JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow

BMC Bioinformatics. 2006;7(1):513 DOI 10.1186/1471-2105-7-513

 

Journal Homepage

Journal Title: BMC Bioinformatics

ISSN: 1471-2105 (Online)

Publisher: BMC

LCC Subject Category: Medicine: Medicine (General): Computer applications to medicine. Medical informatics | Science: Biology (General)

Country of publisher: United Kingdom

Language of fulltext: English

Full-text formats available: PDF, HTML

 

AUTHORS

Martinez Veronica
Vizoso Paula
Guziolowski Carito
Saba Juan
Silva Herman
Latorre Mariano
Maldonado Jonathan
Morales Andrea
Caroca Rodrigo
Cambiazo Veronica
Campos-Vargas Reinaldo
Gonzalez Mauricio
Orellana Ariel
Retamales Julio
Meisel Lee A

EDITORIAL INFORMATION

Blind peer review

Editorial Board

Instructions for authors

Time From Submission to Publication: 19 weeks

 

Abstract | Full Text

<p>Abstract</p> <p>Background</p> <p>Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task.</p> <p>Results</p> <p>In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project.</p> <p>The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses.</p> <p>Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access.</p> <p>Conclusion</p> <p>JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in fruit exportation". However, due to its ability to organize and visualize data from external pipelines, JUICE is a flexible data management system that should be useful for other EST/Genome projects. The JUICE data management system is released under the Open Source GNU Lesser General Public License (LGPL). JUICE may be downloaded from <url>http://genoma.unab.cl/juice_system/</url> or <url>http://www.genomavegetal.cl/juice_system/</url>.</p>