James Fellows Yates
jfy133.genomic.social.ap.brid.gy
James Fellows Yates
@jfy133.genomic.social.ap.brid.gy
Bioinformatician in #Metagenomics, #Palaeogenomics / #aDNA, #Microbiomes. Loving #nextflow and #OpenScience. @MPI_EVA_Leipzig / @LeibnizHKI. Core team member of […]

🌉 bridged from ⁂ https://genomic.social/@jfy133, follow @ap.brid.gy to interact
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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]
Reposted by James Fellows Yates
On the Value of Informal Communication in Archaeological Data Work
Archaeological data simultaneously serve as formal documentary evidence that supports and legitimizes chains of analytical inference and as communicative media that bind together scholarly activities distributed across time, place, and social circumstance. This contributes to a sense of “epistemic anxiety,” whereby archaeologists require that data be objective and decisive to support computational analysis but also intuitively understand data to be subjective and situated based on their own experiences as participants in an archaeological community of practice. In this article, I present observations of and elicitations about archaeological practices relating to the constitution and transformation of data in three cases in order to articulate this tension and document how archaeologists cope with it. I found that archaeologists rely on a wide variety of situated representations of archaeological experiences – which are either not recorded at all or occupy entirely separate and unpublished data streams – to make sense of more formal records. This undervalued information is crucial for ensuring that relatively local, bounded, and private collaborative ties may be extended beyond the scope of a project and, therefore, should be given more attention as we continue to develop open data infrastructures.
www.degruyterbrill.com
December 14, 2025 at 7:27 AM
🎉 Huge shout out to everyone who instructed and participated in yesterday's online Meta-*omics #nextflow Pipeline Community Exhibition Day!

🧑‍🏫 Over 9 hours, we had 15 different pipelines demo'd by their lead developers, and giving an international cohort of […]

[Original post on genomic.social]
December 11, 2025 at 5:23 PM
Reposted by James Fellows Yates
Making my way from Copenhagen to Leipzig for a workshop on #radiocarbon data and metadata organised by @jfy133. I'm looking forward to the workshop but---strangely maybe moreso---10 hours of focused time on the train.

I unfortunately haven't done so much solo #CrossBorderRail this year. It's […]
Original post on archaeo.social
archaeo.social
December 3, 2025 at 1:05 PM
Reposted by James Fellows Yates
It might seem intuitively more empowering to generate a thing that works without issues, but it's not! It's empowering to make a thing you understand.
November 20, 2025 at 10:20 PM
Reposted by James Fellows Yates
This makes me sad and makes me want to revisit the idea I made a half arsed version of on glitch where you remixed a project that was broken and had to fix it.. avoidance of debugging is avoidance of the learning that opens up opportunities through software […]

[Original post on glasgow.social]
November 20, 2025 at 10:19 PM
Reposted by James Fellows Yates
November 19, 2025 at 10:45 AM
Reposted by James Fellows Yates
Day 17 #30DayMapChallenge - Sussex Street Network Orientation

I used {OSMnx} in #Python which can be used to visualise street network orientations using polar plots. Some places (e.g. Haywards Heath) are sprawling while others (Brighton & Hove) are more clearly organised grid-like.

#dataviz
November 19, 2025 at 10:44 PM
Reposted by James Fellows Yates
50 % weniger Todesfälle und schweren Verletzungen von Fußgängern und Radfahrern bei Kollisionen mit Lkw dank der Londoner Sicherheitsvorgaben Direct Vision Standard (DVS). Lkws ohne diesen Standard dürfen im Großraum von London nicht fahren.
tfl-newsroom.prgloo.com/news/pedestr...
November 18, 2025 at 11:14 PM
Reposted by James Fellows Yates
RE: https://mastodon.social/@dkz2r/115536945968755413

THAT is some intro slide for research data management 101!

#rdm #rdmtraining
mastodon.social
November 12, 2025 at 1:55 PM
Reposted by James Fellows Yates
Day 2 #30DayMapChallenge - Road Conditions in York

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

#rstats #dataviz
November 2, 2025 at 11:29 PM
Reposted by James Fellows Yates
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 […]
Original post on fediscience.org
fediscience.org
October 29, 2025 at 6:45 PM
Reposted by James Fellows Yates
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 […]
[Video] Original post on gts.burning.homes
gts.burning.homes
October 21, 2025 at 9:25 PM
Reposted by James Fellows Yates
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 […]
Original post on archaeo.social
archaeo.social
October 22, 2025 at 6:57 PM
Reposted by James Fellows Yates
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 […]
Original post on mastodon.social
mastodon.social
October 21, 2025 at 11:50 PM
Reposted by James Fellows Yates
Profile HMMs and other Hidden Markov Models explained from we @weratedags.com at #bsky
#bioinformatics #generativemodels #probability #latentvariables #statistics
October 17, 2025 at 9:01 PM
Reposted by James Fellows Yates
October 19, 2025 at 5:51 AM
Reposted by James Fellows Yates
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 […]
Original post on archaeo.social
archaeo.social
October 17, 2025 at 2:55 PM
Reposted by James Fellows Yates
Words I never thought I'd see in the same sentence:

TK Maxx presents
Halifax
Opeth
October 16, 2025 at 5:49 PM
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]
October 16, 2025 at 9:57 AM
Reposted by James Fellows Yates
Nextpie: A web-based reporting tool and database for reproducible #Nextflow pipelines academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/bishwaG/Next...
October 13, 2025 at 4:40 PM
Reposted by James Fellows Yates
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 […]
Original post on infosec.exchange
infosec.exchange
October 12, 2025 at 4:47 AM
Reposted by James Fellows Yates
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]
October 10, 2025 at 8:21 PM
Reposted by James Fellows Yates
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 […]
Original post on hachyderm.io
hachyderm.io
October 9, 2025 at 3:13 PM
Reposted by James Fellows Yates
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
October 9, 2025 at 1:23 PM
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]
October 8, 2025 at 1:33 PM