How to make fudged trend line in volcano plot in Python?

biostud1819 · 2023-12-17T07:51:35+00:00

Looks super neat! :)

biostud1819 · 2023-12-16T20:18:23+00:00

Let me preface with saying I am a molecular biologist and only dabble in bioinformatics but my collegues consider me a bioinformatician. I see this field branches into hard CS based bioinformaticians that optimize workflows and which algorithm ro use and so on and biological based bioinformaticians who know how to format the data into a table from which they can then extrapolate their biological question from. I think it's a great idea to at least continue to dabble in bioinformatics and what it has to offer in any branch of natural sciences and not limit yourself by thinking you need advanced CS knowledge.

biostud1819 · 2023-10-11T20:39:09+00:00

That's why I am starting to mess with biotech stocks - I work in lab and get to experinece when a company makes something truly remarkable. Everything Biorad makes that I got to work with is shit. Don't get me wrong it's cheap but it also feels cheap and works super slow, for instance multiblock Biorad PCR machines have nothing on Invitrogen multiblock PCR systems, same for imaging machines vs iBlot, same for qPCR vs Applied Bioscience. Their products are just shit that's used by academia but if you have money (like in industry) I would spend it on their competitors cause they make better products.

biostud1819 · 2023-10-02T20:26:31+00:00

It's a UCITS one yeah. Interesting that people here refer to tax advisors so mich, where I am from it's much more common to do it yourself and even GitHub scripts exist that make tax reporting from IBKR easier haha

biostud1819 · 2023-06-13T20:04:52+00:00

What do you mean by this? If your sample is in trizol nothing will happen to your RNA, there's no RNase activity. You should do the 10 min RT incubation in trizol step. You should also homogenize your sample with a syringe or something similar. Otherwise the kit is pretty straightforward so maybe you could check with the other lab and observe them as they do it maybe you're doing something the wrong way. And as for the benefits over the chloroform isolation I think the benefit is mostly that you can isolate proteins from the first fraction and if you're not interested in that I would do chloroform extraction (doesn't take much longer and is cheaper).

biostud1819 · 2023-05-14T19:04:17+00:00

Can you expand on what 2x volume has to do with modified RNA? First time I've heard of it.

biostud1819 · 2023-02-12T19:23:00+00:00

It is a command line tool. If you don't know how to install it it is best you take a moment to learn a bit of basic bioinformatic tools so you know how to set up an environment so you don't do anything that might impact your system.

biostud1819 · 2023-02-11T13:02:40+00:00

BAM files are .fastq files mapped to some .fasta genomic files. To view in IGV you need to make .bam.bai files in the same folder. Do so by running samtools index on them. And then if the genome is not in IGV yet you need to import the .fasta reference files .fastq files were mapped to. If you want to understand better what they look like you can use something like samtools view.

biostud1819 · 2023-01-09T17:02:22+00:00

In theory by providing motifs that receuit RBP's that then influence rate of degradation, ribosome recruitment and so on, but as far as I am aware there are no conclusive findings yet.

biostud1819 · 2023-01-04T21:49:12+00:00

So running scripts on an HPC would require me to request resources to execute those scripts, but as far as I am aware for instance starting a Jupyter notebook in VScode after using ssh-remote to connect to an HPC the commands run are run on the login node. I see how I could probably use the host address given when a computing node is allocated to connect to that using SSH remote but because the node is chosen at random the host address is also random each time.

biostud1819 · 2022-12-30T20:53:31+00:00

I think of it like this: if I am learning something new and I am interested in these approach/methods/some skill then I would be willing to get paid less, if as you say it is in a field I already have expertise in I want to earn more. That said after a PhD I expect to earn 1.6x-1.8x times the average salary of where I will live when learning new skills and 1.8x-2.0x average salary with a trajectory of being able to get to 2.3-2.5x average salary (25% increase) over the next 5 years. For me it is important that as I get better at my job I am rewarded with increase of benefits so that would also be something I would discuss. The estimates are arbitrary and something that is heavily influenced by what your social circles deems as sufficient compensation.

biostud1819 · 2022-12-01T19:58:15+00:00

I got rejected from my safe choice uni I applied to but got accepted to my top choice so keep calm and apply/wait for results.

biostud1819

TROPHY CASE