Vladimir Mikryukov

Sandboxing Applications with Bubblewrap: Securing a Basic Shell Everybody knows that allowing different applications unlimited access to each other’s data is not exactly optimal from a security point of view. While servers have enjoyed containers to isolate applic...

Nice read on sandboxing with bwrap: sloonz.github.io/posts/sandbo...

10.11.2025 09:14 — 👍 0    🔁 0    💬 0    📌 0

Run shell commands in a lightweight sandbox (using `bubblewrap`) Run shell commands in a lightweight sandbox (using `bubblewrap`) - sbx.sh

Safeguard yourself: do backups (yes, now!), don't run random code on production systems. If you must run untrusted pipelines, you can bubblewrap them in a bwrap sandbox - here is an example (works transparently with conda envs & system tools): gist.github.com/vmikk/08212e...

10.11.2025 09:14 — 👍 2    🔁 0    💬 1    📌 0

Terminal screenshot showing a minimal bash loop demo: starting in $HOME/project, a for loop runs cd subdir (which fails if missing), then rm * in the current directory, followed by cd .., so on the next iteration it climbs to $HOME and rm * risks deleting files there.

20+ years on #Linux, 🧬🖥️ #bioinformatics pipelines daily - and one relaxed moment running a colleague's script nearly wiped my $HOME 😅 Here's how a silent cd+rm combo escaped my project dir, the original script was quite tangled, but it hid this construct [ ⚠️ danger zone, don't run 🔥 ]

10.11.2025 09:14 — 👍 3    🔁 0    💬 1    📌 0

New fungal phylum-level system, with red font indicating novel taxa and size taxonomic diversity.

Fungal phylum-level classification update now available! Used "innovative taxonomy" to describe >100 taxa, from species to phylum, based on long reads, characteristic nucleotides and env-samples.
mycokeys.pensoft.net/article/1616...

#fungi #taxonomy #PacBio #classification #eDNA

20.10.2025 17:27 — 👍 23    🔁 12    💬 0    📌 1

New article on equitable reuse of public sequencing data, published in @natmicrobiol.nature.com!
Led by the Data reuse core team @lhug.bsky.social @environmicrobio.bsky.social Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and with Anke Heyer and The Data Reuse Consotrium!

26.09.2025 19:34 — 👍 34    🔁 20    💬 0    📌 4

Who lives underground?

Find out now in our new paper published in @nature.com.

Key finding: 90% of predicted mycorrhizal biodiversity hotspots lie outside protected areas.

Read here: buff.ly/WmDqAP3 🧵

23.07.2025 15:20 — 👍 39    🔁 28    💬 1    📌 3

Post-Doc position for 3 years available jointly between University of Tartu (Estonia) and University of Aarhus (Denmark) on soil microbiome and biogeography. Skills required: bioinformatics, metagenome analysis, microbiology
Contact: leho.tedersoo@ut.ee

23.01.2025 06:54 — 👍 54    🔁 38    💬 0    📌 0

AM fungi are vital for plants but their global richness remains underexplored. In our latest study, out in Fungal Ecology, we analyzed 4,733 sites, revealing 8,517 G-AMF OTUs (5–15x previous estimates) & 600 E-AMF OTUs, the first global count. Read it for free authors.elsevier.com/c/1kJ7y6ExPy...

22.12.2024 09:11 — 👍 11    🔁 1    💬 0    📌 0

A newly discovered fungal species emerges from the open pages of a scientific book, surrounded by various lab journals and books, with research tools scattered around. The image highlights the connection between scientific discovery and publishing.

🍄📖 Do high-impact journals lead to more fungal species discoveries? Think again! Low or even no-impact factor journals contribute significantly! Let's value research quality over impact metrics in funding and hiring decisions! Read more @MycoKeys: mycokeys.pensoft.net/article/136048

21.11.2024 11:05 — 👍 6    🔁 1    💬 0    📌 0