Viewing profile — benjamin-lee

>> 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 v…

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 th…

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 Co…

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. …

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…

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 aff…

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 fo…

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…

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 `+`.…

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 tr…

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 cod…

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 o…

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 simplic…

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…

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 …

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 jus…

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 DNAVisuali…