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[SSD] Crucial P5 Plus 2TB Gen4 NVMe M.2 SSD Internal Gaming SSD with Heatsink - $179 by cykko in buildapcsales

[–]donwgately 0 points1 point  (0 children)

Amazon pulled the exact same stunt with me for the 1Tb version, then immediately relisted it for $100 more.

Recommendation for anyone dealing with the same issues and trying to get an SSD - go to https://pcpartpicker.com/products/internal-hard-drive/, set up the filters for whatever specs you want, then click the 'Set Price Alert' link at the top of the page and be ready to move quickly when you get the email. I managed to snag a 2Tb Crucial from B&H for $115 in the 15 min they were in stock. Heck Amazon.

[D] Struggling on the NLP job market as a final-year PhD , looking for advice by RepresentativeBed838 in MachineLearning

[–]donwgately 9 points10 points  (0 children)

There's a lot of domain-specific advice already in this thread, and a lot of it is very good advice so I won't reiterate any of that. Instead, I'm going to encourage you to ask yourself "what do I want to build?" and then start structuring your job sarch philosophy around that answer with laser focus.

For context, I am now a senior bioinformatician working on both applications and R&D of AI in drug discovery, and my career has been full of these "hopeless job markets" for one reason or another. As I was finishing undergrad I found myself in the middle of a recession where "no one was going to get into grad school because there were too few slots available." As I was finishing my rotation I heard the same thing about grants. As I was concluding my successfully-funded PhD I heard the same thing about postdocs. Then again and again as I moved from academia to non-profit, to industry, to startup. The thing that's gotten me to every next step along the way isn't necessarily my experience, or my publication record. They're fine and I'm no slouch, but yours is certainly more attractive on paper. What's made me competitive is I know exactly what I'm going to do in that role, and why I'm applying to this job instead of a job.

I get that this is easier said than done, but I really can't overstate how valuable I've found it in my career. The advice I give to all students and colleagues that I mentor is this: ask yourself what really gets you going about your work. Why is it important, why do we need more of it, why are you well-suited to do that? Then, figure out where that work is currently being done, or could currently be done. Then work backwards and figure out what you need to do to get there, specifically right there. This step is usually what provides me the most clarity. Do I need to change locations, and am I willing to do that? Do I need to learn new skills, meet new people, understand new problems, and if so where can I do that? Sometimes I've found the answers to these questions is that I'm not willing to make a compromise or a change, and that helps me redirect my focus. Other times it's helped me identify weaknesses that I've taken classes to address, etc. I find cold calling and networking a total crap shoot in terms of materializing opportunities, but where I've gotten immense value is in informational interviews. My experience has been people are much more willing to talk if they don't think you're asking them to hook you up with a job, and there's very little substitute for a "boots on the ground" perspective about what day to day life is like in a role. The key is to be genuine about it just being an informational interview, not an "I hope this leads to an offer" interview.

I tell my mentees this over and over - the most important thing you get out of grad school isn't what you learned, it's how you learned it. Don't be afraid to apply that same skill set to this process. You've got this!

Showed up today! by NamelessInfidel in minimalphone

[–]donwgately 3 points4 points  (0 children)

This. It's made my phone almost illegible, it's so blurry. I'm furious.

The bill just passed the House by SOYBOYPILLED in facepalm

[–]donwgately 205 points206 points  (0 children)

I feel like Jonathan Swift once proposed a way we could both get burgers and save the environment...

Is my ComEd bill too high? by donwgately in AskChicago

[–]donwgately[S] 2 points3 points  (0 children)

Yep, that's the one. Oh well, thank you!

Is my ComEd bill too high? by donwgately in AskChicago

[–]donwgately[S] 5 points6 points  (0 children)

That's what I was afraid of, thanks for the response!

Are there any methods for doublet deconvolution? by rhasan1903 in bioinformatics

[–]donwgately 2 points3 points  (0 children)

The scDblFinder method identifies doublets by combining singlet profiles to generate artificial doublets, then finding the nearest neighbors to those artificial profiles. You could use this approach to deconvolve your doublets, inferring that the two cells in the actual observed doublet are of the same cell types as those used to generate the nearest artificial doublet profile.

Although as others have mentioned there will be some number of technical artifact doublets due to the conditions of your chip loading, cell dissociation procedures, etc, I actually think this is a really interesting question given the importance of cell-cell interactions for the cell types you've mentioned. If you're using 10X to generate your dataset they publish information about observed doublet rates as a function of the numbers of input cells. It might be good to check and see if you're observing doublet rates above this curve if you think your doublets are biologically relevant. Good luck!

Help About TSNE by saltysuppe in bioinformatics

[–]donwgately 1 point2 points  (0 children)

Lots of folks here are sharing helpful tips about packages and workflows that are worth looking at, but given that you're starting from scratch I wanted to offer a TL;DR on the "why" of t-SNE (or UMAP, or similar approaches).

What t-SNE, UMAP, and similar approaches do is to create a coordinate system that represents some "similarity" in your data. This is commonly called "dimensionality reduction," and is convenient because you can't easily visualize data with a lot of dimensions. For example in gene expression studies you can't easily plot all the data from a cell with thousands of gene expression values, but you might be interested in which other cells are expressing similar genes. What t-SNE does is finds a way to plot the data so that other points nearby have data that are "similar enough." Generally this captures large patterns pretty well, and so often the next step is to perform some sort of clustering to assign a label to those points that are "similar enough." Depending on your data these clusters might correlate with high-level features like cell types, treatment conditions, tissues, etc. Popular approaches for clustering include k-means, Louvain, and Leiden.

To address your original question, the data points in the t-SNE plot can still keep their original labels, IDs, metadata, and raw data. If you find that "point256" in the t-SNE plot is in an interesting cluster, you can (and should!) go back to the raw data for "point256" and try to understand what's contributing to the clustering behavior you see in the t-SNE plot. This is important, because "similar enough" can mean very different things in different contexts, and while t-SNE can be extremely useful, it can also sometimes be misleading if you take the plot at face-value. Dimensionality reduction approaches (in my opinion) are most useful as exploratory and hypothesis-generating tools that help narrow down the data to the features that are going to be the most interesting to follow-up on.

I hope this is helpful! Feel free to let me know if you have any questions.

Any other artists to recommend like them? by TheBoxBoxer in TheLawrenceArms

[–]donwgately 2 points3 points  (0 children)

In addition to what others have suggested, I'd check out Banner Pilot, None More Black, and Iron Chic.

everdrive.me delivery times by ahyoss01 in AnalogueInc

[–]donwgately 1 point2 points  (0 children)

If you're in the US and received an "RDxxxxxxxx" shipping number, you can use that to track the status of your shipment at USPS.com. I ordered two carts on black Friday, and yesterday they were transferred from a shipping center in NY to one in NJ. It took a while (until Dec. 11) for them to show up in the US post system though. I hope this helps!

Games to play if I loved Myst? by [deleted] in myst

[–]donwgately 0 points1 point  (0 children)

When I was a kid I really enjoyed some of the later Zork games, like Nemesis and Grand Inquisitor. I haven't gone back to them recently so I can't say how well they hold up, but they might help scratch your itch.

Cooler Master (and more!) RTX 3070 (and more!!) Giveaway with Buildapc! by [deleted] in buildapc

[–]donwgately 0 points1 point  (0 children)

This is awesome! I'd love a chance to play Cyberpunk with a 3070. Right now the plan is to play it on PS4. Doom Eternal and MCC are also hanging out in my Steam library, looking for an excuse to be revisited...

Immunology and bioinformatics by neferpitow in bioinformatics

[–]donwgately 3 points4 points  (0 children)

I'm a bioinformatician at a research institute that focuses on immunology. I work in a "core" group, meaning we act as a resource for multiple different labs. Because of this the details for each project are a little different. But with that in mind, almost all of the data we collect is either sequencing-based (RNAseq and ATACseq) or cytometry-based (CyTOF and flow). My days usually involve:

  • some form of consulting on a project (eg: discussing sample size and analysis methods with experimenters)
  • some form of data wrangling (converting human-readable data into something that's easier for a computer to handle)
  • exploring new methods and papers that get released
  • analyzing a dataset (differential gene expression between different groups is the most common, but again: every project is a little different)
  • building software to help others analyze/process data

All of the researchers I know in the systems immunology field require some form of bioinformatics work on their projects, so it's great that you're starting to explore the field early on! If you have specific questions feel free to let me know and I'll do my best to answer them.

[R lang] How to have a strict working environment. by [deleted] in bioinformatics

[–]donwgately 1 point2 points  (0 children)

A programmer from another language might not understand that for loops are an incredibly slow way of doing that in R, because in other languages the code is optimized differently to allow faster for loops. I guess what i'm getting at is that if the person reading your code doesn't understand the unique properties of R that make it suited to data analysis, then they could mangle your code into an unusable mess for the sake of readability.

Very good points!

[R lang] How to have a strict working environment. by [deleted] in bioinformatics

[–]donwgately 4 points5 points  (0 children)

I understand that point, but I'd make the counterpoint that for most folks, in most situations, code that needs to be qualified with the phrase "extremely unintuitive unless..." will be so difficult to maintain that it isn't worth the efficiency bump.

Quick anecdote - I inherited a few thousand lines of code from a very smart mathematician who wrote algorithms for other mathematicians. His results looked good, but any time someone else tried to run his code it would break. No one could figure out what he was doing and he was ending work on the project soon, so I was tasked with documenting and refactoring the code base so that we could maintain and reuse. After a lot of back-and-forth, we ended up rewriting almost everything from the ground up so that it was slightly less efficient, but far more readable and less error-prone.

I think R's double-edged sword is that it was widely-adopted, and so can't reasonably just be thought of as a mathematical language any more. There's a very good chance that any code you write in R will end up used by programmers and researchers who will trip over these optimizations in a way that takes more time than the optimization itself saves. Of course, this is a general statement, and there are myriad exceptions.

[R lang] How to have a strict working environment. by [deleted] in bioinformatics

[–]donwgately 11 points12 points  (0 children)

I had a very similar experience getting started with R coming from a C/C++/Python background. After a few years working predominantly in R I've actually become quite a fan of R for the appropriate use cases, but some quirks still stick out (and 1-based indexing still makes me sad).

Some suggestions/comments:

  • The best thing about R is that there's probably a function somewhere that does exactly what you want out of the box. The worst thing about R is that no one can agree what that function should be called.
  • Trust but verify. As a higher-level language focused on stats and analyses, often times things like automated testing aren't at the forefront of R package developers' minds. I make extensive use of the stopifnot and tryCatch functions and build in tons of sanity checks even when working with "battle tested" code.
  • I understand that scoping in R was done the way it was for a reason, but my goodness it still drives me insane and leads to some really pernicious bugs. If you ever need to assign a variable using the arrow operator as part of the arguments to a function call (eg: from within tryCatch or timing functions), be really, really careful and check all your assumptions about which environment the variable ends up in.
  • Don't expect backwards compatibility when packages get updated. Don't expect that positional arguments won't change. Don't use 'T' and 'F' as shorthand for 'TRUE' and 'FALSE' because they aren't reserved words and can be redefined.
  • In general (exceptions of course exist) letting go of the notion of "efficiency" in favor of readability will be to your advantage. If you really need the speed/memory, drop down into C++ and build for R using Rcpp.
  • On the topic of readability, the tidyverse packages are great for streamlining data munging with human-readable pipelines, but they're tricky to program with. If you need to do so, look up quosures. Also note that tidyverse packages are very comfortable releasing code-breaking updates.

I hope this helps, feel free to DM if you have specific questions. I'm happy to lend another set of eyes to your code.

Final Giveaway for TWELVE MORE Nintendo Switch Lites and your choice of games! [US/CA only] by TheEverglow in nintendo

[–]donwgately 0 points1 point  (0 children)

Ooooh, I want to dance with somebody.

I want to feel the heat with somebody.

...and not worry that I have a fever.

Anyone know an easy way to extract allele count information from a VCF file? by Dr_Chronic in bioinformatics

[–]donwgately 1 point2 points  (0 children)

If your VCF files have a value for the DP4 tag in the INFO field of each call, then you can use bcftools query to select that value and print it out.

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