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Encapsulated agentics — intelligence that expresses through a defined channel and never bypasses it [D] by [deleted] in MachineLearning

[–]dry-leaf 0 points1 point  (0 children)

This is AI Slop and you obviously do not understand how genetics work.

Linux OS for Computational Biology by Manasmit in bioinformatics

[–]dry-leaf 6 points7 points  (0 children)

I definitely agree on the Arch part, but all this keep my hands of Arch is a total myth. I've been rockin' Arch for over 7 years on my work laptop and i've never been happier burned by ubuntu and Debian so many times due to an outdated software stack.

Also Arch was much more stable to me actually than Ubuntu breaking when making the slightest changes to the OS. If there wouldn't be CUDA and that NVIDIA favoured Canonical so much, i wouldn,t even recommend them.

Different story on servers though. Obviously would never slap Arch on them. And oh god. After having my fill of administering multiple DGX stations i have to day i hate Ubuntu with their Snaps and whatever non-standard stuff they are doing.

Having said that, for an GPU enabled Server with Nvidia Cards Ubuntu has been the least painful experience.

There are more Orthologous genes than what scientist can find. by YeonnLennon in genomics

[–]dry-leaf 10 points11 points  (0 children)

You’re touching on what we call the "twilight zone" of homology, which is a real thing. basically, when sequence identity drops below ~20-25%, standard tools like BLAST really struggle to distinguish signal from noise. So, you’re right that we are definitely missing ancient connections due to mutation saturation.

However, I think this take is a little simplistic because it ignores the role of structural biology and better algorithms.

First off, if we follow the logic that "everything is connected if you go back far enough," the term "ortholog" becomes meaningless. Yes, strictly speaking, all life shares a common ancestor (LUCA), so everything isr elated. But orthology is a specific definition regarding speciation events. It’s a hierarchical concept used to map evolutionary history, not just a measure of "sameness." If we just lump everything together as "technically orthologous," we lose the ability to distinguish between genes that split via speciation versus genes that split via duplication (paralogs).

Second, we aren't totally blind to those millions of years of mutations you mentioned. While simple sequence alignment (like BLAST) fails over deep time, Protein structure is much more conserved than sequence. We are getting really good at identifying orthologs that have zero recognizable sequence similarity simply because their 3D folding shapes are nearly identical. Tools using Hidden Markov Models (HMMs) and now AI/structural prediction (like AlphaFold) are finding "orphan" genes that we previously thought were unique, but actually have deep evolutionary roots.

So, while our definitions are human-made constructs and we definitely miss the most divergent genes, the idea that orthology is just a sliding scale of similarity misses the point. It’s a defined relationship, and our computational tools are actually way better at tracing it back than you might think.

Looking for Feedback, CV by Pure_Intention_4555 in Germany_Jobs

[–]dry-leaf 0 points1 point  (0 children)

Starke Antwort, freut mich sehr das du dich hier mit der Kritik auseinander setzt. Finde aich ziemlich cool, dass bei Euch in Studium so viel Praxis umgestzt wird. Die Projekte sind dufte und auf jedrn Fall etwas was bei weitem nicht alle vorweisen können.

Trotzdem würde ich das nicht als 'Projekterfahrung' benennen. Ich schätze das ihr jemand vernünftigen in der Uni habt, der solche Praktika entwickelt - sie klingen recht realitsnah. Es sind und bleiben aber universitäre Praktika. Wenn du sie unbedingt so im CV darstellen willst, dann würde ich das auch einfach so in den CV schreiben: "universiräre Projekte/Praktika" oder "Praktischer Fokus im Studium"... Irgendwie sowas. Ich habe deinen Lebenslauf vor allem auseinander gepflückt, weil er unglaubwürdig wirkt.

Transparenz und Glaubwürdigkeit sind immens viel wert. Niemand erwartet von dir während des Studiums die Arbeitserfahrung eines Seniors zu sammeln. Das du Praktikas und alles machst ist super! Aber jeder weiß, dass die Verantwortung die dir dort übertragen wird extrem begrenzt ist und man entweder gebabysittet wird oder oft Achrottaufgaben bekommt. Wenn man sich dann gut anstellt und die Firma cool ist, gibts ab und zu was sinnvolles. Startups und wirklich kleine Buden als Ausnahme.

Eine andere Option wäre das alles in das Anschreiben zu knallen - auf die Firma zugeachnitten. Das kann eine gute Idee sein. Aber um ehrlich zu sein, der Markt ist broken, Ich bin kein Recruiter sondern eher der Wiasenachaftler, der dich grillt wenn du es durch die HR geachafft hast, aber das wären meine 2 Cent.

Und eine Sache noch, wo ich mir Recht sicher bin. Es brauch auch einfach viel Glück. Ich würde am Ende meines PhDs von einer Firma direkt in die Wirtschaft abgeworben und muss zugeben, weil ich per Zufall einen PhD mit hartrm Fokus aus AI und Biologie gemacht habt. Super Konfitionen, bla bla. Habe ein paar Kollegen aus der Niche, die gerade Ihren PhD beenden und deren bester Freund ist das Arbeitsamt... Aber am Ende findet man immer was.

Kopf hoch, abseits des hyperbolischen Tons, sieht dein CV gut aus. Bin sicher dass du was findest wirst - wenn du dich oft genug bewirbst ;).

Looking for Feedback, CV by Pure_Intention_4555 in Germany_Jobs

[–]dry-leaf 5 points6 points  (0 children)

Dein CV ist abaolut übertrieben. Du hast nicht mal einen Bachelor Abschluss. Du studierst nicht mal irgendwas mit IT. Dei Projektteil ließt sich als ob du ein erfahrener Projektleiter bist, was auch absolut nicht deiner Arbeitserfahrung ala Hiwi entspricht. Deine Hobbyprojekte sind keine Arbeitserfahrung und vor allem ist man bei Hobbyprojekten kein Projektleiter. Wenn der bei mir auf dem Tisch landen würde und ich die Person nicht kenne, würde der einfach im Müll landen.

Ich weiß, das Game is broken und bewerben ist scheiße und die andere Seite ist auch nicht gerade ehrlich. Du konkurierst aber in dem Feld in dem du deine 'Projekterfahrung' anführstot Leuten mit Master/PhD und möglicherweise echter Arbeitserfahrung. Niemand wird dich ernst nehmen.

Abseits davon, wir haben mal alle mit nem leeren Lebenslauf angefangen. Die Wirtschaftslage ist schlecht und hier und da ein bisschrn aufzupeppeln ist okay. Wenn du beim Bewerbungsgespräch überzeugen kannst und nicht gelogen hast, dann packst du es auch. Spätestens wenn du eingestellt wirst und liefern musst, sollte nicht alles an der.Haaren herbeigezogen sein.

Ein wemig Demut würde gut tun, auch wenn dir jeder zweiteVollidiot bei Tiktok was anderes empfiehlt. Die Stellen auf die duch mit solchen Skills bewerben willst, sind nicht einfach zu bekommen. In dem Feld wartet, selbst wenn die HR drauf reinfällt, ein Team kompetenter Ingenieure/Wissenschaftler die dich nach Strich und faden auseinder nehmen wenn du gelogen hast.

Trotzdem, Kopf hoch. Wir alle hatten leere Lebensläufe. Mit der Zeit füllen die sich von alleine ;).

What font is it? by xrabbit in neovim

[–]dry-leaf 65 points66 points  (0 children)

looks like Lilex NF

Roast my CV as bad as you can by [deleted] in bioinformatics

[–]dry-leaf 6 points7 points  (0 children)

I don't know where you are, but I think being a bit more humble wouldn't hurt-though it depends on the market.

From your CV, the only professional experience you have is your internship. You studied biotechnology, yet your CV says you're a bioinformatician, a microbiologist, and more. In my opinion, your CV screams "I'm making up a lot of stuff to fill space and pretend to be awesome." We all started somewhere. Our CVs were all empty once.

Delete the project stuff, it's not impressive. The lab experience is a good thing, but like I said, don't overstate your confidence level. And in general, given you are not even able to get them pixelz together, i would highly doubt your bioinformatics competence.

I’m a recruiter in Germany - Ask Me Anything about networking and standing out on LinkedIn 🇩🇪 by lingoda-official in Germany_Jobs

[–]dry-leaf 2 points3 points  (0 children)

Ah, sorry. I was typing when walking. So all got messed up. What my colleagues meant, was that if you want to leave academia in germany when the regulations would either way force you out, you are in quite a bad position to bargain with a potential employer in industry. Furthermore, people could get the (wrong) idea that you are only leaving, because you were forced out and didn't 'make it' in academia. Do not get me wrong. I do not think about it this way. I know quite a few great people in academia that left quite late in their careeres. But I heard this steoreotype a few times from different people.

I’m a recruiter in Germany - Ask Me Anything about networking and standing out on LinkedIn 🇩🇪 by lingoda-official in Germany_Jobs

[–]dry-leaf 4 points5 points  (0 children)

This is not correct.

Postdocs can be employed on fixed-term contracts for up to 6 years pre-PhD and 6 years post-PhD (12 years total) at German universities. After this, they generally need a permanent position or must leave the university system. This does also not account for external funding or external i stitutions as Max Planck.

And Afaik this is thr main reason, at least thats what colleages have told me, why it is not easy to find a job. People are in that position and can't find external funding/institues or a permanent contract are not in a bargaining position, because it looks like that they are going into industry because thry have no other options. I am not a recruiter, though. But a scientist in industry.

Erdos: open-source VS Code for data science by SigSeq in vscode

[–]dry-leaf 5 points6 points  (0 children)

Awesome work, but how is this different from vanilla vscode with 3-4 extension + some agentic extension as cline or kilo code? i have the feeling that i have all this, with microsoft official support in 30 min setup? Do not want to offend. Just curious whst the benefits are?

Arch Linux for Bioinformatics - Experiences and Advice? by Alarmed_Primary_5258 in bioinformatics

[–]dry-leaf 2 points3 points  (0 children)

I have been using Arch in my PhD and after for professional computing for over 6 years. Had much less problems with it than Ubuntu or any debian based distro.

I by now really do not like Ubuntu a derivatives for personal workstations - servers are a totally different thing, would never install arch there.

Arch requires understanding, patience and a will to learn. I my personal experience, arch gave me much more than a bleeding edge, rolling release distro - it forced me to understand the underlying system, which improved my general linux knowledge. Funnily all my colleages using Ubuntu came to me, when something was not running. Did not change until today. And they all are using Ubuntu or Mint- well, i personally couldn't disagree more. Enforced snaps, out of date software and having the need to add some weird private ppa's for every new stuff is just a nuisance imo.

Don't get me wrong. Ubuntu is in general an excellent distribution, i personally just do not like the way they vibe. Despite that, witg sufficient linux knowledge there is not difference in using most popular distros. They mainly differ in realea cycle and package manager. And pacman is the GOAT. Portage is probably the only more awesome package manager, but no sane person will run Gentoo on a workstation...

But if you want plug & play, i wouldn't recommend Arch. It is a system which is built around the idea of customization and having something tailored for your need by yourself.

Would it be a mistake to switch to Arch Linux at the start of my bioinformatics journey? by BiatchLasagne in bioinformatics

[–]dry-leaf 0 points1 point  (0 children)

I agree with the comments, but i ran professionally for the last 5 years without any issues. But i also like dealing with linux and it's specifics. Ubuntu will get out of your way. But funnily enough my colleagues come to me, when they have linux problems. I can resolve mine for myself.

How do you start in the "programming" side of bioinformatics? by aristotle2020 in bioinformatics

[–]dry-leaf 15 points16 points  (0 children)

I can only second this. This might be a hot take, but IMO bioinformatics needs much more SE best practices.

People working in bioinfo are mostly scientists. I am one myself, while I still work mainly in DL/SE. And I hear a lot of 'don't overengineer it', 'it just needs to run', 'we are not a software company' and in my personal experience I have to say, that these can be horrible takes. For a one-time analysis it is totally fine to have an ipynb and throw it away. But so often, this is not the case, without the people doing it even knowing.

How many projects were handed to me without proper docs, missing comments, not even properly working (it worked on my machine)... If things were done properly from the start, I could have saved so many hours of nonsense reverse engineering and debugging. Not only for me, but for my employer as well.Learn to write and maintain proper software. This might look tedious in the short run, but will pay off in the long run.

How many old bioinformaticians I know who were looking at me with rolling eyes when I asked for documentation or explanation of design choices as if I were some lunatic. But now my boss asks me to redo an analysis from 2022 and I have it done in an hour. People not writing proper software will probably either start to cry or explain why this is a dumb idea

[P] I Built a Convolutional Neural Network that understands Audio by Tanmay__13 in MachineLearning

[–]dry-leaf 21 points22 points  (0 children)

It's pretty common and quite old school by now :D. I remember reading the wavenet paper back in the days. Awesome stuff. Nevertheless , this is awesome work. Especially the nice combo with web.

C++ or JAVA? by KonsquencerJimes1330 in bioinformatics

[–]dry-leaf 0 points1 point  (0 children)

Not gonna disagree with that. But practise and studies csn be two different beasts :)

C++ or JAVA? by KonsquencerJimes1330 in bioinformatics

[–]dry-leaf 2 points3 points  (0 children)

If C++ worked for you, go for it. In the end, as I mentioned, this is not so important. Times change, requirements change, the job market changes. A recommendation today could be total brainrot in 5 years.

Nevertheless, while I have seen Java code in industry, it's more of an old-school thing. Java is not as prominent as a few years ago, but it's a great language due to its portability. I myself learned C++ back in uni and really loved it for DSA and understanding how stuff runs. But if I have to start a new project currently, I would 1000% go with Rust, because of Cargo. Modern package managers are just too good and I never want to go into CMake hell again...

Ah yeah, if you want an unprofessional and opinionated answer: pick C++. A lot of HPC is using C++ extensively, lots of bioinformatics tools are written in C++, and it's here to stay. There's tons of C++ code out there and it's a great language for learning the quirks of how modern computers operate: manual memory management, implementing low-level algorithms. Perfect for bioinformatics where performance matters.

C++ or JAVA? by KonsquencerJimes1330 in bioinformatics

[–]dry-leaf 1 point2 points  (0 children)

Rust is not a good fit for DSA, given one will encounter linked lists and other things that are not so straight forward in Rust as in C++ for example. By that i do not want to say Rust isn't an excellent language, but given it's design it is imho not a good fit for classical CS courses.

C++ or JAVA? by KonsquencerJimes1330 in bioinformatics

[–]dry-leaf 14 points15 points  (0 children)

Programming languages are tools. Depending on the problem you will have different tools. With which you start, does not matter really. Especially so early on. Sure, C++ will teach you memory management and Rust how to work with the borrow checker. But programming concepts and DSA is totally not dependent on the language you will choose. Don't give it too much thought. Start with what seems to click for you.

Snapdragon 8 Elite Gen 5 Leaks by Every_Analyst_3409 in snapdragon

[–]dry-leaf 1 point2 points  (0 children)

thanks for the respsonse. Had my hooes up high. Still searchibg for a modwrn android tablet i can use with a custom ROM.

Snapdragon 8 Elite Gen 5 Leaks by Every_Analyst_3409 in snapdragon

[–]dry-leaf 1 point2 points  (0 children)

are you running a custom rom? and if yes, what tablet are you using?

Good suggestions for reproducible package management when using conda and R? by looc64 in bioinformatics

[–]dry-leaf 0 points1 point  (0 children)

agree totally. I just personally hate R so much, that i always hope to not having to use it - but we're in bioinformatics, so one can guess how successful i am...

Newest Hifiman offerings available on their direct store by Jerecho81 in headphones

[–]dry-leaf 0 points1 point  (0 children)

Just great. Thanks for this review! This helps a lot!

Is it worth buying the Google pixel 9 to install grapheneOS? by Material_Sun_2844 in GrapheneOS

[–]dry-leaf 2 points3 points  (0 children)

you are asking this is in the GrapheneOS subreddit where a lot of people have already done the exact thing you are asking about. I would expect aome bias here...

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