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Bioinformatics Advance Access originally published online on January 12, 2005
Bioinformatics 2005 21(9):1754-1757; doi:10.1093/bioinformatics/bti246
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

AGML Central: web based gel proteomic infrastructure

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

1Department of Biostatistics, Bioinformatics and Epidemiology 135 Cannon Street, Suite 303, P.O. Box 250835, Charleston, SC 29425, USA
2Division of Nephrology, Department 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.

Summary: AGML Central is a web-based open-source public infrastructure for dissemination of two-dimensional 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

Contact: stanisrc{at}musc.edu


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