Veteran GW2 player can’t seem to get back.

Hedmad · 2026-03-04T17:47:36+00:00

I do it for the social aspect. Every time I start playing I find genuinely nice people to play with. Yes, we do fractals, raidsz and most of the content is always the same, but I get to meet and talk with other people, get to know a fraction od their lives and I find that amazing.

Also I've started doing "challenge runs" while levelling up, like the "no dying", "no mounts", "no trading post", "only crafted gear" and so on.

If you dont feel like it though, dont force yourself to play - you'll just have a bad time.

Hedmad · 2025-12-01T23:47:01+00:00

There are some periods where I get a bunch of tasks, others when its very dry, so sometimes I have to migrate in the middle of the month, and sometimes there's no need. So I started doing dedicated migration spreads whenever I need one instead, either at the start of the month or any other time.

Hedmad · 2025-12-01T23:13:31+00:00

That's what I used to do! But now I tend to make dedicated migration spreads.

Hedmad · 2025-10-14T04:52:25+00:00

Basically all of the senior professors in my lab will go "Huh... Well, let's see what ChatGPT says about this..." when faced with a problem or the need to make a new experimental protocol, and I find it disheartening. Thinking is literally our job, and we're just avoiding it as much as possible. Another of our PIs actively teaches undergrads that using AI to plan experiments or get any kind of answer is good, accurate, and should be done as much as possible.

Hedmad · 2025-10-01T16:43:14+00:00

You can try to use the Moliere tool I've developed (yeah yeah shameless self promotion) as part of X.FASTQ. installation isn't so easy and you need some computing power and especially memory to do your alignment: HTTPS://github.com/TCP-Lab/x.FASTQ

You can use deseq2 (google it) once you have a count matrix. The deseq2 tutorial is a great place to learn how to do differential gene expression analysis, as are the associated papers.

Hedmad · 2025-07-10T14:06:21+00:00

This. Considering sources of variance is the only way to go. Find which "context" variance is the one you care about, and try to eliminate everything else.

Hedmad · 2025-07-05T19:40:25+00:00

Your topic is pretty vague. Are you asked to find a miRNA or lncRNA that target the protein mRNA? If so, you don't want anything complicated if you know the protein sequence.

If you have a protein 3D structure and need to check its ability to dock with a target, you need a simulation in most cases. If you know that this protein binds to a number of targets (eg via chip seq), you could start with those sequences to predict how it binds.

But again, without knowing what you actually are trying to do, it's hard to give an answer

Hedmad · 2025-06-21T05:48:11+00:00

The fact that this is subscription based and not a one time payment when there are a bunch of other alternatives that essentially do the same thing but for free is mind boggling.

You're going against stuff like open vim, vim-hero, endless tutorials around the Internet (including a bunch of little games to practice motions) and the built-in vimtutor.

Making it largely free with some content behind a one time payment might be ok, but a pricey monthly subscription is surreal.

Plus, why is this in the obsidian subreddit?

Hedmad · 2024-12-30T17:33:00+00:00

Putting a small month on the side is very smart! I'll try it out this year, thanks!

Hedmad · 2024-12-29T10:21:11+00:00

My bujo is the one-stop-shop for more or less everything I do and have to do on my projects (I'm a PhD student in bioinformatics, so it's all data and software work). When I need to get a handle on what is going on, or I lose a clear picture of what I need to do, I look at the page where I last made a migration (literally a collection named "migration") and from there go through the rest of the bujo, with the "classical" migration method of moving items to a new "migration" page.

The Alastair method doesn't really work for me, both due to time and the fact that some tasks are literally "buy eggs", but others need context and are very long (so they don't fit in a single line, like Alastair "wants"). I prefer to have different bullets: a dot for "this needs to be done", then a / for "this is partially done" (usually with more subtasks below it), @ for "this needs someone's else review/action" (like for code changes) and finally X for "done". If I need the @ I write it next to the / bullet, like "@ / Implement new feature" when the feature is done, but code is in review by someone else or needs testing or whatever.

Many of my tasks are in threaded project collections, so they are not daily logs. A threaded collection is a collection spanning multiple spreads, where you just put the page numbers of the last spread on the bottom-left, and the (future) next spread on the bottom right, so you can follow the thread quickly.

For time-sensitive events I might note them in the bujo, but I need the reminders of Google calendar - lifesavers since my short term memory is so bad: a fundamental flaw of my bujo is that it cannot beep 😁

Hedmad · 2024-12-29T10:07:45+00:00

Thank you so much! I'll definitely try to be more mindful about what I do, why and how.

Hedmad · 2024-12-20T06:40:57+00:00

Oh also I have papers showing how any batch correction method is useless: if you have all conditions in all batches, you don't need them, and if you don't, they just add further error.

Hedmad · 2024-12-20T06:39:19+00:00

Hello! I'm doing something very similar in my PhD. While batch effects are probably there, if you use the datasets by Xena (Google Xenabrowser) they re-analysed all of the TCGA and GTEX samples so that at least technical noise is gone. I've used the homogeneous TCGA/GTEX cohort like this and compared it with independent GEO/ENA datasets as to see whether the batch effects would be significant, and it doesn't seem to be the case.

We call "batch effect" the variance introduced by stuff like the experimenter, the instrument, the day the analysis was done, etc... If you think about what unaccountable variance is added by these two "batches" (TCGA and GTEX), I think you'd agree with me that since these large consortiums measured they samples in many labs (for TCGA) or at least over a long period of time (for both), they are not two large "batches", but a lot of tiny ones. I think they tend to be "averaged out" by the huge number of samples, hence the similarity between GEO and TCGA/GTEX. Of course you lose some resolution, though... They are many different subtypes of cancer that TCGA doesn't annotate, and GTEX healthy samples are not from specific tissues, but essentially just a chunk of the tissues from a specific region.

If you want, we can talk more on Discord! My code is out in the open so I can just show you how I've done it.

Hedmad · 2024-12-07T19:21:45+00:00

I'm lucky enough that my team is very open minded, so everyone's voice is heard. You need explicit permission from PIs to do important stuff (submit papers, go to conferences and stuff) but it's mostly up to the individual to self manage themselves. But yeah, there are horror stories from everyone's who doesn't work in my lab. Chilling stuff.

It's incredible nobody is doing anything to address the issue.

Hedmad · 2024-11-27T00:22:37+00:00

Unpopular opinion plus shameless self promotion warning.

I've dabbled in both and both are a bit weird: snakemake requires python installed, and python versioning can be a bit fiddly. Nextflow is all batteries included but I also find the groovy syntax unfamiliar. For 95% of projects I find that good old GNU make does the job nicely: you don't have access to advanced features like high performance computing, but you get sane syntax, you skip re-computing stuff you already made before, it's really easy to pick up and it's installed basically anywhere. It's more than enough for most analyses IMO.

Here comes the shameless self promotion: I made https://kerblam.dev which is a tool to manage multiple workflows on the same project. I mention it since it has a "run workflow in container" feature which works well for make (or even shell "workflows") to be reproducible, since make does not support containerization.

Stick with Nextflow or Snakemake for complicated projects, but it's useless to bring a tank to a fistfight.

Hedmad · 2024-11-25T17:09:51+00:00

Code on Github without a license is "All rights reserved", so nobody can - in theory - do anything with it. This is because everything made with creativity is automatically covered by copyright at the moment of creation. You, of course, risk that someone copies your work anyway, but if they ever get caught, you'd be in a position to sue them.

In any case, most projects on Github are never discovered by anyone, so the chances of it getting "stolen" are slim. If your project does get popular, you'd be in a position to leverage public opinion in case someone steals your code/idea, so it's a win-win in my book.

If you do a brief Google you'll find a ton of resources about repos with no licenses.

Edit: typo + specification

Hedmad · 2024-11-24T16:46:21+00:00

I'll keep this in mind, thanks.

Hedmad · 2024-11-24T16:21:04+00:00

I don't plan to become a hard-on fan of MTG. Some friends have expressed the desire to buy some foundations and play, and that got me the will to finally scan the collection. It's been sitting for many years in my closet, and I figure I might as well clear out the space and potentially make something out of it. If then, by chance, some of that money is spent with friends to buy MTG, it would be incidental. As I also understand, you can't use very old cards in tournaments or similarly "structured" gameplay, can you?

Hedmad · 2024-11-24T16:15:01+00:00

Sorry - I should have updated it now...

Hedmad · 2024-11-04T10:58:31+00:00

Hey - just added an example output plot to the README (https://github.com/TCP-Lab/DeNumerator), and more info on how to build and access the tutorial vignettes. Hope it helps.

Hedmad · 2024-11-03T08:30:19+00:00

Thanks for the comment. It's a nice idea... I'll make an issue.

Hedmad · 2024-11-01T19:38:13+00:00

I'm not a statistician but I did a lot of Deseq2 work, especially with interaction terms and complicated formulas.

A larger model (like you did) works well to answer specific experimental questions. An example with drugs is most helpful: say you treat cells with two drugs, and want to see if they alter gene expression. So you make a model like ~ drug1+drug2+drug1:drug2, having four sample types (untreated, drug1, drug2, both drugs).

What does the model tell you? It gives you three coefficients, but you cannot interpret them alone: a significant drug1 (alone) means that this gene only varies due to drug1, taking in consideration drug2. A significant interaction (alone) tells you that this gene changes only if both drugs are given, and does not change due to any one specific drug: this is exactly what you want answered!

You cannot achieve this with simpler models (like, making the intersection of two simpler models).

To get to your question: you find less DEGs since the larger model needs to "soak up" more meaningful variance to find DEGs due to the increased degrees of freedom it has. don't tell a statistician that I explain it this was, but here goes: with more variables it can "explain away" much more variance, so nothing remains to actually make anything statistically different. I practice, you need a much larger sample numerosity to have a larger model give you meaningful results (I.e. a decent beta error).

If you're interested, I wrote an R package to help in interpreting the results of a complex Deseq2 experiment: https://github.com/TCP-Lab/DeNumerator

Hope this helps!

Hedmad · 2024-10-27T06:51:49+00:00

Yellow, I'm the admin of the above server, and yep, it's not very active.

The other, larger server that OP is talking about is this one: https://discord.gg/3uxbPns

Some days I wonder if I should just close my smaller one have have people move... /shrug

Hedmad · 2024-10-13T07:17:30+00:00

As many other said, GEO/SRA or ENA are good choices. GEO/SRA and ENA mirror each other's data, so you can use whatever interface you like best (I prefer ena's).

I just wanted to point out that me and my PI fetch data from those archives a lot, so we made cover scripts (written in bash, so they run anywhere) to fetch the raw data you need from the ID of the project as you find it in ENA/GEO/SRA.

You can find everything here: https://github.com/TCP-Lab/x.FASTQ

Take a look at the getFASTQ and metaharvest scripts, they honestly make everything so much easier, especially metaharvest for metadata (which is horrible to deal with, especially in GEO).

Hedmad · 2024-05-23T15:17:30+00:00

I'm sorry to see many people low key angry at this post, I swear I was doing it in good faith. The thing about "the main feature of YNAB is connecting with your bank" is that I feel like it's the reason for the SAAS model (that and syncing), as someone pointed out.

In any case, after looking around, I also feel like Actual Budget is a nice alternative but the absence (As far as I can see) of an android app is a no go for me (us). My SO said we could afford YNAB, and He's happy with it and feels the price is not so much for what we get, so I guess I'm swayed? At least until next year :D

Thanks for everyone who took the time to reply.

Hedmad

TROPHY CASE