KOINA - Proteomics machine learning for everyone!

 

There have been some bioinformatics initiatives where the goal has been "any dumbass can do this, even you!" and it has turned out that 

(pronounced doom basses, the latter word sounds like the instruments) 

Is KOINA really something we could all use, regardless of what languages we do/don't know and how very long ago we had any formal training in informatics? I'm not sure, but the authors seems to have tried really really hard to make it so. 

The first problem a lot of people run into when integrating tools into other tools is what language is supported? Machine learning is almost always in Python and proteomics people like Java and various versions  of C. 

30 different tools are integrated into KOINA in an attempt to both make this all more open and to show off that they can take data from and to different languages! 

The next thing is that even within the same programs peptide annotations can be completely different. Ever try to make a Venny from a peptide list from 2 different software packages? Chances are zero overlap because someone's like, "let's absolutely for no reason whatsoever provide the c-terminal amino acid with a period after it AND THEN let's make up a non-standard abbreviation for this PTM and put it in italics while underlining a random letter in this non-standard abbreviation" one of those is absolutely real, the other one probably is, I don't know everything.

So the high school sized list of KOINA authors decided to do something no proteomic informatics person in all of history has ever tried. 

THEY CONSULTED THE PROTEOMICS STANDARDS INITIATIVE (we have a proteomics standards initiative????) (PSI)

I just got back from International Human Proteomics and rumor was that this year's secret meeting of our field's least popular group of people was held in the nosebleed section of the Sabrina Carpenter concert, ensuring that they actually annoyed more people this year with their suggestions of how making up new ways of doing the same things is stupid and we should stop, and that no one who could possibly need this lesson heard them. 

KOINA includes steps to convert peptide level annotations to a standardized format that PSI suggested that we all use at some point and we all pointedly ignored. 

I need to get going, but if you read this far (sorry) you should check out KOINA here!