On Feb 7, 2013, at 3:36 PM, George Hartzell wrote:
> Fields, Christopher J writes:
>> Should put your post on a pedestal :)
>> tl;dr version: I completely agree, but we need help in order to do this.
> And therein lies the [a] problem. Don't look at me....
> I'm not coding on bioinformatics problems these days (though I'm
> available...) so _maybe_ I shouldn't have gotten up on the soapbox.
> But I'm so sick of getting into arguments (or walking away from
> them...) with Ruby and Python [and lisp and *PHP*] fans; Perl is dead,
> you can't write good code in Perl, look - Ruby has GEMS!, etc…
Right, but that's a perception not just in the Bio* world. It's larger and
more pervasive than that.
> Perl of the olden days was an easy language in which to write really
> shitty code. Even the Perl of the BioPerl heyday wasn't really much
> help; role your own OO, role your own distro-building, mountains of
> monkey-work to provide consistent POD, versioning, etc...
> But that's not the Perl that I use. I have Moose and Moo. TAP and
> the things built on it. Dist::Zilla. PerlTidy. PerlCritic. cpanm.
> MetaCPAN. Pinto. GitHub. Perlbrew. Wow.
Yes, and that is the direction we need to go in.
> It isn't any harder to write good code, for measures that I care
> about, using Perl than it is *any* of the other similar languages.
> And it's just as easy, and happens just as frequently, for people to
> write shitty (undocumented, untested, poorly managed, poorly packaged,
> ...) stuff in the other languages.
Oh, I know. I'm working on some very nice looking but terribly implemented
Python code now.
> GET OFF MY LAWN, KID! (Yeah, I know...)
> But BioPerl *is* dying. You might be standing on the shoulders of
> giants when you use it to solve a problem, but you *definitely* have
> those same giants (and their extended families) on your shoulders
> every time I see you try move the project forward. All of that
> history has become the tail that's wagging the dog.
> If all y'all are going to keep the thing alive, moving forward and
> contributing to new great works then make Apple your hero. Deprecate
> the stuff that's holding you back, give folks a path forward and move
> Have fun. Use sharp tools. Do cool science. Build cool things.
> Advance your careers (forgot that one last time). Be reasonable and
> Supporting last year's projects is someone else's business
Right, but this isn't just my show. I can't do this alone; it's simply too
much code and I don't have even 1/4 the time I used to have.
> ps. Are all y'all following this thread?
> Maybe someone should search down for this bit: "Where to start? Any
> list of this [sic] projects?" and insert a plug for the various
> open-bio projects. (But "someone" doesn't work here, he said…).
Read the original guy's post. He's completely delusional (okay, maybe not
*completely*, but he comes across as quite bitter and unrealistic).
Frankly I don't feel so bad if he wants to leave. He doesn't like messy
things. Biology is messy, if one doesn't understand that then
computational biology is not for them.