-core/taxprofiler (nf-co.re/taxprofiler) nf-core/taxprofiler is a pipeline for taxonomic classification and profiling of shotgun short- and long-read metagenomic data. It performs in-parallel taxonomic identification of reads or taxonomic abundance estimation with multiple classification and profiling tools against multiple databases, with standardised output profiles. (and more! Please contact James Fellows Yates for the rest of the list - hitting Alt text limits now)

Do you perform analysis on #metagenomics, #metataxonomics #metatranscriptomics #metaproteomics datasets?

Would you like to find out how to make your #bioinformatic analysis more efficient, scalable, and reproducible?

Join us on December 10th for an online […]

[Original post on genomic.social]

Pipeline diagram in the style of a london underground map for nf-core funcscan. There are three sections 1 for preprocessing, 2 for functional contig screening of ARG, AMP, and BGC with different tools, and finally results aggregation for summary outputs.

🎁 Another week, another pipeline release!

🚀 This week it's the latest version of @nf_core 's funcscan , assembled contigs and genomes for functional genes.

🥐 v3.0.0 French Chocolatine (in honour of @gau ), with major tool version upgrades for antiSMASH (for […]

[Original post on genomic.social]

From 2006. A younger and shell-shocked looking Catherine on a balcony holding a very tiny baby with the mountains of Vancouver in the background. The baby is so new, Catherine still has the pregnant bump.

Conventional wisdom says motherhood should wait for tenure as before you land a permanent post, #academia is just not that family friendly🙁

@carersinstemm.bsky.social are calling for change and to celebrate their new report, a Saturday🧵on parenting & academia! 1/9 👩‍🔬🧪🔭⚛️

ℹ️: carersinstemm.co.uk

R-multiverse: a new way to publish R packages · Community Call Community Call about R-multiverse

🎙️ Resources from Community Call "R-multiverse: a new way to publish R packages" with @landau

✅ video with subtitles
✅ R-multiverse website with guidelines to participate in
✅ collaborative notes

https://ropensci.org/commcalls/r-multiverse/

#RStats @RConsortium

I usually make things for people to use at home, but it seems to me that the only purpose of this bowl is to bob and spin in the Gulf.

#ceramics #pottery #nature #water #beach #Florida #birds #PeacefulMoments

Paulina Przystupa is bringing #archaeology #dataLiteracy instructional materials to the #OER commons!

Here's an example of free teaching materials for you to adapt and reuse:

https://oercommons.org/courses/cow-culating-your-data-with-spreadsheets-and-r

Many more such resources are on their […]

📣 Last call 📣

👨🏾‍💻 Do you develop a #Nextflow #pipeline for #metagenomics, #metataxonomics, #metatranscriptomics, #metaproteomics

🎉 Represent your pipeline at an upcoming community 'meta-omics' exhibition day by giving a tutorial!

✏️ Register your interest to demo your pipeline […]

where this came from is that I made a Git cheat sheet a while back at https://wizardzines.com/git-cheat-sheet.pdf

and then I found out that the folks who make the official Git website are super open to contributions and thought "... wait, the website doesn't have a cheat sheet, I could just […]

added a cheat sheet to the official Git website https://git-scm.com/cheat-sheet

❓ Do you develop a #Nextflow pipeline for #metagenomics, #metataxonomics, #metatranscriptomics, #metaproteomics, etc?

🧑‍💻 I'm looking for #bioinformatics developers to give demos of their #opensource pipelines to the scientific community in a ‘Meta-*omics Nextflow pipeline community exhibition […]

Do you work in #bioinformatics, love #conda & #bioconda, but didn't know how to start adding (or debugging) your/someone else's software to it?

Here's a three-part (opinionated) guide for the #microbifinie blog on just that, based on my own experiences!

Adding […]