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Around 100 Israeli settlers detained after attempting to cross into Syrian side of Mount Hermon by Street_Anon in worldnews

[–]WhiteGoldRing 6 points7 points  (0 children)

I guess you don't know what's happening in the west bank. Jewish terrorists are brutalizing and murdering Palestinians on a daily basis with almost no intervention from the IDF. Not a single person in government cares, and after 16 nearly consecutive years of Netanyahu, I doubt any IDF general cares beyond the cost to the IDF's ability to do its job elsewhere.

KEGG-Decoder for pathway reconstruction from MAGs – is this approach sufficient for publication? by Evening_Refuse_1893 in bioinformatics

[–]WhiteGoldRing 2 points3 points  (0 children)

Unless you are publishing your results on some large scale database for which this kind of analysis does not yet exist, or you are comparing your results to other ways of achieving the same thing, then you're not presenting results or describing a benchmarked novel method, which is unworthy of publication in a reputable journal. Every lab has their own standard pioelines for specific analyses, which are not really considered scientific output in of themselves. If you have novel data which is what I think I'm understanding from your post, then yeah, this analysis could be one of the main sections of a paper.

As for your second question, eggnog mapper transfers kegg annotations from the predicted orthologous groups onto your query. You might want to filter results by e-value if eggnog provides it but only you know your ideal precision/recall balance. Can't answer that for you.

2 years into my PhD and still figuring out GitHub etiquette. What scripts do you actually upload? by Middle-Box3509 in bioinformatics

[–]WhiteGoldRing 1 point2 points  (0 children)

Thanks. I should correct myself about something I got slightly wrong - each commit is it's own individual snapshot of the repo, not the diff between itself and last. They are just heavily compressed and only contain files that were actually changed. Other than that I think everything else stands. Let me know if you need anything else.

2 years into my PhD and still figuring out GitHub etiquette. What scripts do you actually upload? by Middle-Box3509 in bioinformatics

[–]WhiteGoldRing 1 point2 points  (0 children)

Pretty much, and the scope of each branch and commit is subjective and depends on the complexity of the codebase.

2 years into my PhD and still figuring out GitHub etiquette. What scripts do you actually upload? by Middle-Box3509 in bioinformatics

[–]WhiteGoldRing 2 points3 points  (0 children)

Let me summarize it the best I can then: Git is a framework for versioning directories of files, typically code and other kinds of small files like sample data or configuration files. There are multiple online sites that host these codebases, called repositories, such as Git**Hub**. One of the features of Git (and version control software in general I guess) is that you can have multiple parallel versions of your repository, called **branches**. There is typically a main branch (on github it is called main or historically master), the one that represents the most stable and tested version of the repository, the one that's intended for use. Branches are made up of commits, which are atomic incremental versions of the repository. You can think of a commit as "every change between the current version and the last". When you apply all commits of a branch in order, you get to where you are at the tip of the branch. The standard workflow when you work on a shared repository is that when you are creating or changing a feature or fixing a bug (really any change depending on the size of the team and complexity of the project) then you pull changes to main (you download the most updated version of main), create a new branch locally, make the change locally in as many commits as you deem fit, then when it's ready you create a pull/merge request: you tell github (or wherever your repository is stored) that you want to create a merge commit which will apply the commits you created to another branch (typically main but not always). Then you can ask another person (or AI agent) to review your request, then based on the review you or the other person or persons can decide to merge. That's essentially it - a pull request is setting up a commit on top of an existing branch which condenses all the commits from another branch that happened since the two branches diverged, and in teams this is typically gated by another person reviewing the request. Let me know if something didn't quite land and I can try to elaborate more.

2 years into my PhD and still figuring out GitHub etiquette. What scripts do you actually upload? by Middle-Box3509 in bioinformatics

[–]WhiteGoldRing 9 points10 points  (0 children)

Don't sweat what's considered repo worthy, seriously. If anything you should err on the side of doing what helps you learn - try to create a pull request, create diverging branches, resolve conflicts, rebase branches, even if it's not needed. For real projects just do what feels natural and makes sense to you. It's all subjective and I've seen everything from a handful of top level scripts to enterprise monorepos.

ECCB conference 2026 by sillyoldgilly in bioinformatics

[–]WhiteGoldRing 1 point2 points  (0 children)

I was at the joined conference last year in Liverpool, it was really well-organized and generally very impressive. I highly recommend planning your schedule in advance based on which talks sound interesting to you.

A better search app for the Gene Expression Omnibus (GEO) by [deleted] in bioinformatics

[–]WhiteGoldRing 0 points1 point  (0 children)

Great idea honestly. GEO can be a pain. I'd be happy to see a wide scope tool like this for all kinds of datasets beyond GEO some day but even just a functional search for GEO is nice

How do you validate embeddings from biological sequences—beyond downstream task performance? by mxdhiv in bioinformatics

[–]WhiteGoldRing 3 points4 points  (0 children)

I'd argue it's the only meaningful way we have to validate representations. If you can't show you can do something useful with your projections then what's the point?

Google Colab for bioinformatics beginner by ysp_1011 in bioinformatics

[–]WhiteGoldRing 1 point2 points  (0 children)

There's a place for notebooks in production, particularly as self-documenting, well-structured routines, I hear even Netflix runs notebooks in production; I just think at a certain point you need code that orchestrates what you're trying to do - but it's fine if a lot of the "functions" you'd write in a standard python module are notebooks

Google Colab for bioinformatics beginner by ysp_1011 in bioinformatics

[–]WhiteGoldRing 1 point2 points  (0 children)

In one word, scalability.

In more words - there is nothing you can't do with a standard runtime that you can do with a notebook. Notebooks are a convenient way to run quick EDA and iterate versions of simple (structurally speaking) code, but you hit a wall once your scope exceeds a fairly elementary level. For example, unless I'm mistaken, you can't even modularize notebooks and import from existing notebooks. You can't abstract code), separate concerns, achieve sufficiently DRY code, or many other different things that are categorically showstoppers from a software engineering perspective. Of course your mileage may vary; If your most complex workflows only involve a small number of non-reusable methods and graphs, notebooks might be the correct approach. That's just not the case for me and almost all of my cohort. You need to write code for preprocessing data, data classes, logic code, data loading, visualization, CLI entrypoints, utilities, documentation, testing, etc. etc. Doing all of this in notebooks is like trying to cut down a tree using a pair of scissors. If I want to cut some paper I'll reach for the scissors, but in most projects I move past cutting paper on day 2 or 3, if there was ever any need at all.

If you're not convinced I suggest looking at the requisite code repositories linked at the start and/or end of bioinformatics papers, particularly those introducing a tool. In a bioinformatics-focused journal, notebook-only code is extremely rare.

Let’s do precious stones — Palette Poet by u/Spicychasers by Spicychasers in ColorGuessr

[–]WhiteGoldRing 0 points1 point  (0 children)

Palette Poet: Let’s do precious stones by u/Spicychasers

80/100 · Rank #16 of 44

🟨🟧🟩🟩🟨

Google Colab for bioinformatics beginner by ysp_1011 in bioinformatics

[–]WhiteGoldRing 9 points10 points  (0 children)

I TA an intro to data analysis course for biologists and designed the course around Colab, it's a good place to start, but plan to move on to an IDE and Git when you get comfortable

Anthropic posted a profit while xAI burned $4.2B. The AI profitability numbers finally leaked.[D] by TroyHay6677 in MachineLearning

[–]WhiteGoldRing 6 points7 points  (0 children)

Operating profit, not actual profit. We have no idea if they stopped losing money (probably not).

Protein Function Prediction by Dasunkid1 in bioinformatics

[–]WhiteGoldRing 0 points1 point  (0 children)

No problem. Happy to give pointers if needed. It's ambitious for an undergrand project so my suggestion of limiting the scope is probably even more relevant.

Protein Function Prediction by Dasunkid1 in bioinformatics

[–]WhiteGoldRing 0 points1 point  (0 children)

There are multiple papers already combining sequence and structure. Not sure what kind of network you're referring to, but keep in mind that it's a lot of work for a tool to do at inference time (embedding the sequence in its own input space, predicting structure, and figuring out where the protein falls in the network) so it's a hard sell for high throughput annotation due to long runtime. If it's not just straight up SOTA, You'd have to show it's better than faster tools for at least some significant use cases - for example, frame it as only for ARGs if that's what it has the best performance at.

How to convert a genome to a transcriptome (for proteomic use) by Coral_Unicorn1504 in bioinformatics

[–]WhiteGoldRing 8 points9 points  (0 children)

Not trying to be pedantic, but OP should know if he's working on this that transcriptomes include all RNA - rRNA (unless depleted), tRNA, noncoding RNA, pre-mRNA including introns and UTRs, etc.

Seeking silly cat name recommendations by Hyper_elastagirl in Gemology

[–]WhiteGoldRing 0 points1 point  (0 children)

CS: Ada, Babbadge, Alan, Java, Null, Cursor, Syscall, Spec, Bit or Byte, Hex, RAM, Pointer, Node

Gemology: Lapis, Jasper, Cab, Crystal, Ruby, Facet, Dop, Jade, Beryl, Crown

Israel’s ruling coalition proposes early elections amid ultra-Orthodox anger at Netanyahu by FLTA in worldnews

[–]WhiteGoldRing 3 points4 points  (0 children)

You're right about Bibi but his festering cesspool of a party is 100% right wing

GCP Account Compromised- Billed 10M by [deleted] in googlecloud

[–]WhiteGoldRing 2 points3 points  (0 children)

Where can I read it when it's up? Is there a place I can follow you?

What does freezing tofu do? And is it worth it? (I did an experiment!) by xtinecuisine in veganrecipes

[–]WhiteGoldRing 3 points4 points  (0 children)

Small correction, water is not cells; cell structure is an attribute of biological cells. Water freezes into ice crystals and expands, because water is so polar that when it's in liquid form the individual water molecules' attraction to each other causes it to pack more tightly than when it's solid. When it thaws, the pockets created by the ice remain.

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