[bip] Reproducible research

[Giovanni Marco Dall'Olio]

On Wed, Mar 4, 2009 at 1:10 AM, Giovanni Marco Dall'Olio
<dalloliogm at gmail.com> wrote:
> 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.

Hi,
so, just to say that I presented the seminar on makefiles that I was
speaking of before.
I posted it on slideshare:
- http://www.slideshare.net/giovanni/makefiles-bioinfo

Thank you all for all the suggestions and discussion in this thread.
The talk is not the best (it is always difficult to explain make), but
this thread helped me a lot when preparing the slides.




>>
>> 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
>



-- 

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