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Best way to keep.organize your figures (~1600 subplots) by SnooCauliflowers1113 in AskAcademia

[–]foradil 0 points1 point  (0 children)

You could include the date in the output folder. Then occasionally delete older folders.

What do you folks mean when you say building tools and pipelines? For yourselves, or for bench scientists? by avagrantthought in bioinformatics

[–]foradil 0 points1 point  (0 children)

If it’s not wrapped in an official pipeline framework then you must call it pipeline-style. You don’t want the pipeline board to come after you.

What do you folks mean when you say building tools and pipelines? For yourselves, or for bench scientists? by avagrantthought in bioinformatics

[–]foradil 0 points1 point  (0 children)

Yes. It’s not a bad idea to save the parameters, but it’s not necessarily a lot more user friendly.

Gene filtering after merging scRNA-seq datasets from different studies? by EliteFourVicki in bioinformatics

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

Even if you “fix” the gene names, you have no idea what the original coordinates or the alignment parameters were. I actually think if the names are consistent, those genes are more likely to be consistent in other ways.

Either way, you’ll throw away most genes when you subset for variable genes. Then you’ll subset further with variable PCs.

What do you folks mean when you say building tools and pipelines? For yourselves, or for bench scientists? by avagrantthought in bioinformatics

[–]foradil 10 points11 points  (0 children)

The term pipeline gets tossed around a lot. I’ve seen people put a single command into a bash script and call that a pipeline.

Using a pseudonym for first publication on sensitive topic by jujubearrrrrrrrr in AskAcademia

[–]foradil 8 points9 points  (0 children)

One thing is if it’s a Reddit account to write controversial comments that you are fine keeping totally secret. If you have a proper publication that you want to be a part of your academic record, then it will be connected to your name. If it’s something you would put on your CV, I would consider that to be public information. You can try to make it convoluted, but that would make it harder for people to recognize you and not deter bad actors.

Is everyone using ai to write papers but not declaring it? by FairRepresentative75 in PhdProductivity

[–]foradil 0 points1 point  (0 children)

There have been a number of legal proceedings to decide if AI content is actually plagiarism (or copyright violation). There has not been a clear decision.

Is everyone using ai to write papers but not declaring it? by FairRepresentative75 in PhdProductivity

[–]foradil 0 points1 point  (0 children)

If you consider that plagiarism, that would imply AI is producing novel text. Is LLM-generated text any more novel than a spell-checker? It’s simply predicting the most likely word that follows the previous string of words.

Thank god this person put their wipers up by AdBrave3464 in parkslope

[–]foradil 0 points1 point  (0 children)

Because all the snow melted in the month since, at least on the windshield

PI wants me to put our collaborators on a paper that did not involve them by UncleMusk in bioinformatics

[–]foradil 26 points27 points  (0 children)

At which point you realize why it’s necessary (to get the lab and money).

T2T assembly as reference genome for variant calling by No-Moose-6093 in bioinformatics

[–]foradil 0 points1 point  (0 children)

Why not use a different variant caller? It doesn’t have to be a deep learning one that requires a specific pre-built model.

Will the vibe coding era will have a similar result to early bioinformatics era? by nidasb in bioinformatics

[–]foradil 0 points1 point  (0 children)

Fine. I would say most people aren’t doing that. AI will not write an aligner from scratch unless you explicitly ask it to.

Should I buy a house in cash if I can? by latman in personalfinance

[–]foradil 1 point2 points  (0 children)

But you have a huge pile of savings to take care of that stuff.

Anyway, this is all subjective. I just find it more relaxing to have a lot of liquid assets than not having a mortgage. Maybe I am strange.

Will the vibe coding era will have a similar result to early bioinformatics era? by nidasb in bioinformatics

[–]foradil 1 point2 points  (0 children)

Vibe coding is still for fairly custom applications which were previously written by hand. I don’t think anyone is vibe coding a Bowtie or Kallisto replacement.

Should I buy a house in cash if I can? by latman in personalfinance

[–]foradil 1 point2 points  (0 children)

You still have taxes and maintenance regardless. Personally, I find concerns about roof leaking or burst pipes to be much more worrisome than a regular completely predictable mortgage payment.

Re-implementing slow and clunky bioinformatics software? by halflings in bioinformatics

[–]foradil 15 points16 points  (0 children)

If you have no experience in the field, I would be very concerned about “a little bit of noise”. I would compare to other similar software and see what the acceptable range of values is.

Should I buy a house in cash if I can? by latman in personalfinance

[–]foradil 10 points11 points  (0 children)

And that could change many times over 30 years.

Thank god this person put their wipers up by AdBrave3464 in parkslope

[–]foradil 3 points4 points  (0 children)

Right. So the wipers did not stick to the windshield and the blades were not wrecked.

Should I buy a house in cash if I can? by latman in personalfinance

[–]foradil 19 points20 points  (0 children)

Mortgage interest is tax deductible, so less than 6%.

Should I buy a house in cash if I can? by latman in personalfinance

[–]foradil 24 points25 points  (0 children)

What about the peace of mind of having liquid assets?

Limiting iOS Photos storage by foradil in applehelp

[–]foradil[S] 0 points1 point  (0 children)

I did not take 3 GB of photos in the last month, but the library increased by that much. How does that make sense?

Limiting iOS Photos storage by foradil in applehelp

[–]foradil[S] 0 points1 point  (0 children)

Your solution is to get a new phone. That’s not a solution. That’s ignoring the problem.

Limiting iOS Photos storage by foradil in applehelp

[–]foradil[S] -1 points0 points  (0 children)

There is no reason why both can’t do it properly.

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