[bip] Reproducible research

[Giovanni Marco Dall'Olio]

On Tue, Mar 3, 2009 at 9:03 PM, James Casbon <casbon at gmail.com> wrote:
> Hi Bip,
>
> I've been thinking about reproducible computational research in
> biology recently and I thought I'd drop it your way.  There seem to be
> several components of this, some already recognised and some not.
>
> Database and software tools are already known to be badly maintained:
> http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000136
> But that problem is very difficult.  What I am more interested here is
> the day to day work of making an analysis work again and again, and
> applying it to other data.

I have been looking at a few possible replacement for make/scons in
python, and there are a few:
- waf (http://code.google.com/p/waf/)
- paver (http://www.blueskyonmars.com/projects/paver/)

However, I never have enought time to study them and see if they are
really better than scons, or if they are too oriented to compilation
of C programs.
I have also been told of kepler (http://kepler-project.org/) as a
possible alternative to taverna, but I have never used it.

This friday I am going to present a small talk on makefiles to my
labmates, with the purpose of having some discussions over these kind
of softwares... I will let you know if some interesting alternative
comes out.

>
> Makefiles are the obvious way of doing this, and there has been some
> work around this:
> http://skam.sourceforge.net/
> http://biowiki.org/MakefileManifesto
> AFAIK python + make = scons
> http://www.scons.org/


Thank you for these links, they are very interesting.


> And these guys are doing interesting stuff with scons:
> http://reproducibility.org/ (but their tools are a bit domain specific
> for what I want)
>
> Then, there are the workflow engines, of which taverna seems the most
> enterpisey (grid!, Web services!):
> http://taverna.sourceforge.net/
> Galaxy's workflows has been coming on a bit as well:
> http://galaxy.psu.edu/
> But you can't run them from the command line (and looking at the code,
> the controller and the view are so coupled you won't be able to).  And
> you can't parametrize them.
>
> So how is BIP doing this?  I really want something simple, that can be
> used at a command line or the web, and preferably in python.
>
> James
>
> _______________________________________________
> biology-in-python mailing list - bip at lists.idyll.org.
>
> See http://bio.scipy.org/ for our Wiki.
>



-- 

My blog on bioinformatics (now in English): http://bioinfoblog.it