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Here is the source code, AFAICT: https://github.com/DavidPierreEnard/Gene_Set_Enrichment_Pipeline https://github.com/DavidPierreEnard/Gene_Set_Enrichment_Pipe..
by breck 5y ago
Here is the source code, AFAICT: https://github.com/DavidPierreEnard/Gene_Set_Enrichment_Pipeline https://github.com/DavidPierreEnard/Gene_Set_Enrichment_Pipe...
I've been involved in GWAS before, so have an inkling of what's going on. I love the creativity in this paper.
The stuff is super fascinating, but the pipelines are still very primitive—so I encourage programmers to get involved in bioinformatics if you like this stuff! In the future I expect we see work like this accompanied by not only source code but Spore like simulations that let you explore the ideas like a video game.
- UncleOxidant 5y agoIt's written in Perl.
- jacquesm 5y agoSo?
- UncleOxidant 5y agoI have Perl Traumatic Stress Disorder from too much Perl in the 90s. Just looking at Perl code makes me break out in a cold sweat. I wish I were kidding. Otherwise, just noted that it was written in Perl.
- jacquesm 5y agoOk. It came across as a value judgement. Personally I don't much care what its written in, executable line noise or anything else as long as practitioners of that particular language do not find anything wrong with it. Scientists typically don't particularly care about the latest and greatest software development environments and practices, they simply need answers. The best way to deal with that is to help out, I personally think they should be applauded for putting their code out there, which is better than the vast majority. Including CS, for that matter.
- deleted 5y ago[deleted]
- ajsnigrutin 5y agoThe good thing with perl is, that all the code writen in the 90s still works :)
- Y_Y 5y agoPerl is (amazingly) still a thing in 2021 in quantitative biology, at least in big national labs I'm familiar with. See e.g. https://www.amazon.com/Mastering-Perl-Bioinformatics-James-Tisdall/dp/0596003072 https://www.amazon.com/Mastering-Perl-Bioinformatics-James-T...
- CoolGuySteve 5y agoIt’s hard to beat Perl when it comes to string matching performance and flexibility.
- moralestapia 5y agoActually, no. But it's some sort of technical heritage/baggage.
- vlovich123 5y agoI actually dug into it, & it's not clear. Rust & many C libraries do outperform Perl if you can stick to an NFA regex. If you like backtracking & lookaround, then it's not clear that Perl loses that much in performance. The language itself is definitely better suited to writing those regexes all over the place, so if you have two axes of performance & regex usability, I wouldn't discount Perl for those use-cases. I do suspect though that the bioinformatics field overindexes its use of Perl because that's what they know even though it's less well-suited for other things. That being said, that's usually why programmers might choose Python. Something to be said for familiarity & access to a thriving software ecosystem you're familiar with.
- moralestapia 5y agoI actually programmed it, for that exact scenario, and there's some really nice C++ libraries that outperform Perl, even in the cases you mentioned. Sure, Perl it's easier, but not necessarily faster. You can downvote this comment as well, code is code at the end of the day :^)
- mynegation 5y agoCould you please give some guidance on the topic of “what programmers could do for bioscience”? Or point to any resources doing so? Absolutely serious question.