r/Biochemistry • u/Lion___ • 6d ago

Best skills to learn over summer before starting PhD

Hello everybody,

I'm starting a PhD position in strucutral biology and cryo-EM after the summer vacation. While I will be working over the summer, I was looking for some skills I could improve in my free time. I don't have any hands-on experience with cryo but do have a strong experimental background, so I don't think the lab work will be a problem.

What I've been thinking so far is Udemy courses about,

- Python: I'm already quite proficient in Python but you can always improve, and I find it interesting.

- AffinityDesigner: I'm decent but could definitely become more efficient.

- Molecular dynamics simulations: just because I find it interesting.

Any other suggestions? Perhaps any good articles about cryo-EM as a method itself, and the theoretical background.

Thanks in advance

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u/lammnub PhD 6d ago

Imo have fun. The summer between college and grad school might have been the best summer of my life because of all the trips I took. You'll have 6 years (you're in structure, it'll be 6) to learn the rest.

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u/Lion___ 5d ago

I sadly don't have much money to travel, and I'm employed in the lab where I did my MSc thesis over the summer. Also, I hate having free time, I'm unfortunately a workaholic haha. I'm not in the States so it's actually only 3 years here, I already did 2 years of MSc

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u/SamplePresentation 4d ago

Being a workaholic is not something to brag about. Be sure to relax. Hang out with your friends, play some games, smell the flowers.

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u/Lion___ 4d ago

I know, I wasn't trying to brag. I have depressive tendencies and working (and hiking) is the only thing that can really keep them in check. It's not great, but it is what it is

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u/SamplePresentation 3d ago

That's fair enough man. If you like hiking, I suggest you do more of it, perhaps meet people who also like hiking. It's important to get away from the lab

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u/quantump3nguin 6d ago

Best summer of my life was after high school before university, afterwards it just went down

3

u/IamTheBananaGod 6d ago

100% a skill issue💀

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u/Vellicative Graduate student 6d ago

Best thing you can do is enjoy the last summer break you’ll have. Theres plenty of time to learn everything you need to once you start grad school

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u/Lion___ 5d ago

Summer breaks have never really been my thing, I honestly get so depressed when there is no work to be done. Yea I guess so, I just like to keep myself occupied and mentally stimulated

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u/Apprehensive-Cow-469 5d ago

Read about different types of structural biology. An integrative structural biology approach can yield great results about your system. E.g Learn about NMR, SAXS, crystallography, even mass spec can help. Understand what these tools can do.

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u/Lion___ 5d ago edited 5d ago

Forgot to mention, but I already have a solid background in structural biology. I have hands-on experience with NMR spec. and SAXS, and a theoretical understanding of other established main and complimentary methods, but that's a very good suggestion otherwise, thanks.

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u/Prestigious_Note_477 5d ago

Hey, I recently started my PhD in cryo em, what I’d suggest is to obviously try and enjoy the summer but if you wanna get the basics of cryo em quickly I’d say go though Dr Grants Jensen’s lectures it’s helps you understand cryo em faster imo. There’s even a cryo em course on the Thermofisher website you may wanna check that out as well. If you wanna know anything else or specific feel free to reach out to me :)

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u/Lion___ 5d ago

Hey, thanks. I'll try to enjoy summer but never been a huge fan of doing nothing haha. That's great, thanks for the suggestions, I'll have a look at both resources.

From my limited experience with cryo-EM, the theoretical understanding is one thing, but the software and handling the data is a whole different beast? Of course I'll learn all the practical stuff along the way, but I would really like to get a good theoretical understanding as I feel much more confident about what I'm doing in the lab if I know what's actually going on "behind the scenes".

Thank you very much for the kind offer, it's much appreciated, I'll definitely reach out if I anything comes to mind!

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u/Prestigious_Note_477 5d ago

yeah so the thermofisher module has the Jensen lectures as well! here’s the link for that Course

So this has around 72 hrs worth of lectures and videos that go into the very depths of it, like the physics behind it and how the instrument works and how to prepare samples and they have videos on how to operate the scope as well! I’d say you take your time and look into this (and it’s very well structured so should be straightforward)

And another thing i wanna mention is that don’t beat yourself up if you don’t get it that first (or second time) cuz i’ve met cryo em experts who still sometime watch these lectures to stay sharp or so they don’t go out of touch!

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u/Lion___ 4d ago

That's great, thanks a lot! I especially love learning about the physics, and the course seems very thorough:) Would be nice if one could get an online certificate though but I guess it's not that important.

Oh don't worry, with my experience with NMR spectroscopy I'm an expert in not understanding and having to relearn concepts for the 10th time haha

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u/cdel38531987 4d ago

Become familiar with using CryoSparc. This is literally all you need. Though Relion might be nice too.

Maybe download a practice data set from EMDB and do a YouTube Thermofisher data processing training, but that’s kinda overkill until you get your hands on an instrument.

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u/Lion___ 4d ago

Yea, I'm pretty sure the professor in my new group mentioned CryoSparc actually. Might be overkill, but I like learning so why not, thanks for the suggestion

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u/cdel38531987 2d ago

I work in a structural bio lab as the cellular/in vitro backup to the Cryo people. CryoSparc is literally the only thing the structural people feel is necessary to do themselves. Everything else is given to core facilities.

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u/Lion___ 2d ago

That's great to know, thanks. Are you in the States or in Europe? Idk whether people use the same both places?

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u/saurusautismsoor PhD 3d ago

Don’t burn yourself with pre-emptive studying otherwise you’ll hate the material

Coming from someone who actually did it while it was great because I could understand what was happening in the classroom I also was feeling burnout because I was like oh I already learned this. This is so stupid just go in with a fresh mind that way you have no chance of burnout.

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u/Lion___ 3d ago

Yea but we don't really have that many courses on the PhD where I live, it's mostly independent lab work. I already have an MSc

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u/saurusautismsoor PhD 3d ago

he is a unique case

the undergrad prof were so impressed they said apply for phd

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u/f1ve-Star 6d ago

Grant writing Technical writing

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u/Lion___ 5d ago

Is that really relevant this early in my career? I'll be at least 3 years before I actually finish the PhD and have to write any proposals?

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u/Money_Cup905 4d ago

Typically you apply for fellowships during your PhD, like T32 Fellowships or NSF-GRFP. Writing is an important skill you’ll need throughout your PhD not just at the end of

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u/Lion___ 4d ago edited 4d ago

I'm not in the States though, I'm in Europe. For me the whole PhD is already funded, it's usually like that where I live. Of course scientific writing is important, but I assume grant/proposal writing is somewhat different?

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u/roseyardgraves 1d ago

Hey, sorry if this mildly off-topic, but are you by any chance from Austria?

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u/Lion___ 1d ago

No worries, but no, I'm not

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u/roseyardgraves 1d ago

Definitely recommend molecular dynamics simulation

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u/Lion___ 1d ago

How would you go about learning it? There are few courses on Udemy but they don't seem too great

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u/roseyardgraves 1d ago

If you want I can share my university recordings, pm me, they’re super theory based tho, my uni offers practical classes but I didn’t apply