%0 Journal Article
%T GTC: A web server for integrating systems biology data with web tools and desktop applications
%A Dan Tenenbaum
%A J Christopher Bare
%A Nitin S Baliga
%J Source Code for Biology and Medicine
%D 2010
%I BioMed Central
%R 10.1186/1751-0473-5-7
%X There are hundreds of public databases for systems biology data, and an equal number of applications for working with that data. However, it is often difficult to work with data of interest in the desired applications. Databases may not offer programmatic access, or require special scripting. Software tools may imprison the data in such a way that it can only be analyzed by a particular application. Data available for one organism may not be available for another. Individuals may have to download their own copies of databases in order to work with them in nonstandard ways, forcing them into the role of curator. Software tools may not allow users to work with their own data. Applications may only accept data in arcane formats, requiring special conversion.Here we describe Gaggle Tool Creator (GTC), a web application which addresses these problems by providing public data for hundreds of organisms, and making it instantly accessible to many popular, unrelated web resources and desktop applications. This in turn allows sophisticated analyses and novel discoveries to be achieved with just a few mouse clicks (Figure 1).GTC is composed of a number of MySQL databases, regularly updated by scheduled scripts which download systems biology data from public sources. These sources, and the method used to download data from each, are as follows: NCBI (web services), STRING[1] (flat file download), BioNetBuilder[2] (flat file download), KEGG[3] (web services), and the UCSC genome browser[4] (flat file download). We currently have data for 500 organisms, with the eventual goal of having data for all sequenced organisms. The core of GTC is a Java web application which makes available links to several applications suited to the analysis of particular types of data. These applications are launched using Java Web Start, a technology which seamlessly pushes software updates to the user's computer. All of these applications implement the Gaggle framework [5] for sharing data between app
%U http://www.scfbm.org/content/5/1/7