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Make2D-DB II

The Make2D-DB II Package

current version: 3.10.2 -- December 2011

Make2D-DB II is an environment to create, convert, publish, interconnect and keep up-to-date two-dimensional gel electrophoresis (2D-PAGE) databases. It converts data from various formats into a relational format. The tool offers the possibility to automatically update data related to numerous external data resources in a highly consistent manner. It is also possible with this tool to dynamically interconnect several remote databases or projects to form a virtual global database accessible from one single entry point. 

Make2D-DB II can also be used without any local data, as a personal and a configurable Web portal, to link simultaneously to several remote 2D resources. Finally, this tool can be easily used to build up a 2-DE repository, accessible by any one from the Web.

The tool is open source and is free of charge.

Related documents:

What is the Make2D-DB II Tool?

Make2D-DB II is an open source software (cf. license) to create, convert, publish, interconnect and keep up-to-date 2D-PAGE databases. With this tool, one can easily convert any personal federated 2-DE database, or any 2D-PAGE database following the SWISS-2DPAGE conventions, into a more reliable format. The tool also handles XML exports from Melanie, common spreadsheets reports (e.g. Excel CSV exports), as well as simple text lists. It is also possible to create new relational databases from scratch. The tool runs on most UNIX-based operating systems (Linux, Solaris/SunOS, IRIX). Being continuously maintained, the tool is evolving in concert with the current Proteomics Standards Initiative of the Human Proteome Organization (HUPO).

Make2D-DB II is designed to ensure high consistency of data. It allows dynamic interconnection between any number of similar remote databases and offers many other features, including automatic data updates related to external data, dynamic cross-references to similar databases, intuitive Web-based search engine, and data visualization combined with exports in various formats. In addition, the tool extends the concept of 2D-PAGE databases to cover a more elaborate description of proteomics experiments and analysis. Currently, it can integrate various annotations and documents (e.g. sample and gel preparation), as well as many common analysis and identification file formats (common mass spectrometry formats, MIAPE documents, etc.). References to other remote repositories can also be easily integrated (e.g. PRIDE for MS/MS data). Users can also define their own types of annotations and easily integrate them within their data representation. Moreover, any laboratory can easily build up its own Web portal in order to access as many remote 2D-PAGE resources as desired.
Moreover, The Web interface appearance can be personalized for everyone's taste. Data can be marked to be public, as well as fully or partially private. An administration Web interface, highly secured, makes external data integration, data export, data privacy control, database publication and entries version control a very easy task to perform.

Some 2-DE databases constructed with Make2D-DB II:
  • SWISS-2DPAGE - The world famous reference database -- Swiss Institute of Bioinformatics
  • WORLD-2DPAGE Repository  A public standards-compliant repository for gel-based Proteomics data linked to protein identification published in the literature -- Swiss Institute of Bioinformatics
  • WORLD-2DPAGE Portal - A dynamic portal to query simultaneously world-wide gel-based Proteomics databases -- Swiss Institute of Bioinformatics

  • UCD-2DPAGE - 2D-PAGE Database of Escherichia coli -- Conway Institute Proteome Research Centre (CIPRC) University College Dublin, Ireland
  • SIENA-2DPAGE - Multi-species 2D-PAGE Database -- Department of Molecular Biology, University of Siena, Italy
  • KAIKO-2DDB - The Silkworm Genome Research Program -- National Institute of Agrobiological Sciences, Japan.
  • COMPLUYEAST 2D-PAGE DATABASE - The COMPLUYEAST 2D-PAGE DATABASE -- Department Microbiology II, Universidad Complutense Madrid, Spain
  • REPRODUCTION-2DPAGE - 2D-PAGE database (Human ovary, Mouse testis) -- Lab of Reproductive Medicine, Nanjing Medical University, PR. China.
  • 2DBase - 2D-PAGE Database of Escherichia coli -- Fermentation Engineering Group, University of Bielefeld, Germany