BioSequences.jl

A while back, user xvilka posted a short list of OS tools used to combat diseases. I've got some free time to contribute to some issues, what are the OS tools used to combat diseases and epidemics? xvilka's list: https://biojulia.net/ https://github.com/BioJulia https://biopython.org/ https://github.com/biopython/ https://github.com/BioJulia/BioSequences.jl/issues https://opencollective.com/biojulia#backer

If you are not a scientist this doesn't mean you can't help fighting this particular or any other infectious and non-infectious disease. It is easy - just help to improve the tools that scientists and laboratories use. For example, something like BioJulia[1][2] and BioPython[3][4] - both have some issues[5][6] that need help with or accepting donations[7]. Or R packages, like survival[8]. There are many other tools that are used, feel free to list them in the comments. [1] https://biojulia.net/ [2] https://github.com/BioJulia [3] https://biopython.org/ [4] https://github.com/biopython/ [5] https://github.com/BioJulia/BioSequences.jl/issues [6] https://github.com/biopython/biopython/issues?q=label%3A%22h... [7] https://opencollective.com/biojulia#backer [8] https://cran.r-project.org/web/packages/survival/index.html

Response from the BioJulia developers: https://biojulia.net/post/seq-lang/. High-level points: * they were able reproduce the performance comparison between Seq and BioJulia * BioJulia spends most of its time on these benchmarks validating and transcoding data into a more compact, efficient representation of gene sequences * Seq, on the other hand, operates on the raw ASCII input data and does no validation * BioJulia devs implemented Julia types that representing gene sequences the same way as Seq does in less than 100 lines of Julia code [1] * when using the same representation in as Seq, BioJulia was significantly faster than Seq * BioJulia devs were able to further optimize transcoding of gene sequences to get a 10x performance improvement [2] * with these improvements BioJulia reaches similar performance to Seq while still doing vali

If you are not a scientist this doesn't mean you can't help fighting this particular or any other infectious and non-infectious disease. It is easy - just help to improve the tools that scientists and laboratories use. For example, something like BioJulia[1][2] and BioPython[3][4] - both have some issues[5][6] that need help with or accepting donations[7]. There are many other tools that are used, feel free to list them in the comments. [1] https://biojulia.net/ [2] https://github.com/BioJulia [3] https://biopython.org/ [4] https://github.com/biopython/ [5] https://github.com/BioJulia/BioSequences.jl/issues [6] https://github.com/biopython/biopython/issues?q=label%3A%22h... [7] https://opencollective.com/biojulia#backer