4 ms·

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

by xvilka 7y ago

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/ https://biojulia.net/ [2] https://github.com/BioJulia https://github.com/BioJulia [3] https://biopython.org/ https://biopython.org/ [4] https://github.com/biopython/ https://github.com/biopython/ [5] https://github.com/BioJulia/BioSequences.jl/issues https://github.com/BioJulia/BioSequences.jl/issues [6] https://github.com/biopython/biopython/issues?q=label%3A%22help+wanted%22+is%3Aissue+is%3Aopen https://github.com/biopython/biopython/issues?q=label%3A%22h... [7] https://opencollective.com/biojulia#backer https://opencollective.com/biojulia#backer

bordercases 7y ago
Are these tools really used by disease labs?
- Fomite 7y ago
  Yes. I run an infectious disease modeling lab - while I don't use these tools, I know people who do. In my lab, we use R, Numpy, SciPy, StochPy, etc. You could also just see about donating directly to a lab at a nearby university.
  - yread 7y ago
    Scary username!
  - zhdc1 7y ago
    What are some of the R libraries that your team uses? I wouldn't mind donating some time to help with bug fixes. I have no idea though which R libraries/projects are being used.
    - Fomite 7y ago
      Lets see... survival, parallel/snow, Amelia2, nlme,vioplot,ggplot2 and deSolve are the big ones.
- DangerousPie 7y ago
  In my anecdotal experience almost all new comp bio methods are implemented and used in R. Python is starting to become a bit more common but is still the minority. When performance matters people sometimes go for C/C++. I have never seen anyone actually using Julia but I guess there may be one or two.
spectramax 7y ago
Does anyone use Julia in production?
- floatingatoll 7y ago
  Yes.
  - soVeryTired 7y ago
    Maybe you can elaborate on that?
ChrisRackauckas 7y ago
And an interesting note of Biosequences versus the new Seq language: https://biojulia.net/post/seq-lang/ https://biojulia.net/post/seq-lang/

by xvilka 7y ago

bordercases 7y ago

Are these tools really used by disease labs?

Fomite 7y ago
Yes. I run an infectious disease modeling lab - while I don't use these tools, I know people who do. In my lab, we use R, Numpy, SciPy, StochPy, etc. You could also just see about donating directly to a lab at a nearby university.
- yread 7y ago
  Scary username!
- zhdc1 7y ago
  What are some of the R libraries that your team uses? I wouldn't mind donating some time to help with bug fixes. I have no idea though which R libraries/projects are being used.
  - Fomite 7y ago
    Lets see... survival, parallel/snow, Amelia2, nlme,vioplot,ggplot2 and deSolve are the big ones.
DangerousPie 7y ago
In my anecdotal experience almost all new comp bio methods are implemented and used in R. Python is starting to become a bit more common but is still the minority. When performance matters people sometimes go for C/C++. I have never seen anyone actually using Julia but I guess there may be one or two.

spectramax 7y ago

Does anyone use Julia in production?

floatingatoll 7y ago
Yes.
- soVeryTired 7y ago
  Maybe you can elaborate on that?

ChrisRackauckas 7y ago

And an interesting note of Biosequences versus the new Seq language: https://biojulia.net/post/seq-lang/ https://biojulia.net/post/seq-lang/