What is PARIS 2.0?

PARIS (Proteomic Analysis and Resources Indexation System) is a suit of software to manage and analyse the data from 2D electrophoresis based proteomic analysis. It stores information about experiments and analysis procedure, allows the user to search and navigate in genomic and proteomic data, supports visual verification and validation of the analysis results, and provides tools for cross multi-experiment and multi-experimenter data validation and exploration.

Based on a 3-tier architecture, PARIS consists of a PostgreSQL based database server, an integrated research engine and a graphical user interface. The database server manages data regarding experimentation, including sample preparation through biological interpretations of the results while passing by parameter settings of used analysis procedure. It also stores information necessary to connect with external genomic and proteomic resources such as GenBank, SWISS-PROT and KEGG.

The search engine analyses the queries formulated by biologist, provides fast, highly selective access to internal and external data sources, and structures the search results. From information provided by the biologist, it defines a search strategy taking into account the availability of local data and external sources, starts appropriate processing, and structures the provided information in order to facilitate its reading and interpretation. An important feature that distinguishes our system from others is that queries implemented in PARIS are not limited in means for accessing the needed entries in the database, and they also discover relations that were not explicitly noticed in the data but can be derived from them.

Based on Java 2D Graphics, the graphical interface enables users to visualize, to compare, and to correct or validate the results of analysis. It provides most of the basic functionalities of an image manipulation tool such as zooming, scrolling, region-of-interest (ROI) selection and image contrast enhancement as well as spot emboss and gradient computing. Other functions give helps to understand the relationships which exist in the proteomic data. The spot where the mouse cursor is over is highlighted, and the associated genomic and proteomic information is displayed. Given a term such as spot, protein, physiochemical characteristics, etc, we can retrieve all gels having relationships with this term, display the gels in a set of windows, and highlight, by using pseudo-colors, particular relationships such as spot matching, deduced spot matching, and matched spots ramification, etc.

PARIS is particularly designed for maximizing the system usefulness. It exploits the Web Services technology and assists the users to formulate their queries . Users can either select queries from a established list or compose queries by combining previous queries. Complex queries can be formulated from elements directly selected on the images and be previewed before being submitted to the search engine.

Getting PARIS

PARIS is an open source, freely available software released under the CeCILL Licence Version 2. To download the different components of PARIS from this site, please refer to the listing on the right of this page.

PARIS has been tested on Mandrake Linux 8.0, Mandriva 10.0, and Windows XP Professional under the following environment: SUN, Java(TM) 2, Standard Edition. We strongly recommend you to use that environment. Although we're not sure its compatibility when working with other operating systems, PARIS should be JAVA compliant.

If the Java Web Start tool has been installed in your machine, you can try the client component of system PARIS by simply clicking here.

Referencing PARIS

Examples of applications and technical information about the system PARIS can be found in the publications as follow:

Juhui Wang, Christophe Caron, Xuefeng He, Audrey Carpentier, Michel-Yves Mistou, Alain Trubuil, Christophe Gitton, Céline Henry, and Alain Guillot. A system for integrative and post-planned analysis of 2DE-MS centred proteomics data , «2005 Year-Book of Integrative Bioinformatics» , Editor, Dr. Ralf Hofestädt, Publisher Shaker Verlag, April 2006.
Christophe Gitton, Mickael Meyrand, Juhui Wang, Christophe Caron, Alain Trubuil, Alain Guillot, and Michel-Yves Mistou. Proteomic signature of Lactococcus lactis ncdo763 cultivated in milk. Applied and Environmental Microbiology, November 2005, pages 7152-7163, Vol. 71. No. 11.
Juhui Wang, Christophe Caron, Xuefeng He, Audrey Carpentier, Michel-Yves Mistou, Alain Trubuil, Christophe Gitton, Céline Henry, and Alain Guillot. A system for integrative and post-planned analysis of 2DE-MS centred proteomics data, Journal of Integrative Bioinformatics, November, 2005.
Juhui Wang, Christophe Caron, Michel-Yves Mistou, Christophe Gitton, and Alain Trubuil. PARIS : a Proteomic Analysis and Resources Indexation System. Journal of Bioinformatics, 20(1):133-135, January 2004.
Juhui Wang, Christophe Caron, Michel-Yves Mistou, Christophe Gitton. Integrative and post-planned analysis of proteomics data . In International Workshop on Integrative Bioinformatics : Complex Metabolic Networks, pages 17-20, Bielefeld, Germany, July 2005.
Juhui Wang, Christophe Caron, Michel-Yves Mistou, Christophe Gitton, and Alain Trubuil. PARIS : a system for 2-DE based proteomic data management, ECCB’2003, Paris, France (Oral Presentation).
Juhui Wang, Christophe Caron, Michel-Yves Mistou, Christophe Gitton, and Alain Trubuil. A System for Proteomic Data Management and Post-Planned Analysis, HUPO First World Congress, 2001, Versailles, France (Poster Presentation).

Latest Version
PARIS is an open source, freely available software released under the CeCILL Licence Version 2. Download the latest ersion v2.0 by clicking : here

User's Guide
The User's Guide can be viewed on-line via here or downloaded as a pdf file via here.

OS Requirements
PARIS is Java compliant. It runs on the Microsoft Windows, Linux, or Mac OSX operating system and requires Java 1.4.1 or higher.

Technical Support
If you need help, please contact {Juhui.Wang}@jouy.inra.fr.

Credits
PARIS is developed by the units of MIA and MIG , INRA-Jouy, Domaine de Vilvert, 78352 Jouy en Josas, FRANCE. Numerous biology laboratories have contributed to its maturation such as BIOBAC, FLEC , etc.

Fundings
This work has benefited from the following grants:
1) "Collaborative analysis of electrophoresis gels", inter-EPST Program on bioinformatics, CNRS, INSERM, INRA, INRIA, Ministry of Research; 2001.
2)"Statistical methods for genome profiling from electrophoresis gel", inter-EPST Program on bioinformatics CNRS, INSERM, INRA, INRIA, Ministry of Research, 2002.
3) "ProteHome", Program of the RNG (Réseau National des Génopôles), 2006.