Still Just a Rat in a Cage - Laboratory Chat!

The Something Awful Forums > Discussion > Ask/Tell > Business, Finance, and Careers > Still Just a Rat in a Cage - Laboratory Chat!

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mycomancy: Oct 16, 2016

I cut my teeth on Geneious way back in 2008. The software has gotten pretty advanced, but their subscription model is loving garbage and I won't patronize a company who pulls that poo poo. Either I own this software or I don't, I'm not renting it from you fucks.

I have yet to find a replacement. Benchling works but I feel like it's missing something and I can't narrow that down.

# ¿ Aug 2, 2021 12:19

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# ¿ May 7, 2024 02:58

mycomancy: Oct 16, 2016

Bastard Tetris posted:

Benchling scales HORRIBLY. In HTS environments the browser chokes hard when handling large datasets.

Lol lmao I build my own HTS pipelines using python and command-line software. Geneious and Benchling are mostly relegated to annotation visualization and primer design/storage.

# ¿ Aug 5, 2021 12:49

mycomancy: Oct 16, 2016

Bastard Tetris posted:

my man

also you don’t work with a bunch of protein scientists on the edge of retirement that don’t give a fuuuuuuck about any of this

Ugh, old biochemists are some of the crankiest of all the life scientists. I think only old female ecologists are crankier, though they usually have much better reasons to be cranky.

# ¿ Aug 10, 2021 21:01

mycomancy: Oct 16, 2016

That Works posted:

Old microbiologists, at least the ones who aren't sexpests, are generally high functioning and cheerful alcoholics.

Good company usually.

I feel seen

# ¿ Aug 12, 2021 13:40

mycomancy: Oct 16, 2016

Cardiac posted:

Or do cold shocks (not on the undergrad) with calcium competent cells.
I have horrible memories of an electroporator.

Chem comp cells are a pain in the rear end for anything other than Gibson cloning.

As for the electroporator, how is it broken? I've actually repaired one before that simply had a bent electrical contact. Once I straightened it out it worked great.

# ¿ Oct 5, 2021 17:48

mycomancy: Oct 16, 2016

mycomancy posted:

Chem comp cells are a pain in the rear end for anything other than Gibson cloning.

As for the electroporator, how is it broken? I've actually repaired one before that simply had a bent electrical contact. Once I straightened it out it worked great.

I say this as I literally am walking to lab to dunk cold cells into warm water like a loving caveman.

# ¿ Oct 5, 2021 17:49

mycomancy: Oct 16, 2016

married but discreet posted:

Well what happened is that the undergraduate jammed in a cuvette sideways like the huge brute he is, it got stuck and the whole thing had to be taken apart and the cuvette needed to be cut out with a knife. Now the contacts seem to be misaligned but not to the point where anything is obviously wrong, apart from the fact that there's no transformants. We'll see if its repairable and in the meantime just use some other labs electroporator.

Are you getting strange time constants from empty cassettes or cassettes filled with millique water?

# ¿ Oct 5, 2021 18:18

mycomancy: Oct 16, 2016

married but discreet posted:

The opposite, I can literally spit into a cuvette and get normal time constants/no arcing. It's probably the contacts not touching anything.

Yeah the copper clamp inside is bent. Open it up, bend it back into place, and I bet it works fine. My clamp was bent the other way, was sparking on an empty cuvette.

# ¿ Oct 6, 2021 01:00

mycomancy: Oct 16, 2016

Grad school is like surgery. Don't do it unless not doing it will kill you.

# ¿ Nov 8, 2021 14:07

mycomancy: Oct 16, 2016

Dik Hz posted:

I'd love to know this mythical grad school where you learned project management. I've never seen anyone in an academic setting do even the slightest bit of competent project management.

I feel attacked by this post.

In all seriousness, how does one learn good project management skills? Is this something you can learn from a course?

# ¿ Nov 16, 2021 01:43

mycomancy: Oct 16, 2016

Development posted:

annual harassment training is wild

...the lab manager is in the wrong here?! What on earth.

# ¿ Nov 22, 2021 17:58

mycomancy: Oct 16, 2016

I've been having some serious angst about my scientific career lately. A lot of it comes from learning about Marxist perspectives on labor, which I did not have when I started graduate school. All my advisors, and probably most of y'all's, 100% abused my labor and the labor of my peers to produce data to elevate their position without providing nearly the quality or quantity of training necessary to produce a functional scientist at the end of it. I mostly got very very lucky with my connections to enable me to get this far in a scientific career without ever winning a single finding award. Still, I'm so sick of this career and the god drat rich coastal cunts who infest it.

I don't really know what I'd do outside of science though. I loving hate teaching, or really any job where I have to interact strongly with people because I think the last two years have shown the kinds of people with which this world is populated.

Maybe I'll just hike into some woods and never come out.

# ¿ Dec 16, 2021 00:35

mycomancy: Oct 16, 2016

Epitope posted:

Take enough food and gear to support a return, maybe bring back a spiritual awakening. Or at least some good posts.

I think you missed the part about never coming.

It's a fantasy regardless, I'm the sole breadwinner for a family of four, so I'm trapped.

# ¿ Dec 16, 2021 01:14

mycomancy: Oct 16, 2016

Epitope posted:

I saw that, and figured it was a joke, but kinda felt obligated to say "don't do it." Of course what I'm really doing is trying to exploit your posting labor

Posting is a pleasure, sir/madame/mixter.

# ¿ Dec 16, 2021 02:11

mycomancy: Oct 16, 2016

Cardiac posted:

There is a life outside academia, you know.
Of course exploitation is a fact, but at least it is not hidden by a veneer of science as it is in academia.

I'm actually not in academia per se anymore. What I'm saying is that I feel all the bullshit that begins in academia pervades the entirety of modern science and it loving bums me out.

Bastard Tetris posted:

PM me if you wanna talk candid HTS career chat

If HTS = high throughput sequencing, that's technically already part of my career. Nanopore-seq owns.

# ¿ Dec 16, 2021 13:13

mycomancy: Oct 16, 2016

Epitope posted:

Working in science is still very much in service to the empire/capital. The myth that we're somehow separate or above that, "building the body of human knowledge" or whatever, is probably part of the scam to exploit labor. I'm no revolutionary, so, well, despite all my rage I am still just a lab rat in a cage

# ¿ Dec 16, 2021 18:26

mycomancy: Oct 16, 2016

You're absolutely right Epitope. I hear people at my new job whinge about the current trend to disallow scientists to sponsor postdocs and grad students, and my retort is always "good, do the work your own god drat self."

Well I don't say it in those meetings, but I think it very strongly.

# ¿ Dec 16, 2021 18:27

mycomancy: Oct 16, 2016

global tetrahedron posted:

Any posts/goon-recommended resources concerning leaving academia forever with a PhD and related job prospects/ideas for careers?

My partner recently finished her evolutionary biology degree and cannot stand academia and wants out. She has a temporary visiting professorship position currently, and perhaps a postdoc if she wanted to continue to commit, but at this point it's all very clearly deleterious to her mental health so she's basically saying "gently caress it". All her friends in her department are trying to get out as well, i know she can't be alone since the politics and working conditions of academia seem absolutely appalling.

She has some coding experience, and is vaguely interested in science communication, but that doesn't seem like a field that you can break into easily. A lot of what's coming up are corporate data analysis jobs, which she isn't completely adverse to, she's just open to any creative or non-intuitive ideas, and still would like to do something vaguely 'pro social' which a job with a bio med company probably wouldn't provide.

She hadn't thought she'd be in this position even a couple years ago and feels a little stuck. It really sucks to watch her struggle! I don't think I could ever internalize what spending years of your life on something for what ends up feeling like nothing would do to your psyche.

e: she also likes teaching a lot! if the field were just educating the Youth she would love it, it's the cutthroat bullshit and publishing she can't stand

Three words: liberal arts university. There's a number of them that have strong biology programs, you just have to look around.

# ¿ Jan 14, 2022 02:58

mycomancy: Oct 16, 2016

So over the last 10 days I've attempted to fragment eleven gDNA samples from two different people using NEB's fragmentase. I have eaten piles of poo poo each time, but the E. coli HMW extraction I made myself works great!

Turns out fragmentase is just a finicky little bitch of an enzyme. I amplified all my samples with Qiagen's Repli-G kit, magbead cleaned the products, and bam! worked like a charm.

The moral of this story: no one can extract clean DNA anymore, kits have turned two generations of scientists into slackjaws. Guess I'll just clean every sample I get ahold of because I can't lose two weeks at a time just because Jimbob at NREL decided he didn't wanna wash that column twice.

# ¿ Feb 2, 2022 03:46

mycomancy: Oct 16, 2016

global tetrahedron posted:

thanks! she's definitely looking into getting everything onto github. the decision to exit academia came a bit quickly so she's playing catchup a bit.

here's her redacted resume, she's primarily looking for feedback on how to translate the academic research into project descriptions, the work was very theoretical and seems hard to explain simply and has no real practical applications. academia sounds like a real bitch! she hasn't made a resume in ages, was always a CV so this is our first stab.

Oh my dude, that's all just way too dense for business dumbasses. Like 10 word max sentences with a 10-grade vocab level and lots of white space.

# ¿ Feb 6, 2022 02:08

mycomancy: Oct 16, 2016

Dobbs_Head posted:

Yeah, this is too dense. It’s actually hard to extract information from it. Make it way more linear, and it’s ok to go to 2 pages but make sure the most important bits are at the front.

Break it into sections. Since she’s coming from a grad program put education on top. Follow with projects an publications, etc.

Make the project titles bigger and cut down the descriptions. The goal is to communicate the core skills she got from the project and the gist of the topic. Also, if the project resulted in a publication LINK IT (doi, github address, patent #, etc.).

(Not a big deal but I kinda chuckled at calling 20 GB a large dataset.)

Lol I missed that

*glances at my 300 GB MinION run still accumulating reads*

# ¿ Feb 6, 2022 02:45

mycomancy: Oct 16, 2016

Dobbs_Head posted:

It’s the code itself. Look how the dude reads files. He iterates over folders and reads the files with pandas like a normal human and then concats them. I mean, he winds up reading them 3 times each because he doesn’t use open / readline to parse the headers but that is normal hacky stupid.

Rather than passing the list of dataframes directly to concat, he hard coded lists up to length 15 and then raises an error if there are more than 15 files. There is no earthly reason for this, other than he didn’t know that concat can take a variable sized list.

Then look at the model functions. He has functions with names like RC37, where he literally hard coded a finite sum from a list with 37 elements. It’s bonkers, and the only explanation is he didn’t know how for loops and zip work. Thousands of lines of code where he needed only a few serving as a monument to the author’s determination to not learn the basics of iteration.

Then there is how analysis is done. Rather than cleanly splitting model definition, fitting and display he’s got monster functions that do it all at once. The tool can’t be adapted outside the scope the author imagined because of this design choice. Imagine trying to systematically fit a few thousands EIS curves and having the tool write a ding dang matplotlib figure for each!

The worst part is he put his name and contact information in every docstring, so you remember exactly who thought writing that buggy crap was a good idea.

I'm a terrible coder, but at least I'm ashamed enough to not have a GitHub.

Also gently caress me I'm way better than this clown.

# ¿ Feb 9, 2022 13:12

mycomancy: Oct 16, 2016

Greatest Living Man posted:

lmmaaaaooo you weren't kidding

code:

        # adds individual dataframes into one
        if len(self.df_raw0) == 1:
            self.df_raw = self.df_raw0[0]
        elif len(self.df_raw0) == 2:
            self.df_raw = pd.concat([self.df_raw0[0], self.df_raw0[1]], axis=0)
        elif len(self.df_raw0) == 3:
            self.df_raw = pd.concat([self.df_raw0[0], self.df_raw0[1], self.df_raw0[2]], axis=0)
        elif len(self.df_raw0) == 4:
            self.df_raw = pd.concat([self.df_raw0[0], self.df_raw0[1], self.df_raw0[2], self.df_raw0[3]], axis=0)
        elif len(self.df_raw0) == 5:
            self.df_raw = pd.concat([self.df_raw0[0], self.df_raw0[1], self.df_raw0[2], self.df_raw0[3], self.df_raw0[4]], axis=0)
        elif len(self.df_raw0) == 6:
            self.df_raw = pd.concat([self.df_raw0[0], self.df_raw0[1], self.df_raw0[2], self.df_raw0[3], self.df_raw0[4], self.df_raw0[5]], axis=0)
        elif len(self.df_raw0) == 7:
            self.df_raw = pd.concat([self.df_raw0[0], self.df_raw0[1], self.df_raw0[2], self.df_raw0[3], self.df_raw0[4], self.df_raw0[5], self.df_raw0[6]], axis=0)
        elif len(self.df_raw0) == 8:
            self.df_raw = pd.concat([self.df_raw0[0], self.df_raw0[1], self.df_raw0[2], self.df_raw0[3], self.df_raw0[4], self.df_raw0[5], self.df_raw0[6], self.df_raw0[7]], axis=0)
        elif len(self.df_raw0) == 9:
            self.df_raw = pd.concat([self.df_raw0[0], self.df_raw0[1], self.df_raw0[2], self.df_raw0[3], self.df_raw0[4], self.df_raw0[5], self.df_raw0[6], self.df_raw0[7], self.df_raw0[8]], axis=0)
        elif len(self.df_raw0) == 10:
            self.df_raw = pd.concat([self.df_raw0[0], self.df_raw0[1], self.df_raw0[2], self.df_raw0[3], self.df_raw0[4], self.df_raw0[5], self.df_raw0[6], self.df_raw0[7], self.df_raw0[8], self.df_raw0[9]], axis=0)
        elif len(self.df_raw0) == 11:
            self.df_raw = pd.concat([self.df_raw0[0], self.df_raw0[1], self.df_raw0[2], self.df_raw0[3], self.df_raw0[4], self.df_raw0[5], self.df_raw0[6], self.df_raw0[7], self.df_raw0[8], self.df_raw0[9], self.df_raw0[10]], axis=0)
        elif len(self.df_raw0) == 12:
            self.df_raw = pd.concat([self.df_raw0[0], self.df_raw0[1], self.df_raw0[2], self.df_raw0[3], self.df_raw0[4], self.df_raw0[5], self.df_raw0[6], self.df_raw0[7], self.df_raw0[8], self.df_raw0[9], self.df_raw0[10], self.df_raw0[11]], axis=0)
        elif len(self.df_raw0) == 13:
            self.df_raw = pd.concat([self.df_raw0[0], self.df_raw0[1], self.df_raw0[2], self.df_raw0[3], self.df_raw0[4], self.df_raw0[5], self.df_raw0[6], self.df_raw0[7], self.df_raw0[8], self.df_raw0[9], self.df_raw0[10], self.df_raw0[11], self.df_raw0[12]], axis=0)
        elif len(self.df_raw0) == 14:
            self.df_raw = pd.concat([self.df_raw0[0], self.df_raw0[1], self.df_raw0[2], self.df_raw0[3], self.df_raw0[4], self.df_raw0[5], self.df_raw0[6], self.df_raw0[7], self.df_raw0[8], self.df_raw0[9], self.df_raw0[10], self.df_raw0[11]], self.df_raw0[12], self.df_raw0[13], axis=0)
        elif len(self.df_raw0) == 15:
            self.df_raw = pd.concat([self.df_raw0[0], self.df_raw0[1], self.df_raw0[2], self.df_raw0[3], self.df_raw0[4], self.df_raw0[5], self.df_raw0[6], self.df_raw0[7], self.df_raw0[8], self.df_raw0[9], self.df_raw0[10], self.df_raw0[11]], self.df_raw0[12], self.df_raw0[13], self.df_raw0[14], axis=0)
        else:
            print("Too many data files || 15 allowed")
        self.df_raw = self.df_raw.assign(w = 2*np.pi*self.df_raw.f) #creats a new coloumn with the angular frequency

Aaaaaaaahahahahahaha hahahahaha Jesus H. Christ this is terrible!

# ¿ Feb 10, 2022 13:28

mycomancy: Oct 16, 2016

Lazy enough to write code to do it for me, too lazy to Google Stack Exchange.

# ¿ Feb 10, 2022 13:29

mycomancy: Oct 16, 2016

Dobbs_Head posted:

More lab oriented: just spent a day sorting through working electrodes. Every ding dang one had scratches and chips in them and was useless in CV (our system reverses in the presence of an H2 catalyst, so scratches make an electrode worthless)

Spent hours polishing and couldn’t rehabilitate a single one. Going to need to just toss like $5-10k in electrodes because we couldn’t be bothered to take care of them.

# ¿ Feb 11, 2022 00:59

mycomancy: Oct 16, 2016

street doc posted:

Use your slow hours to get a masters; then move on.

This is a good answer.

# ¿ Jun 13, 2023 23:11

mycomancy: Oct 16, 2016

I have two interns in my lab right now. I told one of them "label these four tubes *plasmid name* then A through D."

I checked today, all four tubes were labeled "*plasmid name* A-D". Four different colonies picked into four tubes with an identical label.

So that's how my weekend is kicking off. If you'll excuse me, I have an appointment with a throw pillow into which I need to scream myself hoarse.

mycomancy fucked around with this message at 20:45 on Jun 16, 2023

# ¿ Jun 16, 2023 20:33

mycomancy: Oct 16, 2016

# ¿ Jun 16, 2023 22:06

mycomancy: Oct 16, 2016

Johnny Truant posted:

I had a master's in biotech ask me if they needed separate pipette tips for different samples when processing blood.

They lasted maybe 2 months, thank gently caress.

what is wrong with people nowadays? I feel like I can't trust anyone to do anything anymore.

# ¿ Jun 17, 2023 12:57

mycomancy: Oct 16, 2016

Alright, my interns have been corrected and I feel much better about my life. Think I'll wait on taking any more rotrons in my lab until my postdoc arrives in October, I can't do all my work while I'm wiping grad student asses.

# ¿ Jun 19, 2023 15:53

mycomancy: Oct 16, 2016

Zudgemud posted:

Repeating an old experiment for a user now and our values fluctuate a lot creating very noisy data compared to the last run. Turns out it is because the tubes we use for sampling are of a different brand since last time because our procurement supplier changed it, likely for cost reasons. So now the tubes vary in weight up to 30 milligrams per tube and the stated dimensions are probably also differing slightly from reality because some tubes can't fit our freeze racks which fit the old tubes of ostensibly the same dimensions

We've been having similar fun times with culture tubes and other "store brand" plasticware. VWR branded items seem to be the most egregious offenders, particularly their electroporation cuvettes and their falcon-style culture tubes. I've had to swear off plastic completely for my thermophile work, as I kept having cultures spontaneously fail for no other discernable reason; I moved to glass culture tubes and it stopped. I suspect they're using a different chemical to release plasticware from the molding, but I don't know for sure.

# ¿ Jun 22, 2023 12:33

mycomancy: Oct 16, 2016

Buy an RNA oligo and see if it degrades in the tube.

# ¿ Jun 22, 2023 18:17

mycomancy: Oct 16, 2016

Washing pipette tips is the maddest loving thing I've heard about in a while.

# ¿ Jun 23, 2023 13:35

mycomancy: Oct 16, 2016

Had a similar experience with electrocuvettes. Ran out of an old batch of VWR cuvettes, opened a new bag then everything started failing either with short time constants or at 6 ms, indicating an open circuit. Switched to Bulldog Bio cuvettes and everything started working again.

# ¿ Jun 23, 2023 14:16

mycomancy: Oct 16, 2016

Johnny Truant posted:

If any of the hospital labs I worked in ever suggested this I would say no and begin polishing up the CV. That's like "no more free coffee" levels of

Were you washing your gloves with methanol and hanging them on a clothesline, too?

Horrible image in my head of de-agaring, washing, and UV sterilizing polystyrene petri dishes

# ¿ Jun 23, 2023 14:17

mycomancy: Oct 16, 2016

Also what on earth requires precision at 20 uL that a non-adjustable pipette can't deliver? Are you counting individual heme molecules in blood?

# ¿ Jun 23, 2023 14:19

mycomancy: Oct 16, 2016

DildenAnders posted:

Hello, I'm a 24 year old who graduated
2 years ago with a BS in Biology from a highly regarded public university (3.9 GPA for what it's worth) currently working in a quality control lab for a pharmaceutical company. The pay isn't great and I really hate the environment, but I've had a lot of trouble in my job search over the last 8 months. I really love lab work (Microbiology in particular) so I was hoping people would have advice for me here.

I'm not looking for anything too specific, as long as I can support myself financially and expand my lab skills. Covid very much hosed me over in terms of networking and bench experience in college (for example, I've only performed 1 Western Blot, and I've never performed DNA extraction, PCR, etc. and I only have 1 iffy reference from 4 years of school) but professionally I have experience with a decent amount of microbial techniques.

I'm also a bit constrained as I need a baseline salary (~$55k) I need to maintain in order to support myself and family members. Since I doubt I can make this kind of money without working full-time, the prospect of going back to school is daunting, but I don't know where else I can develop my lab skills to further my career. Paying for school is another concern as I am not in a position to assume a ton of debt. So, any advice on where I can look to further my prospects? Appreciate any and all input.

Only place I know of that will pay $50k for a guy with two years real life experience to work in a lab full time is one of the national laboratories.

# ¿ Jun 27, 2023 01:15

mycomancy: Oct 16, 2016

The Aardvark posted:

Whistling while skipping to the gun store

# ¿ Jun 27, 2023 02:16

mycomancy: Oct 16, 2016

pmchem posted:

Most fields graduate a sufficiently high number of PhDs that not all, or perhaps not even the majority, will end up gainfully employed at six figure wages. This has been the case for decades. Postdocs have been paid low wages for lots of well known positions forever.

That’s not the system breaking down, that’s how things have worked for like 30+ years. Literally nothing new here.

This is correct. I started my postdoc in Madison making NIH scale, which was $30k. Scientific labor organization is highly similar to that of drug cartels, just with less murder and more humiliation. We should be structured like the trade professions are, but then that might fix the massive class problem in science and we can't have smart, talented people recognizing that they're class bound. That could be bad!

# ¿ Jun 27, 2023 15:49

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# ¿ May 7, 2024 02:58

mycomancy: Oct 16, 2016

CuddleCryptid posted:

What is a postdoc if not a highly educated intern with the pay scale to match?

PhDs can land six figure jobs pretty easily but that is also helped by the fact that they can go into business roles like sales and customer support with a large paycheck fairly well. At least in the large chemical companies I have worked in they were packed to the gills with PhDs in roles that had little to do it with their actual education. You functionally could not be in middle management without a Dr. in front of your name. The B.S/M.S. did the lab work while the PhDs called on customers, with only a few select PhDs in R&D roles that did actual research and design.

I remember once having a manager who would proudly say that he has neither knowledge or experience with the material we were handling and did not want to learn. He was a PhD but it was utterly transparent that he was a ladder climbing scumbag, for that and other reasons.

Unfortunately this isn't true for Bio, and it's definitely not true for postbaccs.

# ¿ Jun 27, 2023 15:57

The Something Awful Forums > Discussion > Ask/Tell > Business, Finance, and Careers > Still Just a Rat in a Cage - Laboratory Chat!

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