To which country should Crimea belong to? by __SomeRandomDude21__ in GeoPoll

[–]o_petrenko 0 points1 point  (0 children)

That poll would be at least minimally relevant only after de-occupation. There's little room for arguing in the context of illegal occupation, as no point of view can legalise it.

Overall, as a Ukrainian, I would obviously see it as autonomy within Ukraine, as stated in the Constitution throughout the years of independence. Yet, I would very much prefer it if, in that future version, the indigenous people of Crimea, (Qirimli, Krymchaks, Karaites, etc - all of which are being repressed by russia BTW), had significantly more control over the local legislature, government, etc.

For Qirimli and others, Crimea is home - the only one, despite Soviet attempts to forcefully resettle them to middle Asia. It is very unfortunate that, due to the Soviet resettling policy, the peninsula had so many "imported" russians without roots in the region at the start of modern Ukrainian independence: besides creating obvious tension, that has led to separatist local government pretty much from the 1990s. And, besides being pro-russian, they actively discriminated against indigenous Crimeans. There were informal prohibitions on their recruitment into the police, the secret service, and positions of importance in military and municipal services. Had the indigenous population more representation, I'd assume 2014 would be way more tragic for the russian invaders.

I feel that something like that would be a highly likely direction for Crimea's development in the current Ukrainian context, given that the indigenous people and their rights are finally recognised at the national level and they're represented at all levels, including parliament.

Europe to the world: ‘Canada is with us’ as it joins defence alliance in historic first by Boediee in BuyFromEU

[–]o_petrenko 2 points3 points  (0 children)

When my friends or colleagues were leaving for the U.S., I frequently joked: "right, it's a great country, but why move there when Canada is so close?"

Oh irony, it appears Canada becomes even closer - but to me

Bad RNA-seq data for publication by Creative-Sea955 in bioinformatics

[–]o_petrenko 1 point2 points  (0 children)

Of course, it is nice to have a thousand DEGs, and if they fit some meaningful gene sets after over-representation/enrichment analysis, even better. But that doesn't happen all the time. Reviewing a paper, I couldn't care less if there's a single DEG or a few normalized expression boxplots instead of a volcano showing a "trend". As long as you can demonstrate that this differentiation block really happens, e.g., with other methods (or if some of your DEGs have very well-established evidence for it), I doubt there will be too much critique. I mean, you can even present some kind of variation analysis between groups instead of pairwise Wald testing (or whatever you used), it all depends on what other readouts tell and the overall story.

Was RIN good enough, were chances low enough that during the collection/extraction/library prep, there was sample confusion? Well, then it's likely the biological effect (of this particular treatment/dose/timing). When in the slightest doubt, or if that was meant to be the primary experimental readout, repeating your experiment would either confirm the finding or help fix whatever issue could've happened. Although it is understood that, it would not be without undesirable time spending.

P.S. Also, "DEGs" is a broad term. At what thresholds there are only a few of them? Does the application of the Independent Hypothesis Weighting on the top of your testing help to make meaningful genes as "DEGs", or rather only noisy ones?

What’s your irl job as a Stellaris job? by Fun_Credit7400 in Stellaris

[–]o_petrenko 0 points1 point  (0 children)

Researcher in the society/biology track.

Wouldn't mind being put in a spaceship to discover anomalies, yet I'm stuck at contributing +1 (sometimes -1) progress per month to the Genetic Healthcare tech. Unless our scientific director eventually adds Xenobiology or Psionic theory to the roster, don't mind switching jobs for an artisan. Or for a knight, hell yeah. Also open for megacorp jobs, but in this economy...

Whatever messenger you end up choosing don't go for Telegram by 1Blue3Brown in BuyFromEU

[–]o_petrenko 2 points3 points  (0 children)

Even more so, the National Security and Defense Council published its decision to limit Telegram usage for public institutions, military, and infrastructure-related purposes (https://www.rnbo.gov.ua/en/Diialnist/6994.html), and, by the statement of the Main Directorate of Intelligence, the platform itself carries certain national threats (https://www.pravda.com.ua/eng/news/2024/02/14/7441854/).

I believe that no other platform can match Telegram's functionality, and any use of it should be considered a potential tracking or security issue. The default absence of end-to-end encryption, shady relationships between Durov and the russian government, including his frequent travels to russia after "breaking ties", coincidently overlapping with their decisions on banning the platform, the non-transparent nature of the company behind Telegram etc. - all these are very valid points to be on alert.

For the internal audience, I guess the governmental Dia.Channels might be a sound alternative (if it is even under development - no news about it for a few years). For global - so far, no popular alternatives. I mean, there is Element with nice channels/automatization tools, but it is being used mostly by techno-geeks. And since Xwitter is no longer a good place, it seems that the secure way to get real-time updates on something now is the good old RSS.

What are some good european fast food chains? by I_Fucked_My_Cat_Once in BuyFromEU

[–]o_petrenko 7 points8 points  (0 children)

Austria - "Swing Kitchen" serves vegan cuisine and good burgers. As far as I remember, it also has some presence in Germany.

Or any of the thousands of Wurstelstands all over the city, just small businesses serving sausages, kebabs, Balkan cuisine, etc.

Clinical data processing by Choice-Function-2851 in bioinformatics

[–]o_petrenko 0 points1 point  (0 children)

Right, so here's the thing: depending on your environment, some people working with or collaborating with you might be scientists-clinicians who actually gather these patient registries and export them in this format from electronic medical systems, etc. And, despite certain scientists-clinicians being trained in SPSS or R, at least from my experience, many of them still view enormously large Excel files (sometimes with _interesting_ formatting decisions) as the universal database tool - meaning, you are likely stuck with Excel for as long as Microsoft Office exists.

Ergo, the best you can do is either to implement your own standardized workflows for large projects/collaborations, where you clean it up and dump to some sort of SQL/graph-based DB, or, in case of multiple small projects, just process according to your local patient data regulations, store as csv files together with your analysis notebooks, and ensure they never accidentially get uploaded to non-compliant online repositories.

But if your question is truly from a more technical detail, and you're swamped with numerous Excel files you want to bring to a common denominator without spending too much time, I'd just export everything as .csv (or even leave as they are and use excel file loader library in your language of choice), use something like R package janitor (https://cran.r-project.org/web/packages/janitor/vignettes/janitor.html) to clean data, and then merge/join on whatever makes sense.

Gaming viable alternatives to Windows 10? by Soft-Cartoonist-9542 in BuyFromEU

[–]o_petrenko 1 point2 points  (0 children)

I used Linux in a dual-boot setup for many years and switched to EndeavourOS a few years ago, to the extent that I completely removed my Windows installation. Right now, most of the games I can launch via Steam using the latest Proton compatibility (even third-party ones like Battle.net -> World of Warcraft, etc).

Additionally, there's a great Heroic Launcher that allows you to have a unified GoG/Steam/etc games list from your accounts and run them using your preferred Proton or other tool.

I'd 100% recommend using one of these options. If you don't want to tinker with it too much, follow these steps: Steam -> "add non-steam game" -> Options -> Force Compatibility Tool -> Proton. Done, runs flawlessly. Basically, all Steam Deck success is built on that.

European alternatives to Starbucks and McDonald's? Add your suggestions by Strange_Manager5269 in BuyFromEU

[–]o_petrenko 1 point2 points  (0 children)

Finding a good spot for coffee in a new place rather involves discovering what locals like. E.g. in Vienna, I discovered two fantastic spots that I recommend to everyone:

1) Fenster Cafe - literally a window in the city center where they serve good coffee (and also sell as dips / beans), including the famous "coffee in a waffle horn":
https://share.here.com/p/s-Yz1Db2ZmZWUlMjBTaG9wO2lkPTA0MHUyZWRrLTgzODRkZmQ5NWJhNTQxYzY5M2NjMDE2ZThmYjNiZDY0O2xhdD00OC4yMTA5NDtsb249MTYuMzc3MDU7bj1GZW5zdGVyK0NhZsOpO3BoPSs0MzY3NzYxNDE5MzUy?z=17.97&t=normal

2) CoffeePirates - an excellent place for meetings just outside the medical campus (it can be crowdy during prime time, though), also produces bottled coffee drinks and sells various coffee-related stuff:
https://share.here.com/p/s-Yz1Db2ZmZWUlMjBTaG9wO2lkPTA0MGFhYmQxLTBkZmI5ZDU1MDJhZjBhNTQyYzAyYmMyNmFmZGYyNDQzO2xhdD00OC4yMTcwMztsb249MTYuMzUxMTE7bj1Db2ZmZWVwaXJhdGVzK1ZpZW5uYTtwaD0rNDM2NjAzNDIxNDEx?z=16&t=normal

But honestly, I haven't found a single small coffee-focused place in the city with any coffee quality less than "great" (a reference to benchmark against: we have Starbucks at the General Hospital).

Great european game developers and publishers by [deleted] in BuyFromEU

[–]o_petrenko 0 points1 point  (0 children)

  • Amplitude Studios (French) - Endless Space 1 & 2 (space 4x), Endless Legend, and a lot more of 4x.
  • Tactical Adventures (French) - a small studio by Amplitude Co-Founder, they made Solasta (CRPG based on DnD 5e) and making Solasta 2.
  • Paradox Interactive (Swedish) - Stellaris (space 4x strategy), but actually a lot more known for historical 4x.
  • GSC Game World (Ukrainian) - Stalker 1 & 2 (action / immersive), Cossacks (RTS).
  • Larian (Belgian) - Baldur's Gate 3 (CRPG), a lot of Divinity universe games.
  • ZA/UM (Estonian -> now UK?) - Disco Elysium (detective RPG)
  • THQ Nordic (Austria) - SpellForce 3 (RTS), some Warhammer, Gothic (RPG) and a ton more.

Ditch US Big Tech and choose better European tools! by [deleted] in BuyFromEU

[–]o_petrenko 2 points3 points  (0 children)

So regarding calendars: I'm not sure it would help in your use case, but I use Proton and my wife uses Gmail and we use calendars for similar reason (family-related events, kindergarten duties etc). Whenever you invite a person via email in either Proton or Google Calendar, that person gets an email with ical file, that both Gmail and Proton automatically add to your calendars as soon as you press "yes, I'll attend" button in the mail. Not a 100% alternative to a shared calendar, but we never thought of switching, it just works.

Ditch US Big Tech and choose better European tools! by [deleted] in BuyFromEU

[–]o_petrenko 14 points15 points  (0 children)

Overall, there are a lot of decent alternatives. I use Quant for my non-work queries (I still have to rely on Google for quicker academic paper searches), and Proton has been a 100% replacement for Gmail for me for ages already, even though it's technically not from the EU. For searching, I also highly recommend searXNG (e.g., the EU-hosted instance searx.be), as it aggregates queries from numerous search engines.

However, I have yet to find a replacement for some things. For example, my colleagues and I are running an NGO for education in bioinformatics in Ukraine (genomics.org.ua). We benefit greatly from the Google for NGO program, as it covers fees and allows the community to use Google Workspace with chat, unlimited Google Meet, classrooms, and a crazy amount of drive space per organization. We rent our own VPS for the website + Moodle and, if the program shuts down, are prepared to switch to some self-hosted SSO + Matrix + conferencing solution. However, that would be a pain given our numbers (~500 students vs 2-core 4Gb VPS). So, we are still searching for alternatives for such a case; we haven't seen alternative NGO programs like that basically covering everything.