ADF MAGE-ML Tool Project Page

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Version française[fr]

This project has been made for the European Bioinformatics Institute (E.B.I). It has been developped during my six months Master training period from May 2004 to November 2004.

The goal of this project is to check and convert array design data file, from ADF to MAGE-ML and from MAGE-ML to ADF. There is a ADF MAGE Tool project page hosted by sourceforge.net: http://adfconverter.sourceforge.net. The official EBI project page is http://www.ebi.ac.uk/adf.

The project has been presented in a poster[en] for MGED7 in Toronto (Sept 2004).

Project Description

Aim of the project is to develop a module for converting ADF files (a tab delimited file representing microarray design layout) into MAGE-ML format and generating an ADF from an array design described in MAGE-ML format. The module will be built upon the ADF specifications and using of MAGE-Stk APIs (Perl or Java). MIAME-compliance check, logging system and integration of LifeScience Identifier (LSID) specifications will be key components of the module.

Project parts

This project is composed of two parts:

  1. Checking: Verify data file (file structure and data type) -- Check controlled vocabulary (MGED Ontology terms, database Tags/accession numbers - using ArrayExpress approved database list).
  2. Converting: Convert array design data file from a file format to the other one.

Project presentation

The tool has been developped in the Java Language using the Java MAGE software tool kit (MAGE-stk).

This project has been concluded by an oral presentation in french and a report in french/english for my Master. My Master presentation can be download from here (french[fr]) (HTML). The report in french[fr] is available in pdf [pdf] format (about 1mo) made with LateX and Lyx.

Presentation Dess Ebi
View more presentations from Pierre Marguerite.

The project has been also presented during a Microrray Team friday seminar (Microsoft PowerPoint diaporama format[en] or in html (for Microsoft Internet Explorer)).

Friday Seminar 15 10 2004.

The project development has been presented every thursday during student meeting (slideshare).

Documentation

Project specifications

Early specifications can be found there.

Technical documentation

A description of the XMLSchema used for XML describing ADF file structure

Project files

There is currently no official release. Development release can be found on my EBI home page.

The project can be followed on the sourceforge project site: http://adfconverter.sourceforge.net and release should be shortly available here.

The project has been developped under Eclipse 3.0 (IDE) with the Sun JAVA J2sdk 1.4.2_05. The project has not been tested with older versions. The project has been tested under GNU/Linux (Debian - Red Hat) and Microsoft Windows XP (with cygwin (a Linux-like environment for Windows)).


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