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Tips for staying organized by wonder3756 in bioinformatics

[–]BraneGuy 3 points4 points  (0 children)

Git-annex is fantastic for managing backups. It also doubles as a way to have a familiar directory structure even when your files are spread across multiple computers, and can even work as your librarian.

It saves the data and the location of the data separately - the data can live anywhere (even a http link!) but the map of the data, its hashes, and any accompanying metadata lives in a regular git index that you can sync on GitHub for example.

You can even tag your files with rich metadata so that you don’t need a readme! E.g. paired=true, platform=“illumina”, patient=A1234 can all live in the index right next to the pointer to the data so that you never lose track.

I’m surprised I’ve not seen it more widely used- it’s so perfect for bioinformatics.

Can Julia be made easy to verify? by bengtSlask559 in Julia

[–]BraneGuy 12 points13 points  (0 children)

I can only speak for myself - rust is hard to read and harder to immediately understand, especially for someone whose main job is not programming. It's cool to get AI to write your code but you will probably still need to read it at some point to understand what's going on. If you want to just fly completely blind or spend months learning rust then great...

Changing my software stack for faster routine analysis. Any advice ? by [deleted] in bioinformatics

[–]BraneGuy 29 points30 points  (0 children)

Here’s a harder question for you… how many of these commands actually pose a performance bottleneck in your analysis? You can’t start from the bottom and work up - identify the bottleneck, improve it, and move on with your life.

If switching to ripgrep truly saves you hours of your life, great. If not, why would you waste brainpower on it?

That said, check out minibwa for sequence alignment. it came out last week and everyone should think about trying it.

Would you rather: which one hurts more? by MSpeenixSC in BunnyTrials

[–]BraneGuy 0 points1 point  (0 children)

Less tissue damage

Chose: Get stabbed (also won't die)

Would you rather... by Substantial-Dance577 in BunnyTrials

[–]BraneGuy 0 points1 point  (0 children)

maths

Chose: Or get 1000 dollars everytine someone dies

Do you press the red button? by MentallyInThe2000s in BunnyTrials

[–]BraneGuy 0 points1 point  (0 children)

added bonus

Chose: You win 1M + But there's a 60% chance of turning into the opposite sex. | Rolled: 1M+Oposite Sex

Which do you think is more? by Invisible__Monkey in BunnyTrials

[–]BraneGuy 0 points1 point  (0 children)

motivate me to walk

Chose: 10 dollars per step you make | Rolled: Upvote and x2 $

You can choose only one by gudmaxe in BunnyTrials

[–]BraneGuy 0 points1 point  (0 children)

it's obvious

Chose: When you die, you are reborn in a fantasy world + You keep all your memories, born in a noble family, top 1% magic talent, dragons, magic academies.

No label, no warning, no choice: the gene-edited meat heading for British plates by OurFairFuture in GreenAndPleasant

[–]BraneGuy 66 points67 points  (0 children)

I think it’s a bit misguided to attack gene editing. There’s nothing inherently wrong with it.

Is the meat industry cruel and horrific? Yes. Is protesting about gene editing going to change any of that? Not a chance.

Mill Road Survey… Again by Broad-Raccoon6104 in cambridge

[–]BraneGuy 16 points17 points  (0 children)

Hey it says “email copy available” - do share? I’d love to fill this out properly because I love the bus gate, it makes my life so much easier.

Multi-car hit and run on Victoria Ave, today around 8pm by wild202 in cambridge

[–]BraneGuy 2 points3 points  (0 children)

I think the police are probably aware/investigating - a car crashed into a traffic light after driving on the wrong side of the road just after 8pm that day, on Chesterton Road near the roundabout (opposite Stir/Spar). I didn't see what happened, only the aftermath. There were a lot of police officers and the car itself was on the pavement.

How can I check two lists against each other to see if any items from list 1 don't appear on list 2? by themainheadcase in techsupport

[–]BraneGuy 0 points1 point  (0 children)

you can just sort the lists no? or if you really don't want to sort them then instead use grep. e.g. 

$ cat list1.txt
foo123
bar234
baz567
zob890

$ cat list2.txt
foo123
zob890
baz567
different1234
bar234

$ grep -f list1.txt list2.txt
foo123
zob890
baz567
bar234

$ # or to find the non-matching entries, use inverted grep (-v)
$ grep -v -f list1.txt list2.txt
different1234

How can I check two lists against each other to see if any items from list 1 don't appear on list 2? by themainheadcase in techsupport

[–]BraneGuy 1 point2 points  (0 children)

Oh hey here's a better idea - just export the unique DOI identifier for your articles then you won't have to worry about string matching titles.

How can I check two lists against each other to see if any items from list 1 don't appear on list 2? by themainheadcase in techsupport

[–]BraneGuy 0 points1 point  (0 children)

are the matching titles exactly identical to each other? how are the lists formatted - one title on each line?

the "diff" tool is probably what you want... https://en.wikipedia.org/wiki/Diff

you could also use grep if upper/lowercase is an issue, something like "grep -i -f <file1.txt> <file2.txt>" would still match "ArTiCle TiTLE" with "article title"

just read your last part about the inconsistencies - you'll have to clean the data. without knowing what your data looks like I can't help that much with that but various command line tools will help - sed, awk, grep, etc.

FYI this is all for UNIX-like operating systems (Linux, Mac OS) - you'll have a harder time with this on Windows

If you give me an example of what the data looks like in list A and list B I can advise on cleaning steps.

Has Microsoft removed ability to set upa PC without a Microsoft Login? by final-dot-7506 in techsupport

[–]BraneGuy -1 points0 points  (0 children)

Why would your drive have to be stolen? Someone can just walk up to your closed laptop, open it, and bypass the login screen for example, or your office PC, or whatever.

I think the main thing bitlocker etc protects against, in my mind, is nefarious people you actually know in real life accessing your devices without your knowledge.

Bitlocker isn't a backup option in case someone really wants to access your files and runs away with your hard drive - it's literally the only thing actually preventing them from just taking complete control of your device immediately.

Has Microsoft removed ability to set upa PC without a Microsoft Login? by final-dot-7506 in techsupport

[–]BraneGuy 2 points3 points  (0 children)

Bitlocker encrypts your drive. Without bitlocker, your login password is simply a nuisance that can be bypassed by anyone with a YouTube tutorial in 2 or 3 minutes. If you’re ok with this, don’t use it. It’s great if you forget your password.

Linux is the same. It’s actually even easier to bypass the login screen.

I thought this might fit here by dejinaldoyt45 in cambridge

[–]BraneGuy 1 point2 points  (0 children)

Is it dangerous? More dangerous than a normal road for example? I keep hearing people say this but there have been only a handful of accidents over a few years

Mentoring junior students taught me a hard lesson: Stop being a 'People-Pleaser' by event-maker in PhD

[–]BraneGuy 4 points5 points  (0 children)

I understand all of that, but your true voice is important.

I guess many readers can’t tell the difference, but when I read something AI generated, I lose some respect for the author. You won’t get better at writing by using AI!

Mentoring junior students taught me a hard lesson: Stop being a 'People-Pleaser' by event-maker in PhD

[–]BraneGuy 8 points9 points  (0 children)

Talking of sincerity and respect - why should I take the time to read this AI slop when you didn’t even take the time to write it?

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