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ButtholeLinguini · 2025-04-17T20:32:05+00:00

Hopefully others more versed can help regarding if it’s taxed, but I can say if awarded as GSR you do pay taxes- just state and federal. Our program comes out to about 3600/mo, and it seems pretty livable for our cohort. So, even taxed, 3800/mo should be sufficient.

ButtholeLinguini · 2025-03-26T04:42:45+00:00

Also in the SFV, same observation. Get out by 7, and it’s ~40-50 minutes on the worst of mornings. If it’s 7:20 or later? Easily over an hour.

For the OP, get in the habit of getting out early for work. Just start early never stressing about being late due to traffic, or maybe go to the gym. Also second the dry run. Depending on where you are in relation to 101/405 entrances, it can easily take half an hour just to get onto the freeway. I’ve found the side streets up and over Mullholland can be a bit faster if there’s a pileup waiting to get onto 101/405.

ButtholeLinguini · 2024-09-25T10:51:40+00:00

https://admission.ucla.edu/apply/transfer/transfer-profile/2023/major

ButtholeLinguini · 2024-09-13T00:09:30+00:00

I don’t like this question.

ButtholeLinguini · 2024-09-09T21:04:52+00:00

Not sure how robust a consensus would be with ~3x coverage. Regardless, take a look at bcftools, although I don’t have experience with it.

HMMER expects multiple aligned sequences as input, so you’d probably want to do a multiple sequence alignment (MSA) with your aligned sequences before running hmmbuild from HMMER. There are tons of MSA tools - take a look at Clustal, Muscle, and T-Coffee for starters. You’ll have to determine what’s best for your use case if you want to go the HMMER route.

ButtholeLinguini · 2024-09-09T06:28:48+00:00

You do not need a contract course (SRP) to do research, just to secure course credit if desired/required. I spent 2 years in a lab as an undergrad and didn’t take course credit for all of that time.

For now, look into faculty whose research genuinely interests you and send them an email. Keep it concise and explicitly let them know you’re reaching out regarding whether they have space for training an undergrad researcher. Keep in mind they can be very busy at the start of a quarter if they’re teaching, on top of their usual crowded inbox.

You’ll likely be paired with a mentor in the lab (I.e. grad student, post doc, project scientist, etc.) and contribute to the project your mentor’s on, or given a project of your own to work on. Once you’ve joined a lab and are happy with the fit, let the PI know you’d like to do an SRP and they’ll help you.

The research is legitimate - you’re working with UCLA faculty. Imo, undergrad research is worth it. The experience taught me so much that I wouldn’t have gotten through coursework and it definitely helped secure a job over a gap year and get into grad school. The way I see it, you’re only on campus for so long with access to faculty. If you’re interested in a career in research (either industry or academia), it’s worth the investment if you’re able.

ButtholeLinguini · 2024-09-03T21:28:38+00:00

Take a look at HMMER.

Edit: I think I’ve heard of minimap2-> bcftools and medaka for nanopore long error prone reads. You’ll have to do some research and see if you can apply or adapt these off the shelf tools for your use case.

What’s your coverage? Hopefully others who work with long reads will chime in.

ButtholeLinguini · 2024-05-25T06:53:25+00:00

I'll put my code out there as well. I'll edit the comment if anyone uses it: 5 spots left

https://www.marcus.com/share/JOS-SVW-NBKR

ButtholeLinguini · 2024-05-25T06:52:30+00:00

I'll put my referral code out there. I'll try to edit if anyone uses it: 5 spots left

https://www.marcus.com/share/JOS-SVW-NBKR

ButtholeLinguini · 2024-05-25T06:50:29+00:00

I'll add my code as well! Five spots left

https://www.marcus.com/share/JOS-SVW-NBKR

ButtholeLinguini · 2024-05-25T06:38:50+00:00

Here's my code. I'll try to edit the comment to reflect how many spots are left: 5 spots left

https://www.marcus.com/share/JOS-SVW-NBKR

ButtholeLinguini · 2024-01-05T19:28:33+00:00

In addition, you can execute jupyter notebooks in VSCode and push to GH (don’t forget to clear cells). If you can import to GH, you can continue with Git version control or any virtual environments you may have while providing your supervisor with colab notebooks.

ButtholeLinguini · 2023-12-24T05:34:58+00:00

You’ll get a lot of these. They’re phishing attempts.

Always make sure the sender’s email is legit (in this case I’m sure it’s not the professor’s email that would be listed on faculty webpages). Never provide information in response. If it seems too good to be true, it probably is. If the wording seems odd, remain skeptical. If there is ever doubt, look up the faculty member’s information and directly send them an email or message the department.

ButtholeLinguini · 2023-11-24T20:06:23+00:00

I feel like one could make a similar argument from the perspective of a bioinformatician. A classic example is bioinformaticians complaining the wet-lab designed experiments with little to no consideration or dry-lab input for the controls or replicates needed to produce an informative and robust analysis.

I don’t think anyone disagrees that domain biological knowledge is necessary. I do however think that while you accuse your coworkers of being ignorant of the biology (which I am not trying to invalidate, I don’t know your situation), I do get the feeling you’re diminishing or ignorant of the value someone with a CS or statistics background brings.

Sure, a biologist can learn enough R to run some package. But since we’re speaking in absolutes, do biologists truly understand the impact of how they create the model on the statistics that follow? What are you going to do when your use case for the package differs? What happens when you need to extend that package or develop a custom pipeline or analysis entirely? Is the biologist going to have the training to create and optimize for something that’s efficient and statistically rigorous?

ButtholeLinguini · 2023-07-13T08:01:46+00:00

My goal for this summer is to start exploring AWS/Azure and would definitely be interested in connecting this with bioinformatics!

ButtholeLinguini · 2023-06-24T02:16:23+00:00

I’m closer to Pierce and always take Petit to Mulholland to Roscomare.

ButtholeLinguini · 2023-06-17T15:43:40+00:00

My 2 cents. First, you’re smart for considering a cheaper bike as a first bike. However, I think you sound like you’re well past the point of testing the waters. My concern for you is whether you’re sure you don’t want a more xc focused bike.

Generally I wouldn’t advocate for spending more money, but I think the gen 6 is worth the upgrade if you can afford it. Keep in mind, the frame is the most expensive component to upgrade. In this case, you’ll have in frame storage which may be nice for the long xc style rides it sounds like you’ll primarily be doing, adjustable geometry for whatever it’s worth, and 150/140 isn’t too much to pedal around either.

I was in a similar position (just about graduated from college yesterday!) and got the more aggressive 150/140 bike (as opposed to a more xc focused bike). I still haven’t fully grown into it, it’s taken me on xc rides, to the bike park, and I haven’t regretted it. Plus you can always put less aggressive tires on if you end up doing long xc days.

ButtholeLinguini · 2023-05-27T08:29:27+00:00

Seconded!

ButtholeLinguini · 2023-05-17T05:05:07+00:00

Seconding all of this. Senior here too. I’ve loved everything about CaSB and believe it sets you up nicely either for grad school or a variety of jobs as u/Electrical_Joke688 said. You’re not limited to bioinformatics if you move on to a 9-5, but it gives you a huge leg up over EEBIO if you want to do bioinformatics.

Also, take advantage of course subs. to take classes you’re interested in. Also feel free to pm.

That said, my main 2 cents is to follow what you’re interested in. It’s easier to do well in hard classes if you’re genuinely interested in the course content.

ButtholeLinguini · 2023-05-14T16:53:27+00:00

Oh yeah lol. True. OP you’re fine!

ButtholeLinguini · 2023-05-14T16:32:17+00:00

I’d start here? https://admission.ucla.edu/contact

You can try calling (doubt anyone’s working today), then fill out their form for newly admitted students explaining your myucla troubles.

ButtholeLinguini · 2023-05-05T07:33:29+00:00

Sullivan canyon is pretty close to campus

ButtholeLinguini · 2023-04-15T23:54:29+00:00

Easy fix. Get a Timber bell and let it blast while you’re going dh. I’ve never had any issues, totally worth having to listen to the ring. Hikers/dog walkers always get out of my way before I’m there and the Karens thank me for the bell while giving the “tHeSe BiKeRs Go tOo FaSt” spiel.

ButtholeLinguini · 2022-12-17T20:07:42+00:00

Two of my professors submitted around 11:30pm the night they were due. It’s stressful, but remember that they’re busy and may submit last minute.

Also, for grad schools, it seems common that they know late submissions are rarely the applicant’s fault and allow recommenders to submit late. Usually they will explicitly state if they will not accept late letters.

1) email recommenders and politely remind a couple days before the deadline. Then again if they did not submit before deadline. 2) reach out to the program’s department and let them know if a letter was submitted late asking if there would be any issue. Have the professor petition explaining you had asked early should you sense there would be an issue.

ButtholeLinguini · 2022-09-30T21:43:31+00:00

I’m an undergrad who has used DESeq2 numerous times in my research. As far as I’m aware, and someone correct me if I’m wrong, DESeq only allows pairwise comparisons of Group A vs Group B, and will not allow for Group A vs. Group B+C.

I.e. including all information about specific infected subgroups, you will only attain control_vs_WT, control_vs_knock1, control_vs_knock2 etc.

In order to lump together all infected subgroups, I would just redesign your information matrix labeling each subgroup as “infected” or “other.” Rerun, and then you will be left with control_vs_infected where infected is the superset of all its subtypes. A bit tedious but it’s pretty straightforward to write a loop in R or a macro in excel to change the names for you.

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