benjamin-lee

4 ms·

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by benjamin-lee 2y ago
>> so it’s usually not worth spending a ton of time optimizing single-threaded performance for a single experiment when I can just perform a big MapReduce. Is this the scientific version of "rich people problems"? > Is th
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by benjamin-lee 2y ago
Author here. I love the type system. By using distinct strings to represent DNA, RNA, and protein, I can avoid silly errors while still using the optimized implementations under the hood. This is what the `bioseq` library (about two hundred
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by benjamin-lee 2y ago
Author here. This is basically the approach I am using these days to get maximum multithreaded performance for when it really counts (inner loops) [1]. I draft in Python and use Copilot to convert it to Rust, then optimize from there. Howev
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by benjamin-lee 3y ago
Not the author of this paper but am current PhD student focused on viroid discovery. There's no TEM but there are good methods such as RNAfold [0] for predicting their structures. In the case of rod-shaped RNAs, the prediction methods
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by benjamin-lee 4y ago
This looks excellent for my use case, which is visualizing viroid and viroid-like circular genomes. Right now, I reluctantly use the R version but am eager to try this out. I spent countless hours making this figure [1] for my last paper an
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by benjamin-lee 5y ago
I’m a huge fan of the moonwatch both for its beauty and history with the space program. Ever since I was 10 I’ve wanted one. However, I’m a PhD student and there’s no way I can afford to get a “real” one. The Swatch release is really attrac
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Obsidian is (almost) a Typora killer(benjamindlee.com)
1 points by benjamin-lee 5y ago|1 comments
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by benjamin-lee 5y ago
I followed this plan and lost over 100 lbs (45 kg) in about a year and have kept it off for the last five years. Even more impressively, I did it while eating the very same junk food that made me fat, albeit in different quantities. I tried
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by benjamin-lee 5y ago
Ah that makes sense. I agree with you; I’m not a huge fan of trying to infer where the types came from myself either when reading code on GitHub since it doesn’t have the inference that my IDE does.
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by benjamin-lee 5y ago
There is some logic as to why that is. Here [1] is an explanation for why it makes sense but the tldr is that you don't want to be manually importing functions such as `$` and `+`. In languages like Python, those are defined as methods
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by benjamin-lee 5y ago
You hit the nail on the head. This is just the lexicographically minimal string rotation with a canonicalization step. I have actually had this on my to-do list for a while. The truth is that the data set I'm applying this to is small
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by benjamin-lee 5y ago
Author here. This is spot on. The majority of the code I write is either piping data around to existing tools using shell scripting and Snakemake or writing the data processing code myself when there isn't a tool that does what I need.
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by benjamin-lee 5y ago
I'm sorry, I completely forgot that the file I used was from six months ago when I wrote the blog post (and then promptly forgot to publish it). In the last half year, the number of coronavirus sequences has increased dramatically. One
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by benjamin-lee 5y ago
I didn't post it because it's quite big (150M) but readily available from the NCBI Virus portal [1]. I would love to see how well other languages compete both for speed and simplicity. [1] https://www.ncbi.nlm.nih.gov&#
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by benjamin-lee 5y ago
I actually use TypeScript/JavaScript a lot for this reason, especially for biological algorithms that I want to run in the browser. The developer tooling is also as good as you can hope for, especially when using VS Code. I actually wr
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by benjamin-lee 5y ago
This is because there's four bases and each can either be included or excluded from a given combination. So there are 4*2 = 16 combinations each of which with their own letter. In all honesty, these are pretty rarely used in practice t
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by benjamin-lee 5y ago
You make a fair point that using optimized numerical libraries instead of string methods will be ridiculously fast because they're compiled anyway. For example, scikit-bio does just this for their reverse complement operation [1]. Howe
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Why I Use Nim instead of Python for Data Processing(benjamindlee.com)
256 points by benjamin-lee 5y ago|178 comments
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by benjamin-lee 6y ago
I'm not the OP but I can confirm in my own project, we found about a 10x performance gap between AssemblyScript and TypeScript. In essence, we're working on a rewrite of DNAVisualization.org[1][2], a serverless web tool for the in