u/extra-plus-ordinary

For context, I am pursuing a PhD in Genomics in Europe (I'm originally Canadian), specifically in using genomic sequencing and downstream tools to diagnose genetic kidney disease patients who go undiagnosed in clinic.

The lab I joined is just breaking into the space (theyre more into wet lab/proteins) and the labs that are bioinformatics heavy here are mostly evolutionary.

In the past half year I've been in my PhD, I've started to realize that I will probably have to learn and explore things myself much more than some of fhe other candidates. I dont come from a computational background; for my MSc I just happened to update my labs variant analysis pipeline to the point where it was quite different (but useful!). Currently I've been looking at some short read sequencing data and I have a pipeline (using a mix of python and R) that annotates from VCF --> filters for rare variants --> uses some online databases to filter for genes that are specific to the patient phenotype.

I want to upgrade my skills. I'm starting to learn Nextflow, but I also want to learn how to analyze long read and RNAseq data (I'm supposed to get patients with RNA and lrGS data as soon as the research center is equipped to perform it, which may be a while). I don't want to just learn though as I only have 4 years, so I was wondering if there were databases I could mine to potentially come up with work related to my project (perhaps something like gene/variant discovery)?

I apologize for what may be simple/dumb questions; whenever I try to explain my ideas to my PI I can see their eyes glaze over, and most of the diagnostic employees here are busy with hammering down a workflow for the research center. If anyone has advice on where to look or even papers to read I'd be eternally grateful.

Preferably a clinic that has a first time or student discount, and of course can speak English 😊. If anyone knows a good one in the Heyendaal area please lmk (farther is fine but close is best yk!)

For context, I'm a Canadian doing a PhD in the Netherlands.

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A while back I was placed on a side project for my thesis (left over from a past student who quit). I was told I was "in charge" but of course there were so many moving parts that were from before my time (talking to other universities etc) that I felt more like the help. There were a few red flags before the actual sample processing happened (my PI wanted me to transport over 10kg of samples in dry ice by train by myself; thankfully a tech helped me out by driving) and I made some mistakes as well (my packing method was confusing to everyone BUT myself).

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The schedule was honestly really hard on me. It involved traveling 2hr each way to the research center that had the facilities needed for this processing. The 2 techs that were helping lived closer (30 min). I had extreme anxiety over things like missing my train to the city, messing up samples etc that wrecked my sleep, so I had like 3 solid hours or so of sleep per day for almost 2 weeks.

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I became quite fatigued even at lab and became quiet during the processing day, not making eye contact when spoken to and having an impassive face (i have ASD but im usually better at masking). Despite trying to pay attention and/or not do any detailed work in this state (there were other steps I was fine with), I was encouraged to do so and then made about 2-3 mistakes.

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The tipping point came when one of the techs noticed I wasn't doing well with one of the processing steps and basically told me off, saying it looked like I never cared about the project and that I was messing everything up. The other lab tech agreed and said my work was causing her anxiety, even though I would ask multiple times a day if I was doing things right and she would say yes. She also accused me of sleeping as she was talking to me, but I was only sleeping on my lunch break. I was tired and outgunned, so I simply agreed and said I would try harder.

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The next day I was pulled off the project. My PI + 2 supervisors from lab pulled me into a meeting and told me the techs had contacted them and they were disappointed in my actions. I explained my side and I was basically told that was no excuse and that they wanted me to write a reflection on what professionalism in the workplace meant.

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Despite all of this, being able to go home and sleep without worrying about missing a train or fucking up in lab has been a blessing. I'm eating again (I lost almost 5 pounds in 3 weeks without trying!) and have energy to work on my main project. I know I've burned bridges I can never rebuild, but that project was honestly so draining I cant help but be glad I dont have to suffer anymore.

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If anyone has a similar story or advice on coming back from this stronger please let me know 🙏🏾

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Someone very recently posted a checklist for writing a thesis; it was a typed up multi page affair with a beige background and blue text. I thought I saved the post but cant find it anymore, if someone could point me to it id be so thankful

I will soon be receiving data regarding samples sent for mass spec (patients, healthy & disease controls). I want to be able to analyze the quality of the sample data as well as do things like hierarchical clustering & picking up which proteins can be used as biomarkers for disease. Does anyone know where to start reading + what tools & websites will be most beneficial? Thank you!

Despite the tag (this is 100% a vent) I wouldn't mind some sound advice. I'm pretty sure I'm 70% overreacting here.

I'm a first year PhD student from North America, but I'm doing the PhD in Europe. So far things have been great, but recently I was put on a proteomics project that involves dozens of unique & precious samples. I've been really hesitant about this project from the start and I honestly think I've just been holding in a lot of resentment, leading to my current headspace.

This is a mass spec project that requires me to travel every day for 3 weeks to a research center 1.5 hr away by train. The other 2 lab techs on this project (M and E, lets call them) live only 30 minutes away. Since the train only comes once every 30 minutes, if I dont make it to the 7.30 am train I am fucked. I really don't want to be late, and because of my anxiety I've been having really shitty sleep, and I get up at 6.15 to start biking for the train by 7. I've been sleeping on the train (not helpful) and I've been kind of out of it because of this. I haven't been as vocal in lab (M and E love to chat) because I'm trying to save my energy for the actual work of processing the samples. I've made 2 mistakes so far, with one having an effect on the final analysis. Not an excuse, but just an explanation.

M is a lab tech that works in my lab in my home research center. She's really smart and also a bright person in general, and has been a great help to me (my PI was going to have me transport about 10kg of samples in dry ice myself on a train, but she stepped in after I told her the situation). She is also really interested in this project and has been pushing me to speak more during planning meetings, and to ask questions when I have them. Today, she took me aside after a certain step I was having trouble with and really let me have it. She said my work was unacceptable and showed a lack of knowledge on why each step was important. She also said that for the past week it seemed like I didnt know what we were doing and that it felt like she and E had to prompt me for each step. She also said going on my phone during waiting steps instead of reviewing the protocol was rude. E agreed with this and said that she tried to talk to me during lunch break, but I "rudely" fell asleep on her. I wasnt even aware she was trying to broach a topic, she simply asked if she could sit near me and I agreed.

I will say that the step she is referring to (cutting up gel for trypsin digestion) IS important and she's right to point it out, I wasnt doing a good job. I noted that not all of my work hasnt been like that and was told to stop being defensive, which I guess is fair. However, telling me that I don't understand what we're doing seems a bit much. I've been handling a lot of the washing steps and preparing solutions. I ran through the whole protocol with both her and my PI before this started and answered questions on what each solution was for. I can recite the protocol by heart at this point and have noted down deviations every time. I also haven't been on my phone during waiting steps as there's usually something to do (I checked my screen time to confirm).

If I'm honest, I just think that she doesn't like the fact that I've been quiet and sleepy. I know my focused face can also look really creepy to others (its very flat) and I think she read it as uninterested. She also has a very different way of thinking and communicating than I do and seems to get upset whenever I try to do things in ways I understand better, or if I try to reword things. I think all of that added up to her confronting me with all of this. I didn't talk back at the time because I was concerned I would say something sharp and make things worse. She also said she would report this to my PI, and I have no idea how that will go down or how to deal with that. She's been working there for years so I know her opinion will be taken over mine. My current plan is to simply act more friendly and talkative for the next 2 weeks and see if that changes her attitude (I truly think it will).

If anyone notices gaps in my logic or has another view point please let me know. I've been anxious all week about getting this project done and this has honestly made it worse, but at the end of the day it's only for another 9 days 🙃.

I'm starting to notice a lot of video files (particularly anime) are showing up as being taken down for copyright. Some are still okay. I find it annoying to have to sift through all the loaded files to see which one is still up, any way to filter?

Edit: thanks to everyone who's commented so far, I ended up using the AIO addon :). I still have time and points on my RD account so until those run out I'll stick to it, but I'll make sure to remember jumping ship is an option

Currently doing a PhD in genomics. In my old Masters lab, I got really familiar with and good at using Geneious Prime, and I really love the interface and how easy it was to visualize things. I worked mainly with DNA (segregation) and RNA (splicing assays). My current lab uses SnapGene and it is genuinely painful to use (although its good at visualizing plasmids and stuff), and I haven't managed to convince my PI to cough up $200 for the personal subscription. I was wondering if anyone has other alternatives to using Geneious Prime (or if you have a license laying around 👀👀👀). Any suggestions are appreciated!

I recently moved from Southern Canada to the Netherlands, and I've noticed that Isha tends to be very late here (11:30 now) and Fajr is early (3.25ish). I looked ahead in my prayer app and apparently by June, Isha will be after midnight (12:05 AM) and Fajr at 3 AM.

I would like to know how people deal with this. Personally I've just gotten ready for bed and waited until Isha, prayed, and then hopped into bed. I've noticed the impact its had on my sleep quality and quantity but of course I will keep praying, so I'm just curious on how people normally deal. I'm debating sleeping after Maghrib and simply getting up twice at night, but I'm concerned I will miss one by accident because I'm a heavy sleeper and easily disoriented. Any suggestions are welcome!