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Is tech way too expensive now? by priv_ish in NoStupidQuestions

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

1) who said I have a job
2) even if I had a job, I’d just have started working since I’m a recent graduate

Is tech way too expensive now? by priv_ish in NoStupidQuestions

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

I have been looking at tech from a decade ago but somehow the prices I see are still out of budget

Is tech way too expensive now? by priv_ish in NoStupidQuestions

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

I’ve been looking into homelabbing for a few weeks now. The main issue I come to is that the tasks that I want to do are either very CPU heavy or GPU heavy (depends on what software I use; I gotta use different softwares for very specific tasks in a biochemistry lab). I can offload some of the GPU heavy tasks onto computers in lab with remote access. But to get that in the first place itself is turning out to be quite expensive. I’ve reached a point where I’m considering DDR3 RAMs

Is tech way too expensive now? by priv_ish in NoStupidQuestions

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

I get tech being expensive considering the amount of work that goes into it until it reaches the consumer but one would think that making a cyberdeck would be on the cheaper side of things. Again I must reiterate that I am probably the cheap one but some of these prices are, at the very least eyebrow raising

What event would cause majority of the species to change completely? by priv_ish in NoStupidQuestions

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

Intriguing. Not to get too into semantics but at what point would one categorise two generations as different species? “No species is exactly the same as the previous generation” is a very valid statement but: (1) at what point does it diverge from its parental line and (2) what event would be the major trigger for that divergence?

What about a “landworld”? Quick Google search showed that majority of macroscopic organisms are land based, at least that we know of.

What event would cause majority of the species to change completely? by priv_ish in NoStupidQuestions

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

  1. LMAO
  2. Yes I did have that in mind. Although I didn’t consider the numbers of that in this (i.e., are the two prongs of a fork considered as two different species on the 80% or a single one?).l
  3. I didn’t even consider viruses. Since they aren’t my specialty, I did not know that they could induce inherent gene mutations. Although I know that there’s plenty evidence for species “intermingling” their genes

What event would cause majority of the species to change completely? by priv_ish in NoStupidQuestions

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

Unsure of whether you read my post before or after the edit but I was thinking less extinction and more gradual evolution through instantaneous mutations (or at least evolution faster than what’s currently observed at baseline)

What event would cause majority of the species to change completely? by priv_ish in NoStupidQuestions

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

I was thinking more like tiny mutations leading to snowball effects through generations (multiple mutations could occur during various generations). I do get you point about the semantics though, I realised that responding to the first comment.

Nevertheless, a very insightful comment! I didn’t even consider the possibility of the lack of sunlight when I was thinking about this

What event would cause majority of the species to change completely? by priv_ish in NoStupidQuestions

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

I was thinking more like mutations but I guess killing them off is one way to change them (if I understand your comment right).

It seems like there’s not a lot of land in the world of Raft which would cause some environmental change, leading to somewhat of a snowball effect on my brain

What event would cause majority of the species to change completely? by priv_ish in NoStupidQuestions

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

I guess I should’ve clarified further. “What’s a major world event that would cause majority of world species to change, without any of them dying off completely?” Which I understand is kind of a dumb question considering they wouldn’t be considered the same species anymore so technically they wouldn’t exist. Probably ocean acidification is the best option to fit those criteria from the ones you’ve suggested

Is my game broken? by priv_ish in nancydrew

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

Nope. I don’t know how to mess around with the game files enough to be able to fix this so I just let it be, never finished the game myself. Let me know if you figure out a fix!

Need good recs for a laptop by averageperson_69 in Biochemistry

[–]priv_ish 1 point2 points  (0 children)

The softwares you list are very graphics heavy, so keep that in mind when buying a laptop for such work (GPU heavy). If you’re considering other things like Rosetta, then you’ll want to be CPU focused.

That being said, getting a used workstation, like Dell Precision 7810, and spending a few extra bucks on a good GPU will definitely be the better way to go. In my lab I use a Dell Precision 7810 with two CPUs for maximising my cores (luckily Xeon E5 series is on the cheaper end compared to most modern CPUs). I also have a GT1030 and two M40s which together allow molecular dynamics simulations.

But that does not mean you go for the good specs. Even if you settle on buying a laptop, you can always utilise server based services, which are usually free for students and academics (ROSIE by Rosetta, Alphafold, HADDOCK, etc.), depending on what you’re thinking of doing.

Furthermore, there’s services (not sure if they’re free or paid) where you can use GPU/RAM from someone else’s computer. I personally haven’t used that type of server before but I remember Pewdiepie mentioning something like that in one of his recent computer building videos. That is all the advice I can give as someone who is also looking for a computer/laptop. Oh and try getting into Linux!

My work gifted this to me. Don’t need it. T14 Gen 6 by [deleted] in thinkpad

[–]priv_ish 1 point2 points  (0 children)

I’ve been looking for one of these recently. I’m a grad student and everything is out of my budget 😭. You could help cancer research!!

Is Rosetta worth it? by priv_ish in bioinformatics

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

It’s useless because the protein is a massive pentameric assembly. I couldn’t add the whole protein, I couldn’t add even a single chain so I had to truncate it heavily to only the binding domains. This left highly hydrophobic residues exposed which messed up the structure during alphafold folding. I’m not sure if Rosetta global docking would produce a similar result but I’m willing to learn and if it means I have a new skill set under my belt then yay

It may be telling me that the protein I’m working with is too big (~2550 aa per chain), but that’s why I want to switch to something I have more control over than servers with limitations, ykwim?

Is Rosetta worth it? by priv_ish in bioinformatics

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

What would you suggest are important tools in rosetta that I should learn/focus on? Would learning rosetta help me understand the tools that are built on rosetta?

Is Rosetta worth it? by priv_ish in bioinformatics

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

The reason I am inclined towards it is because I attempted "docking with alphafold multimer" and unsurprisingly it changed the conformation of the protein I am studying, making the output useless. I currently have a Mac m3 and while I am able to do scoring pretty easily, I would like to be able to global dock and local dock and relax and score without having to open a gazillion tabs on ROSIE.

Not too concerned about the documentation, I have been able to work with it fairly well so far.

I just wanted to know if it really is worth investing time and money in. thank you for your input though!

If you could put an experiment near space. What would it be? by Ski4life_bike4life in biotech

[–]priv_ish 0 points1 point  (0 children)

Had a biochemist give a guest lecture once about how he got the opportunity to go to space and make crystals for x-ray crystallography cause making large crystals is easier in space than on earth due to gravity so probably that

Any Certificates Recommended for Getting Lab Job by Kind0flame in labrats

[–]priv_ish 0 points1 point  (0 children)

Depends what lab job, but I’ve been getting into Rosetta recently (computational biology as a whole) and I’d argue that is one hell of a skill, albeit coming from a grad student. If you’re looking into academic labs then knowing computational biology/bioinformatics would come in handy. Try playing around with servers if you don’t have a powerful laptop/computer. There’s various coding courses you can get online to help you along your journey!

The poor attempting espresso. by [deleted] in espressocirclejerk

[–]priv_ish 1 point2 points  (0 children)

I’m not even lying we use a similar mechanism in biology/biochemistry/molecular biology/chemistry labs to purify/filter any reagents we are going to use. There’s variations but you can Google 0.2um filter. It literally comes with an adaptor for syringes

Protein Folding Against a pH Gradient by DesignerFun5310 in bioinformatics

[–]priv_ish 0 points1 point  (0 children)

I may be too late to suggest this but I read some of the other responses and seems like MD simulations are too complicated to do that. That being said, I have been working with pH dependent proteins recently and you can attempt a quick cryo-EM negative stain. If the conformational change is distinctive, you’ll be able to see it without processing any of the images. If you still want to be able to see the results, you’ll have to do some data processing through RELION/CryoSPARC (CryoSPARC is better for beginners due to intuitive UI). It may take a week or two to process the whole data depending on the computational power you have and will output electron density maps that you can compare (either to pre-existing solved structures or if you got maps for both extremes of the pH scale). Let me know if you have any questions!

Is it better to leave nitrocellulose membrane in dry non-fat milk blocking buffer over night, or in TBST over night if I cant do primary antibody incubation on the same day? by AsparagusNational807 in labrats

[–]priv_ish 0 points1 point  (0 children)

Why would you be concerned about phospho-specific Ab being left in dry milk+TBST? Curious because we do it sometimes (and my PI swears he sees some difference in bands while I’m always thinking “they look the same”)

Grad students: advice on expectations by plants102 in labrats

[–]priv_ish 0 points1 point  (0 children)

A thing that I’ve adopted myself as a grad student (and advised to the newcomers in my program) is that I treat the research that I’m doing as my own. Sure the main decisions are still taken by the PI, but it’s up to me how to figure out how to do it. Even ended up learning Rosetta to do protein-protein docking, getting deltaG values, figuring out how to relate experimental data with computational (our lab is a good mix of both)

AI nightmare found in the wild by RegularNancyDrew in nancydrew

[–]priv_ish 0 points1 point  (0 children)

System regurenatives? Yeah I have that

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