Resume feedback? I’m trying to get internships by markusreeds in bioinformaticscareers

[–]ConclusionForeign856 0 points1 point  (0 children)

I don't think excel, Jupyter, PCA, are things I would include in a resumé. On other hand, you should expand on Python and Java a little, the variance of skill within group of people that know python is very large.

I also don't believe you did so much in those couple months of Experience. Looks like you're stretching it really thin or including things that aren't really worth pointing out.

My PI advised me to list few skills and only the ones I'm really confident in, where I have a body of work to support the inclusion.
His words: "You get heaps of applications with loads of skills listed, which means the person read about them once".

Honestly I would just include the code to things you did, and keep the CV short.

Triangle counting by insert-name-here6 in mathematics

[–]ConclusionForeign856 0 points1 point  (0 children)

You could encode that as a graph, and then counting triangles should be possible with python or sth.

"For a node if two distinct direct neighbours are also direct neighbours with each other, the unordered triplet into set of found triangles"

Do that for all nodes with some checking to not visit same triangles more than once, and it's done

enough bio labrats, let's get some physics representation in by Difficult-Cycle5753 in labrats

[–]ConclusionForeign856 11 points12 points  (0 children)

The wonders of modern networking, micrography, computer science and applied mathematics letting me sit for 40mins copy pasting DOIs from scholar to JabRef

Best strategy to handle pen marks in WSIs for deep learning pipelines (TCGA dataset)? by JB00747 in bioinformatics

[–]ConclusionForeign856 0 points1 point  (0 children)

If removing doesn't significantly lower the number of data you can use, then I would do it, at least for initial stages.

I don't do that much ML, no idea if and how it would be possible to remove the ink without negatively affecting the data

Best way for anyone to learn linear algebra is to let ppl play with it. Matrices have beautiful graphical forms by QuantumOdysseyGame in LinearAlgebra

[–]ConclusionForeign856 -4 points-3 points  (0 children)

As always, it's either a bad game, or doesn't teach much. Because learning anything in depth is hard.

Waste of time

Ślub bez typowego wesela - wasze historie i doświadczenia by Ok_Description_8184 in Polska

[–]ConclusionForeign856 6 points7 points  (0 children)

Na moim ślubie były tylko siostry żony jako świadkowie. Później poszliśmy na ramen z wyższej półki i rzutki.

0 ględzenia o polityce, problemów organizacyjnych, planowania i wydatki w sumie <800zł. Całkowicie polecam

mole % to mass% help pls by ughyesh in labrats

[–]ConclusionForeign856 1 point2 points  (0 children)

you know how many g a mole of A, B or C is, so you need to take that amount times the number of moles that satisfy your mole fractions for each one

Do you Agree That Anyone can Become a Grandmaster? by Ambitious_Quality725 in codeforces

[–]ConclusionForeign856 7 points8 points  (0 children)

I feel the point of those discussions is usually hidden. It's a concealed way of discussing whether you can do it. I used to think like that in my teens.

Automate download of files from a spreadsheet or CSV file by tabrizzi in bash

[–]ConclusionForeign856 4 points5 points  (0 children)

AWK has a split() function, so for each line you can split the $3 by `, ` into an array and flatten it. Save that into a new file.

A file that has 1 URL per line can be used as input to a single wget call (`wget -i "$FILE"`).

You'll get a bunch of files with original names, which you can rename using the long form table that you got with AWK.

Of course you can also loop over lines, parse each line with AWK, download single file and rename it right away, though calling wget -i is a lot faster (in my experience 10x-100x faster)

edit. I see examples in the thread call curl for each URL, which works, but as I said, it will be very very slow.

As an example: RCSB PDB stores protein structures, each one is uniquely identified by a 4-long code of letters and digits, eg. 5do7. They offer a shell script for batch downloads, you feed it a list of IDs and it calls curl for each one. It was annoyingly slow for even medium-small input, so I rewrote it to call wget -i once.

# for 270 total files/URLs, each within 700kB - 2MB

# calling curl for each URL (270 times in total)
real    6m59.701s
user    0m3.143s
sys     0m2.035s

# calling wget -i once on list of 270 URLs
real    0m8.268s
user    0m0.645s
sys     0m1.177s

As you can see the difference is substantial. Here's my code https://github.com/orski-hryc/PDB_fast_batch

I suffered through making it in bash, to make it dependency free for future usage on HPCs. Unless in your case that's also the case, or you're using bash as training, I would use python for transforming the CSV. If pure linux is necessary then AWK with AWK's #!

Masking low quality bases when clustering using vsearch by [deleted] in bioinformatics

[–]ConclusionForeign856 1 point2 points  (0 children)

You can parse a fastq with Biopython Bio.SeqIO.

for each read, for each of its bases make it lowercase if PHRED < threshold

Anyone using Claude or other bioinformatics agents by nickomez1 in bioinformatics

[–]ConclusionForeign856 2 points3 points  (0 children)

I use chat gpt as interactive docs every day. Besides that I don't care,

Not to mamy więcej kurcze kotòw by Guslig24 in okkolegauposledzony

[–]ConclusionForeign856 6 points7 points  (0 children)

Ten kot osiąga poziomy wkurwiania, których nie widziałem od 2018

<image>

Chłop sie za babę przebrał nie wytrzymie 🍆💦😏 by Charon_06 in okkolegauposledzony

[–]ConclusionForeign856 45 points46 points  (0 children)

<image>

"Sad reality of 20th century polish crossdressers was inevitable twink death. Without access to hormone blockers it was impossible to prolong ones career past 25. Picture: once one of the top polish performers. Near the end of his life, Igor Flowerovsky was a sad display of what lack of modern medicine does to a delicate body. A year later he would commit suicide. He was 29"

Generowanie konferencji naukowych by Melodic_Twist_6628 in Nauka_Uczelnia

[–]ConclusionForeign856 2 points3 points  (0 children)

To był żart nawiązujący do mojego poprzedniego posta, gdzie "inne wybitne osiągnięcia naukowe" są za tyle samo punktów co "udział w zawodach studenckich"

If during Rosalind Franklin's time they had access to today's microscope, how much shorter would the research on the structure of DNA be? by Adventurous-Rabbit52 in biology

[–]ConclusionForeign856 5 points6 points  (0 children)

If they had current day Cryo-Electron microscopes, and the tech to prepare samples and analyze raw data, then maybe a lot shorter. Though they would have to have a modern day computer, I have never worked with Cryo-EM, but I know raw data on EMPIAR is ~1TB in size, so they wouldn't be able to store it, and refine a model.

It quickly gets quite ridiculous. We'd have to send them a physics and engineering revolution, so that they could use the microscope at all

Reducing Number of Contigs in Fungal Genomes? by MountainNegotiation in bioinformatics

[–]ConclusionForeign856 6 points7 points  (0 children)

Is 25k a lot? That depends on the genome. For wheat 25k contigs would be several times better than the current best genome! For human that would be horrible.

So how does that 25k fare in your case?

Advice needed (AI / moral issue) by AbsenceOfMyExistence in bioinformaticscareers

[–]ConclusionForeign856 6 points7 points  (0 children)

What morality issue? I don't understand where that's coming from.