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Anton Savchenko @notgaudi.bsky.social · Aug 16

Keep up the good work!) BTW, I vaguely remember rumors about an ECHO movie - do you know anything new about that?

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Anton Savchenko @notgaudi.bsky.social · Aug 16

not a matchbox, but well worthy

old cigar box reused for specimen storage

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Anton Savchenko @notgaudi.bsky.social · Aug 16

One day your efforts will lift ECHO from the undeserved "mostly positive" zone.)

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Anton Savchenko @notgaudi.bsky.social · Aug 14

QUERY_

phylogenetic tree with way too large font

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Anton Savchenko @notgaudi.bsky.social · Aug 1

RGB values were then automatically translated into color names, which fell rather nicely into color categories assigned subjectively by eye.
Unsurprisingly, most of the failed extracts were dark-colored (and also old!), though ~half of dark extracts performed just fine in PCR and sequencing.

Table comparing subjectively assigned colors to automatically generated, per DNA extract.

Anton Savchenko @notgaudi.bsky.social · Aug 1

Machine vision for poor people, or yet another way to misuse Quantum GIS! I wanted to know if color of DNA extract correlates with sequencing success, and to get the colors I imported a photo of extracts into QGIS as if it was a map, placed sample points, and measured their underlying RGB values.

Screenshot of QGIS program with a photo of PCR plate from underneath

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Anton Savchenko @notgaudi.bsky.social · Jul 29

It often works well for non-fiction academic writing, though not sure if anyone writes entire fiction books in it. Anyway, good luck.)

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Anton Savchenko @notgaudi.bsky.social · Jul 29

Looks like @obsidian.md can work for you. Desktop and mobile versions are free, and for small subscription you can sync them (or just use cloud of your choice). No fancy text formatting, but overall their text editor is sweet.

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Anton Savchenko @notgaudi.bsky.social · Jun 14

ohh no, Ustilaginomycotina is missing, Pucciniomycotina is a single tip, don't show it to mycologists, much drama ensured.)

Anton Savchenko @notgaudi.bsky.social · Jun 7

hah, someone decided to monetize BLAST. Will be funny if it is just MMSeqs in a trenchcoat.

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Reposted by Anton Savchenko

Berna Devezer @devezer.bsky.social · May 27

There is no "science-wide replication crisis" because every word in that phrase carries unfounded assumptions. 🧵

1. There is no evidence that progress has generally stalled in the sciences. Also, no one has actually tried to estimate replicability across fields.

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Anton Savchenko @notgaudi.bsky.social · May 16

Yes, all versions are downloadable unite.ut.ee/repository.php
And also PlutoF (UNITE's management side) has API, it may be more convenient for data retrieval plutof.docs.apiary.io#reference

PlutoF API · Apiary

A place where APIs are kept.

plutof.docs.apiary.io

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Anton Savchenko @notgaudi.bsky.social · May 16

Would be interesting to see the same for UNITE's SHs ;)

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Reposted by Anton Savchenko

ʟᴜɪs ʜᴇʀɴᴀɴᴅᴇᴢ ⚡ @beetlenaut.bsky.social · Apr 7

the beauty of humans is that even if we explicitly attempt to copy something, the noise of our lives and our brains seeps into the work. you still end up with a New messy synthesis of things

AI doesn't live a life, it may have system noise, but it doesn't have a story to tell; because its software

Rick Lane @ricklane.bsky.social · Apr 7

The difference is George Orwell did not steal 7.5 million novels to ghostwrite 1984 for Greg from Stevenage. www.theguardian.com/technology/2...

Mining of authors’ work is nothing new – AI is just doing what creative humans do | Letter

Letters: Creativity has always ‘trained’ on the work of others, says Andrew Vincent

www.theguardian.com

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Anton Savchenko @notgaudi.bsky.social · Apr 27

Antichamber irl? store.steampowered.com/app/219890/A...

Antichamber on Steam

Antichamber is a mind-bending psychological exploration game where nothing can be taken for granted. Discover an Escher-like world where hallways wrap around upon each other, spaces reconfigure themse...

store.steampowered.com

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Reposted by Anton Savchenko

Siobhan Leachman @siobhanleachman.bsky.social · Apr 22

A press release is out about the Biodiversity Heritage Library. From 1 January 2026 the Smithsonian will no longer host the administrative functions of BHL. BHL is looking for a new home. For further information see blog.biodiversitylibrary.org/2025/04/new-...
#ILoveBHL #BiodiversityHeritageLibrary

A New Future for the Biodiversity Heritage Library

The Biodiversity Heritage Library (BHL) is the world’s largest open access digital library for biodiversity literature and archives. A global consortium of over 660 contributors, BHL has made more …

blog.biodiversitylibrary.org

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Anton Savchenko @notgaudi.bsky.social · Apr 5

metsamaja on liminaalnemaja

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Anton Savchenko @notgaudi.bsky.social · Apr 5

One day APIs will get as fine grained as flour, but not today.)

Do you queue also remotely? Some kind of Google/Amazon cloud?

Anton Savchenko @notgaudi.bsky.social · Apr 5

Haha, why it's always like this - any serious work requires downloading the entire resource

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Anton Savchenko @notgaudi.bsky.social · Mar 29

Sampling was... not boring: most of the material is corticioids (sometimes as thin as <100um) the most difficult fungi to sample imo.

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Anton Savchenko @notgaudi.bsky.social · Mar 29

Mycologist: I know a lovely place!

Lovely place in question:

Corridor in herbarium, ending in pitch-black darkness

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Anton Savchenko @notgaudi.bsky.social · Mar 29

The library is on site and very rich, with titles dating back to Linnaeus

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Anton Savchenko @notgaudi.bsky.social · Mar 29

One of a few places with a dedicated collection of spore prints (hundreds if not thousands of them!).

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Anton Savchenko @notgaudi.bsky.social · Mar 29

Spent the last 2 weeks sampling dozens of type specimens in a well maintained, almost fully digitized, and just lovely TAAM fungarium (Tartu).

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Reposted by Anton Savchenko

Berna Devezer @devezer.bsky.social · Mar 16

Six years ago, we published a (thus far underappreciated) study where we showed how scientific communities may generate a literature populated by irreproducible results or may converge on many perfectly reproducible yet false findings *in the absence of QRPs*, challenging popular narratives.

Scientific discovery in a model-centric framework: Reproducibility, innovation, and epistemic diversity

Consistent confirmations obtained independently of each other lend credibility to a scientific result. We refer to results satisfying this consistency as reproducible and assume that reproducibility i...

journals.plos.org

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