IUBio .. Biosequences .. Software .. Molbio soft .. Network News

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IUBio bio-data warehouse and bioGrid

IUBio bio-data warehouse and bioGrid


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.


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/

Data Grids

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