Biosoftware bench
Contents
Overview
The Bioinformatic Software Bench (BSB) for Drupal allows for a rapid and
secure deployment of bioinformatic software. The BLAST, InterProScan,
SSAHA2 and annot8r software are provided by default and plugins for new
software can be readily written. An innovative graphical user interface
guides both end-user and administration of the software, including the
secure provision of pre-publication datasets.
It is available from
http://drupal.org/project/biosoftware_bench or
http://gmod-dbsf.googlecode.com with the latter being
a more complete repository.
Dependencies
BSB is written for
Drupal
6 and it depends on the Drupal gmod_dbsf module
(http://drupal.org/project/gmod_dbsf). The NCBI
BLASTALL package and other relevant software for each plugin are
required in order to provide the relevant facilities but administrators
can choose which software to enable.
Features
It has a number of attractive features:
For the system administrator:
- Secure & fast to deploy: the demonstration required 30’ to setup from
scratch, 10’ of which was the BLAST server. The administrator has to
merely click on a checkbox to activate the software and then choose
which databases will be available to the plugins.
- Secure with private data: We know that laboratories often have two
types of data: those they wish to make public and the unpublished ones
they wish to utilize only in-house. The solution is often the creation
of two separate servers, one password protected. The DBFS takes care
of user management and allows you to choose which datasets are
available to which users. An unlimited number of user groups can be
created included the anonymous/guest visitor who has not logged in.
- Plugin format: It comes with NCBI’s BLASTALL but DBFS is an API
framework and easy to extend, our publication will have a manual as
supplementary material to guide bioinformaticians in writing their
plugins with 1-2 days.
- High Performance Computing (HPC) support: Optionally, it can utilise
the Condor job management system so jobs run on a PC-farm instead of
the often meek BLAST server. A perl daemon manages the submissions
automatically.
- Database API is Chado-compatible: It is GMOD compatible and uses the
robust, normalized Chado database. As Chado is sequence feature-driven
we created sequence-less table set which follows Chado-convention. The
future aim is to be able to integrate multiple website deploying this
software.
For the end-user:
- Build for wet-lab researchers. They can upload a multi-FASTA file to
be used as the query or even the reference database: there is no need
to restrict the user to the administrator’s datasets. The file size
limit is customizable. Users can bookmark their search and re-retrieve
it within 7 days. Further, they can simultaneously run multiple BLAST
algorithm searches.
- Driven by open-source software and adheres to community standards: The
output is driven by BioPerl? (XML, HTML, TXT and a graph using
Bio::Graphics). The database infrastructure is GMOD-compatible and the
visualization is securely managed by Drupal.
Demos and Screenshots
License
This software is GPLv2+ licensed as part of the Drupal package. It is
currently supported by Alexie
Papanicolaou while at CSIRO, the
Australian Commonwealth Scientific and Research Organization
(http://www.csiro.au).
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