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Are there signs of wider BioJulia adoption? Looks like bio frameworks for Python, Go and even Rust still more popular. Disclaimer: I'm just checking GitHub star

by Ambix 6y ago

Are there signs of wider BioJulia adoption? Looks like bio frameworks for Python, Go and even Rust still more popular. Disclaimer: I'm just checking GitHub stars, have no glue what metrics would be more appropriate.

jakobnissen 6y ago
I can't tell how many users we have, or who they are. Unless they directly interact by e.g. raising a GitHub issue, I won't know they exist. In my broader experience, almost no bioinformaticians use Julia. I think we, as a field, are more conservative than e.g. physicists when it comes to technology. My old institute taught me Perl as the lingua franca of bioinformatics as late as 2015 (but switched to Python the year after). I think we, as a field, have been consistently fairly poor at choosing our programming tools. Old bioinfo scripts are cluttered mess of write-only spaghetti-Perl. Most bioinformaticians I know don't use Biopython or Bioperl or anything similar, but rather creates new programs or packages by either re-implementing the basics from scratch, or by duct-taping together static binaries and/or scripts through shell commands. We will never get rid of having to use static binaries or external scripts, but I think BioJulia at least have a decent chance of stopping people from re-implementing the basics again and again, and providing a central "platform" that various external scripts communicate through (e.g. an old Perl script may produce DNA as a FASTA file, when can then be fed into BioJulia). The main issue is to have bioinformaticians understand the current situation is problematic. It doesn't take much to have a big impact, I think. If we had an ecosystem of the most basic data types (biosequences, kmers, phylogenetic trees and protein structures), a collection of well-known fundamental functions to operate on them, and parsers for the 20 most common formats, we would already have a very compelling ecosystem.

by Ambix 6y ago

jakobnissen 6y ago

I can't tell how many users we have, or who they are. Unless they directly interact by e.g. raising a GitHub issue, I won't know they exist. In my broader experience, almost no bioinformaticians use Julia. I think we, as a field, are more conservative than e.g. physicists when it comes to technology. My old institute taught me Perl as the lingua franca of bioinformatics as late as 2015 (but switched to Python the year after). I think we, as a field, have been consistently fairly poor at choosing our programming tools. Old bioinfo scripts are cluttered mess of write-only spaghetti-Perl. Most bioinformaticians I know don't use Biopython or Bioperl or anything similar, but rather creates new programs or packages by either re-implementing the basics from scratch, or by duct-taping together static binaries and/or scripts through shell commands. We will never get rid of having to use static binaries or external scripts, but I think BioJulia at least have a decent chance of stopping people from re-implementing the basics again and again, and providing a central "platform" that various external scripts communicate through (e.g. an old Perl script may produce DNA as a FASTA file, when can then be fed into BioJulia). The main issue is to have bioinformaticians understand the current situation is problematic. It doesn't take much to have a big impact, I think. If we had an ecosystem of the most basic data types (biosequences, kmers, phylogenetic trees and protein structures), a collection of well-known fundamental functions to operate on them, and parsers for the 20 most common formats, we would already have a very compelling ecosystem.