Thursday, September 10, 2015

Run complete programs on any system with BioDocker! Wait...what's a BioDocker?

Okay. I'm going to be pretty excited about this whole thing, cause I knew about exactly none of this 20 minutes ago.

It is totally awesome that we have all these talented programmers and bioinformaticians out there writing interesting new code. A problem is that, just like any expert in anything, they start talking their expert-ese and it becomes hard for outsiders to figure out what they are talking about. I take things about proteomics -terms and such, for granted all the time even though I try very hard not to.

This is an acknowledged problem in their field. That they can't reach users cause sometimes users don't know what a Perl thingy is.  Even worse, maybe someone assumes that you have that Perl thing on your PC because they've had it on every PC they've owned in the last 15 years.

An awesome effort is underway and its called Docker. Its generic for everybody, but what I can understand of it is that its a "container" for a program that includes all the requirements for running it. Say you need that Perl thing and some Perl add-in things, then it would be included in the Docker.

A more focused thing for us is BioDocker. Same goal, but specifically for bioinformatics type stuff.  Sounds great, right?!?

BTW, I'm learning all this from Yasset's blog.
Cause you know what? They've already constructed two awesome proteomics BioDockers.  The first is the all-powerful Trans Proteomics Pipeline and the second is the DIA-Umpire!

Is it simple enough that a dummy like me can use it? Actually...I think it might be...not without challenges, but its getting there!

If it isn't 100% what we need/want right now, its a great step in the right direction. Lets get all these awesome tools and put them into an easily digestible format. They get more users which hopefully translates into more grant justifications and more cool algorithms and we get better data!  Win win win!

1 comment:

  1. Hi Ben:
    As you can see BioDocker has been growing from the proteomics community. We
    already have multiple containers for the protemics community here: Most of the search engines, etc. Please if you think we should include more information, basic examples of how to use the containers, all suggestions are more than welcome.
    Thanks for this post