[Bioperl-l] question about the nature of bioperl

[Wiepert, Mathieu]

Late to the game, not wanting to beat a dead horse, but...

First a commentary.  I always find it interesting that people get scared when things become complicated.  Things always start simple, working the easy 80%.  Then suddenly software bloats, to handle all the hard stuff.  Then a new group says "I can do this more simply", and they do in the beginning.  And then they see all the hard parts, start bloating, and on it goes.  You can pretend that things can be made simple, and they can, for the simple case.  As a newbie looking up (me), it looks like a big black cloud.  As a core developer looking down, I could see someone probably thinking "What is so hard?"

Here is simplicity:  if you are doing bioinformatics (whatever the heck that is these days)and think you need to use perl, use bioperl.  You will learn more in a week of trying to figure out why things are the way there are, and get more than a few "Oooohhh, *THAT'S* why they did that" occurrences (plenty of "Why *did* the do that" as well ;-)  Take Chris' point to heart:  you start simple, then start hitting all those pesky real-life use cases that didn't quite fit.  Add an if/elsif and repeat.  Get scaffolded creaky code.  At least you can count on bioperl (mostly) *not* be the problem.  And if it is, look at all these people ready to give you a hand.  I have no one else to ask around here, I am one of those small labs with no support (not even a supervisor to advise me wrong ;-)  And I have been chided enough to at least try to look at docs before I ask the simple questions.  Problem is sometimes TFM is not that good.  This is open source after all, and not many people are jumping up and down volunteering to document it.  (A great place for a new person to jump in, perhaps blogging how they used it) 

And don't forget, now there is bioperl-pipeline asking for help (use cases) from people just like you, so they can design a better system.  How great is that...	

Lastly, I was really glad to see that you would contribute scripts as you write them.  Modular, simple one-off scripts that read a list of blast files and parse them are really good, easily copied things.  Also, the tutorial is very good, and perhaps as time goes on will develop into the bioperl-newbie tutorial, the bioperl-intermediate tutorial, and the bioperl-guts developer info sheet.  Give all levels a place to go.

Back to lurking...

-Mat

I mean no offense to anyone, especially being new to this 
> mailing list, but
> I
> am starting to wonder just what people expect from this 
> project.  Is this
> supposed to be a do-it-all bioinformatics kit or a set of 
> basic tools that
> people are free to use, fleshing it out with their own code 
> as per their
> specific application?  It just seems to me that, if not 
> already, the project
> is on its way to being what is referred to as a "bloated monster" in
> computer
> science classes.  Everyone has their "bug" catches, specific 
> formats, and
> there are multiple versions flying around with varying degrees of
> documentation and testedness.  Whoa horse.  Stop.  Trying to 
> account for
> every
> single format or user-defined case is in my opinion folly and 
> impossible,
> especially given the nature of bioinformatics.  Define a 
> broad but simple
> suite that is flexible to specifics and leave the rest to the 
> users.  That's
> what Perl was made for by definition: TIMTOWTDI.  This was 
> (is?) probably
> the
> idea with bioperl also, but in browsing the hierarchy 
> diagrams and reading
> the
> emails, it sounds like a big confused mess that several(?) 
> people are trying
> so hard to keep in order but the task is too big.  Simplify 
> simplify.  I
> think
> there comes a point where too many "bugs" (real or not) means 
> more than
> debugging.  Easier said than done I know.  Heh.  Pay me no mind.
> 
> Best regards,
> 
> Nathanael Kuipers
> 
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