3 ms·

How interesting. I’m surprised that I’d never heard of this before.

the_only_law 5y ago
I remember many years ago, outside programming I had a moderate interest in biology. I recall looking into bioinformatics, and reading about Python, but also about how popular Perl was in field. This was 5-10 years ago, though the sources I was reading very likely could have been 15 years old or more.
- leephillips 5y ago
  The first thing that occurs to me, and this may be superficial, is that bioinformatics has a linguistic character to it, with pattern matching of sequences and so forth, and this is something where Perl is more adept than most other languages.
  - etangent 5y ago
    your hunch is correct
  - f6v 5y ago
    Bioinformatics today is much more about complex statistical models applied to sequencing data. There’s some pattern matching when doing low-level FASTQ processing for your fancy combinatorial barcoding. But other than that you need tools capable of processing huge datasets. Python ecosystem fits better in modern era.
    - warlog 5y ago
      Which .env fits better, exactly?
    - MontyCarloHall 5y ago
      Yup. I’ll occasionally still break out Perl for quickly parsing FASTQs/SAM alignments/VCFs on the command line when sed/awk/grep won’t cut it, but for everything else it’s Pandas, NumPy/SciPy, Torch, and TensorFlow.
- gvurrdon 5y ago
  Perl was extremely popular 20+ years ago in biology; I made the jump from the lab bench to bioinformatics with Perl and Bioperl (https://bioperl.org/ https://bioperl.org/). But, after a while I discovered Ruby, and later Python, and moved on, also switching to other fields. The presence of Perl and a "proper" terminal on Mac OS X back then was a big draw in encouraging bioinformaticians to use it (well, that is my recollection, anyway).
  - kingaillas 5y ago
    This tickled a memory... I remember seeing a Bioinformatics for Perl book ~20 years ago. I found it on O'reilly's website: https://www.oreilly.com/library/view/beginning-perl-for/0596000804/ https://www.oreilly.com/library/view/beginning-perl-for/0596... Searching more I see a Python one appears in 2009: https://www.oreilly.com/library/view/bioinformatics-programming-using/9780596804725/ https://www.oreilly.com/library/view/bioinformatics-programm... And now there are several out. Plus expanded topics like Python and Machine Learning, Python and Data Analysis, etc.
    - gvurrdon 5y ago
      That first was a good book - there's still a copy on my shelf in the office, I think, though I've not had chance to go there in person to check recently.
- pvaldes 5y ago
  Perl has its own branch for bioinformatics. The Bioperl modules. https://bioperl.org/ https://bioperl.org/

I remember many years ago, outside programming I had a moderate interest in biology. I recall looking into bioinformatics, and reading about Python, but also about how popular Perl was in field. This was 5-10 years ago, though the sources I was reading very likely could have been 15 years old or more.

leephillips 5y ago
The first thing that occurs to me, and this may be superficial, is that bioinformatics has a linguistic character to it, with pattern matching of sequences and so forth, and this is something where Perl is more adept than most other languages.
- etangent 5y ago
  your hunch is correct
- f6v 5y ago
  Bioinformatics today is much more about complex statistical models applied to sequencing data. There’s some pattern matching when doing low-level FASTQ processing for your fancy combinatorial barcoding. But other than that you need tools capable of processing huge datasets. Python ecosystem fits better in modern era.
  - warlog 5y ago
    Which .env fits better, exactly?
  - MontyCarloHall 5y ago
    Yup. I’ll occasionally still break out Perl for quickly parsing FASTQs/SAM alignments/VCFs on the command line when sed/awk/grep won’t cut it, but for everything else it’s Pandas, NumPy/SciPy, Torch, and TensorFlow.
gvurrdon 5y ago
Perl was extremely popular 20+ years ago in biology; I made the jump from the lab bench to bioinformatics with Perl and Bioperl (https://bioperl.org/ https://bioperl.org/). But, after a while I discovered Ruby, and later Python, and moved on, also switching to other fields. The presence of Perl and a "proper" terminal on Mac OS X back then was a big draw in encouraging bioinformaticians to use it (well, that is my recollection, anyway).
- kingaillas 5y ago
  This tickled a memory... I remember seeing a Bioinformatics for Perl book ~20 years ago. I found it on O'reilly's website: https://www.oreilly.com/library/view/beginning-perl-for/0596000804/ https://www.oreilly.com/library/view/beginning-perl-for/0596... Searching more I see a Python one appears in 2009: https://www.oreilly.com/library/view/bioinformatics-programming-using/9780596804725/ https://www.oreilly.com/library/view/bioinformatics-programm... And now there are several out. Plus expanded topics like Python and Machine Learning, Python and Data Analysis, etc.
  - gvurrdon 5y ago
    That first was a good book - there's still a copy on my shelf in the office, I think, though I've not had chance to go there in person to check recently.
pvaldes 5y ago
Perl has its own branch for bioinformatics. The Bioperl modules. https://bioperl.org/ https://bioperl.org/