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Bioinformatics Advance Access published online on January 12, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti246
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received August 17, 2004
Revised December 17, 2004
Accepted December 20, 2004

Article

AGML central: web based gel proteomic infrastructure

Romesh Stanislaus 1*, Chuming Chen 1, Jennifer Franklin 1, John Arthur 2, and Jonas S. Almeida 1

1 Dept Biostatistics, Bioinformatics & Epidemiology, Medical University of South Carolina, 135 Cannon Street, Suite 303, P.O. Box 250835, Charleston, SC 29425, USA
2 Div. Nephrology, Dept. of Medicine, Medical University of South Carolina, 135 Cannon Street, Suite 303, P.O. Box 250835, Charleston, SC 29425, USA

* To whom correspondence should be addressed.
Romesh Stanislaus, E-mail: stanisrc{at}musc.edu


  Abstract

Summary: AGML Central is a web-based open-source public infrastructure for dissemination of 2-D Gel Electrophoresis (2-DE) proteomics data in AGML format (Annotated Gel Markup Language). It includes a growing collection of converters from proprietary formats such as those produced by PDQUEST (BioRad), PHORETIX 2-D (Nonlinear Dynamics) and Melanie (GenBio SA). The resulting unifying AGML formatted entry, with or without the raw gel images, is optionally stored in a database for future reference. AGML Central was developed to provide a common platform for data dissemination and development of 2-DE data analysis tools. This resource responds to an increasing use of AGML for 2-DE public source data representation which requires automated tools for conversion from proprietary formats. Conversion and short-term storage is made publicly available, permanent storage requires prior registering. A JAVA applet visualizer was developed to visualize the AGML data with cross-reference links. In order to facilitate automated access a SOAP web service is also included in the AGML Central infrastructure.

Availability: http://bioinformatics.musc.edu/agmlcentral.


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