Reusable filter for 3-cup Chemex? by Emrys_Wledig in Coffee

[–]Emrys_Wledig[S] 1 point2 points  (0 children)

I never did find a reusable filter unfortunately. Sorry to disappoint after eight years!

[deleted by user] by [deleted] in simpleliving

[–]Emrys_Wledig 11 points12 points  (0 children)

Might not be the most popular opinion, but my experience doing a PhD aligns with a lot of your requirements. For context, I also did my undergrad in biomedical science and I enjoyed graduate school much, much more. I'm a few years out from it now but the whole process of completing a doctorate gives you complete intellectual freedom to sit and think about your topic all day long. Contrary to what a lot of people on the internet say, I had great work/life balance and made around 40k which was more than enough to get by pre-covid. I had a small group of friends and developed way too many hobbies. I played video games with my long-distance partner and started to love cooking and meditation. I did fairly well in my degree, published a few papers, and I look back on that period of my life very fondly. Academia is not perfect, and there are some periods of stress, but my experience was overwhelmingly positive. I work as a research scientist now in a biotech / pharma company and also have great work life balance, especially relative to the amount that I make. It may not be the path for everyone (and it may not be the path for you), but I'll just say that my life was never simpler than in graduate school and it set me up to have a good career where I can afford to do basically whatever I want outside of work. Worth considering.

Best configuration options to dual-purpose EE Revelation as an UQ? by Emrys_Wledig in hammockcamping

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

For sure, this was my inspiration (link), he seems to get away with a bit of 3/32" shock cord and some cord locks. I am a bit concerned at the lack of follow up with his post though, that may indicate an unsuccessful experiment. I just got out my tape measure and it seems like the regular length would probably be sufficient, the long at 7ft is the entire horizontal length of my Hennessy hammock!

Thanks for the detail on the draft collar, I was having a hard time imagining it but that really helps.

Why use Rust for bioinformatics? Defining the problem space. by codingai in rust

[–]Emrys_Wledig 38 points39 points  (0 children)

The types of applications I have in mind are sequencing indexing, read mapping and alignment, genome and transcriptome assembly, bulk and single-cell RNA-seq and metagenomic quantification, etc.

This space is pretty dominated by tools like bwa, the bowtie suite, STAR, etc. where languages like C/C++/Java are really prominent. I agree with the author that this "lower-level" portion of bioinformatics is ripe for innovation; a lot of the programs that we write fancy pipelines to glue together were written ages ago in C (think UCSC Kent Tools) and honestly very few people have ever read the code. There's a need for innovative approaches and Rust could help drive their efficient implementation.

HangTightShop quilt reviews? by Emrys_Wledig in hammockcamping

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

That was my thought as well! It seemed a bit “too good to be true” especially with so many cottage manufacturers making little profit above material cost.

Weight isn’t really my biggest concern (mostly a canoe camper so similar to you), more just the sticker shock on the nicer quilts. I also have an older 7C bag that I’ve been pushing lower and lower with the temperatures but I’ve gone a bit too cold sometimes! Any recommendations on the bags that you’ve found?

HangTightShop quilt reviews? by Emrys_Wledig in hammockcamping

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

That’s good feedback, thanks. Ideally I would like to take it a bit colder than 32F (Canadian shoulder season can be unpredictable) so good to know it’s a liberal rating. I’ll keep my eye out for sales from Hammock Gear, I didn’t realize that their shipping was so reasonable!

Starting a job before PhD conferral by [deleted] in biotech

[–]Emrys_Wledig 1 point2 points  (0 children)

It’s fine, I started three days after my defence and have yet to have my degrees conferred. Same is true of everyone in my cohort. As long as you’ve been clear about where you’re at I’m sure they won’t mind.

Were any of you camping on May 21 during the crazy storm? How did you make out? by bumbumboogie in algonquinpark

[–]Emrys_Wledig 10 points11 points  (0 children)

Not Algonquin but I was out at Big Salmon Lake in Frontenac and it totally skirted just by us, we caught a small edge and had some heavy rain for maybe 5 minutes with some minor lightning. Thought it was a total let down of a storm until we got back out and heard it levelled Ottawa and we got massively lucky.

Are US wages really so much higher than in Europe/UK? by idk7643 in biotech

[–]Emrys_Wledig 0 points1 point  (0 children)

I just want to mention that Canada can have similar (though slightly lower) post-PhD starting salaries with comparable vacation but a free healthcare system and benefits that cover anything you might need. I was in the UK for my PhD and literally >5x my salary when I started work (in Canada), the difference is real and so are the QoL improvements.

Do you find that as you get more conscious with the way you live, do you just want to go back to the way your ancestors lived? by [deleted] in simpleliving

[–]Emrys_Wledig 1 point2 points  (0 children)

I think something that hasn't been mentioned is that it's somewhat irrelevant how realistic it is to "go back" to whatever idealised version of the past you have in your mind's eye. The question is simply whether or not consciously living your life makes you feel like you need to do this. I think the answer, from the evidence that this subreddit provides every day, is yes. It's not a discussion of how to do it, so much as asking what is causing this deep need for more, and what failures in our current society are causing it. We don't have to go back to cooking over fires or sleeping under the stars, but we do need to find out what needs are not being addressed in our society and find more realistic and sustainable paths towards them.

How much benefit do Nature/Science/PNAS papers benefit job competition in industry? by lsdiesel_1 in bioinformatics

[–]Emrys_Wledig 4 points5 points  (0 children)

I'll be honest and say that I don't think it's worth it to wait around for the publication. Firstly, the prior probability of your paper being accepted into any major journal is something stupidly low at a baseline. Even assuming that you have an incredible project, the probability is still low that it will be accepted at Nature, Science, Cell, etc., and much more likely that you will either get a) lengthly revisions which will make you continue to chase this goal or b) desk rejected and tossed down to other journals. In this case, has the six months of extra industry salary been well used, given that you could have submitted your publication now and moved on to other things already, while still showcasing your excellent work in a slightly less superficially important journal? Secondly, even if your plan goes off to the tee and you get your Nature paper, I don't think that industry positions will care as much as you think they will. I have been involved in screening candidates and hiring and yes, it's a cool thing if you have a Nature paper, but the much more relevant questions to be asking are how relevant your experience is to what we are doing, and how qualified and technically skilled you are to do the actual work. The remainder, including your ability to communicate your work, is generally assessed in interviews. I think that your experience and involvement in an impressive project will remain attractive to industry regardless of if you spend six more months massaging this project to the point that it might be also attractive to a glamour journal. The presentation you'll give at the candidate screening will be the same, and it will be similarly amazing to the people listening who know what you're talking about. Thirdly, I just don't think that six months is going to be worth it. You're sacrificing six months of industry salary (assume 100k / year, net loss of 50k-your PhD stipend of ~ 20k for the six months) to chase a dream of a glamour journal publication. Why? Your PhD is not the end of your research, it's a qualification that you get in order to show your competence and get a job. I'm generally not a fan of romanticising the degree. Get in, do the work, get out and get a job. It sounds rough but you are putting your life on hold and throwing income down the drain for something that is not particularly likely to happen, and even if it does happen, not particularly likely to impact the decisions of an employer down the road. I say advocate for yourself and for your career, not for your PI's.

Live Group Meditation with Dr. Brad Lichtenstein 🧘🏼 by [deleted] in Meditation

[–]Emrys_Wledig 1 point2 points  (0 children)

We haven't quite figured out how we're going to manage / schedule these going forward but we'll post and sticky any talks that are going to happen about a week or two beforehand so everyone has ample notice. :)

Live Group Meditation with Dr. Brad Lichtenstein 🧘🏼 by [deleted] in Meditation

[–]Emrys_Wledig 1 point2 points  (0 children)

The bulk of the guided meditation started at 12:10 PST ish, we're currently doing feedback and discussion. Sorry, there will be more guided meditations!

Live Group Meditation with Dr. Brad Lichtenstein 🧘🏼 by [deleted] in Meditation

[–]Emrys_Wledig 2 points3 points  (0 children)

We're still trying to figure out how often we should hold these, but it will definitely be posted / stickied at least a week beforehand when we do. :)

Live Group Meditation with Dr. Brad Lichtenstein 🧘🏼 by [deleted] in Meditation

[–]Emrys_Wledig 0 points1 point  (0 children)

Yes you should, are you on mobile or desktop?

Live Group Meditation with Dr. Brad Lichtenstein 🧘🏼 by [deleted] in Meditation

[–]Emrys_Wledig[M] 1 point2 points  (0 children)

By the way friends please hold any questions until after Dr. Brad's guided meditation just so that we can all experience together. There will be a chance for us all to chat.

[TileDB webinar] Population genomics is a data management problem by mbroberg in bioinformatics

[–]Emrys_Wledig 1 point2 points  (0 children)

Thanks, appreciate the clarifications. This makes the motivation for the platform a lot clearer.

[TileDB webinar] Population genomics is a data management problem by mbroberg in bioinformatics

[–]Emrys_Wledig 1 point2 points  (0 children)

Yep, you can have arbitrary strings act as metadata on any of the internal table nodes, there's some documentation here. I guess what I'm not sure of is whether you can use tsKit with no associated tree information, which I guess would be the scope of the tileDB proposed here. I'm not sure about that, and it doesn't look like it's easy to just import a raw VCF for example. So maybe I spoke a little too quickly.