[Bioperl-l] cpu time contribution

[Catherine Letondal]

Major Chai Mee Joon MajorLinux wrote:
> Hi everyone,
> 
> 
> I would like to contribute cluster cpu hours on my clusters
> to the bioperl project and also to developers/researchers 
> on this mailing list.
> 
> Just send an email to me with a brief description.
> 
> 
> Best regards,
> 
> Major Chai Mee Joon
> 
> chaimj at majorlinux.com

Hi,

Thanks to Major Chai Mee Joon, some additional Pise servers are now available
for phylogeny and database searches to the bioperl community (as well as
interactive users, and biopython programmers).

Presently, Kun is running 24x7. The parallel mode is planned for about 12
hours each day, from 1600 GMT to 0300 GMT the next day.
(www.timeanddate.com is a good site for time conversion to your city)

For instance, depending on the time of the day, and on the number of 
submissions, a single fasta can complete in about 62 mins. The bottleneck 
is rather on the network bandwith, so setting parameters to recuce blast/fasta 
report size is welcome.

The programs are available through the Pise/bioperl API 
by just specifying the name of the server with the -location
parameter (still -remote parameter in the current bioperl-run
version, sorry for that), e.g:

my $fastdnaml = $factory->program( 'fastdnaml', 
        -location => 'http://kun.homelinux.com/cgi-bin/Pise/5.a/fastdnaml.pl');

Full examples are available in the examples/pise directory or here:

http://www-alt.pasteur.fr/~letondal/Pise/bioperl-examples/blast-kun.pl
http://www-alt.pasteur.fr/~letondal/Pise/bioperl-examples/phylo-kun.pl

For the orignial web interfaces and available parameters, see: 
http://kun.homelinux.com/Pise/5.a/phylip.html
http://kun.homelinux.com/Pise/5.a/fastdnaml.html

Some alignment program are also available:
http://kun.homelinux.com/Pise/5.a/clustalw.html
http://kun.homelinux.com/Pise/5.a/dialign2.html

He has also made blast/fasta available, to run similarity searches 
on Genbank and Genpept. See: 
http://kun.homelinux.com/Pise/5.a/fasta.html
http://kun.homelinux.com/Pise/5.a/blast2.html

We (Major and I) would also like to thank Nicolas Joly for his assistance in 
making the databases available on the site. 

We appreciate any feedback or suggestions 
(see http://www-alt.pasteur.fr/~letondal/Pise/#contact). 

-- 
Major Chai Mee Joon (chaimj at majorlinux.com) -- MajorLinux.com
Catherine Letondal -- Pasteur Institute Computing Center