title: JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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. 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. 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.
  
  
  CONCLUSIONS
  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 http://genoma.unab.cl/juice_system/ or http://www.genomavegetal.cl/juice_system/.
authors.affiliation: Millennium Nucleus in Plant Cell Biology and Plant Biotechnology Center, Andres Bello University, Santiago, Chile. marianolatorre@gmail.com <marianolatorre@gmail.com>
authors.forename: Mariano
authors.initials: M
authors.lastname: Latorre
authors.forename: Herman
authors.initials: H
authors.lastname: Silva
authors.forename: Juan
authors.initials: J
authors.lastname: Saba
authors.forename: Carito
authors.initials: C
authors.lastname: Guziolowski
authors.forename: Paula
authors.initials: P
authors.lastname: Vizoso
authors.forename: Veronica
authors.initials: V
authors.lastname: Martinez
authors.forename: Jonathan
authors.initials: J
authors.lastname: Maldonado
authors.forename: Andrea
authors.initials: A
authors.lastname: Morales
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Caroca
authors.forename: Veronica
authors.initials: V
authors.lastname: Cambiazo
authors.forename: Reinaldo
authors.initials: R
authors.lastname: Campos-Vargas
authors.forename: Mauricio
authors.initials: M
authors.lastname: Gonzalez
authors.forename: Ariel
authors.initials: A
authors.lastname: Orellana
authors.forename: Julio
authors.initials: J
authors.lastname: Retamales
authors.forename: Lee A
authors.initials: LA
authors.lastname: Meisel
mesh_terms: D002845:Chromatography / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D016678:Genome; D023281:Genomics / Q000379:methods; D008331:Management Information Systems; D011381:Programming Languages; D017422:Sequence Analysis, DNA; D012984:Software