[bip] agile software development

[Titus Brown]

On Tue, Jul 31, 2007 at 02:46:22PM +0200, Andrew Dalke wrote:
-> On Jul 31, 2007, at 8:10 AM, Titus Brown wrote:

-> My crazy thought is to have a "code review" track at some conference.
-> Bring in your code and review it with others, and review others' code.
-> Make sure there are some master programmers there who can provide
-> deep review.

I like this idea.

Chris Lee and I are planning to bring some code to the biology BoF at
SciPy.  I don't know that we'll have time for much of a review, but it's
a good idea for the next SciPy.

-> How do we instill a rapid/iterative/agile ;) "peer-review oriented
-> culture" in biology software?

I think it has to be built within a single lab or community, at least to
start with.

-> > See http://genomebiology.com/2007/8/2/103 for one significant  
-> > example of
-> > computational science gone awry.
-> 
-> All I could read was the abstract. [ ... ]
-> 
-> Did anyone blog about the article?  Not that I can find.  Only 20 more
-> months until it's public!  Guess I'll get myself over to the library
-> when I go into town tomorrow.

http://pyre.third-bit.com/blog/archives/877.html

Oh, and while you're at it:

	http://pyre.third-bit.com/blog/archives/864.html

You might also be interested in the Software Carpentry stuff that Greg
Wilson and others (me included) are pushing.  http://www.swc.scipy.org/

-> I think the reference to "waterfall design", when brought up
-> in the various pro-agile/xp debates, is a straw man argument.
-> Very few people use that approach.

... you would be surprised how many people are *taught* that, and how
many teachers will *defend* it.  It's not a straw man to them ;)

-> Have you come across the term "quality without a name", usually
-> written "QWAN"?  It has unfortunate Zen connotations.  I think
-> of it in part as a way to say "but I'm not naming any buzzword."

Yes -- see Richard Gabriel's _Patterns of Software_,

	http://www.dreamsongs.com/Files/PatternsOfSoftware.pdf

for an excellent discussion of software development in general.

-> Compare this chemical informatics, where I spend most of
-> my time.  Lots of graph structures, and nodes and edges
-> in the graph (atoms and bonds) have properties.  This is
-> much harder to do in Perl than in Python.  And you can see
-> there's more Python code in chemical informatics than Perl.

Are you familiar with pygr,

	http://bioinfo.mbi.ucla.edu/pygr

?

-> As long as I'm blabbering on, I think Taverna is a counter-
-> example.  I think it's an example of "throw enough smart
-> people at a project and they can do it".  I've been told
-> that getting up to speed, to write a new Taverna service,
-> will take a newbie several days to do.  While that might
-> have changed in the last 6 months, it doesn't make me
-> feel all warm and fuzzy inside.  I figured it should take
-> a few to 30 minutes.

I'll take a look; I don't know much about it.  I've heard some good
(it's usable!) and bad (it's ugly as sin inside) things about
BioConductor.  Anything else to look at?

Part of the background of this list is that James Taylor (PSU/NYU),
Chris Lee (UCLA), and a bunch of local Caltech people (Diane Trout,
Brandon King, Stefan Materna, Tracy Teal, Andy Cameron, etc. etc.) have
all had problems with biology software.  I'm hoping we can use this list
to at least make contact with other people who care, and down the road
we may be able to foster some sort of common infrastructure.  So this is
definitely an apropos conversation to be having.

cheers,
--titus