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IUBio bio-data warehouse and bioGrid
IUBio bio-data warehouse and bioGrid
BioDirectories
Directories of Bio-data
for efficient, high volume, Grid distribution of bio-data.
This is based on LDAP for a computable, networked search/retrieval
of bio-objects (as opposed to flat file databanks or web pages).
This includes an experimental LDAP-SRS gateway for
query and retrieval of biosequence and genome data housed at
IUBio Archive (/srs/ and /eugenes/ data sections).
Genomes on the Grid
gnomap v2
uses LDAP and DAS distributed directories of genome annotations and
sequence. Find out how this works at
euGenes.
This is experimental; it incorporates
new methods for building common directories of bio-data
that can be automatically searched, a needed component of the
biogrid.
BioGridRunner
Bioinformatics Data Grid application
-- is an experimental distributed computing application
for bioinformatics (biogrid),
incorporating directory services (data and software),
grid computing methods (security, authentication,
data transport and remote jobs),
and gene sequence and genomic data processing methods.
Sources and bioinformatics applications for use with BioGridRunner
are at
ftp://iubio.bio.indiana.edu/biogrid/
IUBio hopes to be part of developing biogrid efforts, with help
from partners with more advanced information grid work. Indiana
U. has a set of researchers actively involved in information grid
efforts: in
computer science, including the Globus grid project), in physics
where grid efforts are essential for their huge data set, and in
information
technology. IUBio also has good network connectivity with the
world.
Biodata to go
We would like to know of your interest for additional bio-data formats
distributed from IUBio archive (http://iubio.bio.indiana.edu) and
Bio-Mirror (http://bio-mirror.net/).
We are now providing GCG + EMBOSS
formats of a standard bio-data set including genbank-embl,
swissprot-trembl and others.
See
ftp://iubio.bio.indiana.edu/biomirror-gcg.
We are also testing the idea of redistributing SRS indices,
and would appreciate hearing of any of this would be of
interest to you.
-- Don Gilbert,
archive@bio.indiana.edu,
august 2001, updated jan 2002