ADF MAGE-ML Tool Home Page

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ADF MAGE-ML Tool aim

The aim of this project is to provide a standalone application for microarray layout data file conversion from ADF format to MAGE-ML file format or contrary.

The application has two functionalities:

• file checking process (syntax and semantics)
• conversion process

The tool is a standalone Java application using the MAGE Software Toolkit (MAGE-stk) from the MGED Open source project.

Documentation

Project specifications

Early specifications can be found there.

Technical documentation

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

Howto

ADF MAGE-ML Tool Wiki Page (can be used as How To, especially for troubleshooting)

External Libraries

A list of used API and version number is available on this page.

Mailing List

ADF MAGE-ML Tool Mailing List (Subscribe)

ADF

Previous ADF format.

New ADF format.

MAGE-ML

MAGE.

MAGE-ML format.

MGED Ontology

MGED Ontology website.

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Project releases

Provided below is a stand-alone application in java for the conversion from ADF format to MAGE-ML file format and vice versa.

(You are welcome to use this documentation and scripts on this page, however, we do not take any responsibilities for their use. Please read  our license for more details.)

Requirements

The tool is developped for Java 1.4 or later. It may work with an earlier version (1.3), but not tested. It has been tested with the Sun Java Virtual Machine, under GNU/Linux Debian and Microsoft Windows 1.5. Tests with free JVM will be done for upcoming version.

Hardware requirements

The tool has been developed to be used on a desktop computer. However, it required a large quantity of memory. For large data file, it recommands to have at least 1 Gb of memory and 1.5 GHz CPU.

Files

• First Development releases >>
  (Release for Jamboree on 13/09/2004)   
• Development release >>
  The current development release is available on the sourceforge.net CVS server.
  To download from CVS - adfconverter-dev module:

  cvs -d:pserver:anonymous@cvs.sourceforge.net:/cvsroot/adfconverter login
    
  cvs -z3 -d:pserver:anonymous@cvs.sourceforge.net:/cvsroot/adfconverter co -P adfconverter-dev
  

  A development cvs snapshot is available.
  Follow development: atom feed
  
• Production release >>
  The tool has been released on the sourceforge website. The tool is available as graphical installer with four packages:
  • base: core files for tool use
  • documentation: documentation files about the tool
  • src: Java source files of the ADF MAGE-ML Tool
  • examples: ADF and MAGE-ML files to test the application

  Or compiled as archive files : tar.gz, tar.bz2, zip. The source code is also available in archive files, with distribution files.

  
  

  Last version: 1.0

  Changes: reported changes

  
  

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Installation

Automatic Java Installer.

The installer (created with IzPack) installs automatically the Tool containing four packages: Base (Mandatory), Documentation, Source, Examples

To install with the installer:

• Double-click on the jar in a file explorer (Usually works on Ms Windows O.S.).
• Or, execute the file with :

  java -jar ADF_MAGEML_Tool-VERSION.jar

Then, follow instructions.

The installer creates automatically the configuration file and the script to launch the tool.

There are two kinds of installer:

• Off-line : All packages are contained in the installer. about 20mb.
• Online /web: Needed packages are download on a website. About 1mb. Requires an Internet Connection.

Archive file ( Tar.gz, tar.bz2, zip).

Instructions

• Uncompress archive file :
  • For Windows, you can use Winrar, Winzip or 7-zip.
  • For Unix/linux,
    • zip:

      unzip ADF_MAGEML_Tool-VERSION.zip

    • tar.gz/tgz:

      tar xzvf ADF_MAGEML_Tool-VERSION.tgz

    • tar.bz2:

      tar xjvf ADF_MAGEML_Tool-VERSION.tar.bz2

• Set the ADFCONVERTERHOME variable to the path containing the ADF MAGE-ML Tool in the script adfconverter.bat/.sh following operating system. (For Unix/Linux user, the adfconverter-configure.sh script can be used to generate the script. Must be called from the directory containing the ADF MAGE -ML Tool files.)
• Check configuration file (adfconverter.properties in etc directory) to match your needs. The default file is fine.

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ADF MAGE-ML Tool script

Command Line

Calling

A script is called to launch the tool. The script sets the ADFCONVERTERHOME variable and calls the tool.

• Under Microsoft Windows O.S.:

  adfconverter.bat

• Under Unix - GNU/Linux O.S.:

  adfconverter.sh

Prior to call the script, please the ADFCONVERTERHOME variable to the path of the directory containing tool files.

Thanks to the ADFCONVERTERHOME variable, the script can be called from anywhere.

Options

ADF MAGE-ML Tool - EBI Tue, 23 Aug 2005
European Bioinformatics Institute - MicroArray Informatics Team
Home Page: http://adfconverter.sourceforge.net/
Developed by: Pierre MARGUERITE
Version  1.0
ADF MAGE-ML Tool [options] file
parameters:
file :  file or directory to convert

Options
        -t || -text :   for text format output
        -xls :  for xls format output
        -c || -conf :   for specific configuration file
        -check :        For checking mode
        -conv : For conversion mode
        -strict :       strict data checking mode
        -relax :        relax data checking mode (default)
        -stepbystep :   step by step checking mode
        -nostepbystep : no step by step checking mode (default)
        -dtd pathtoMAGE-MLDTD:  path to the MAGE-ML dtd path
        -sort:  sorting ADF in the given directory
        -curation:      curation of ADFs and save into file
        -adf:    The application only treats ADF files
        -mage:   The application only treats MAGE-ML files
        -accnumberchecking:      The database accession numbers will be checked
against the database tag
        -ontologychecking:       The MGED ontology term will be checked
        -noaccnumberchecking:    The database accession numbers will not be chec
ked against the database tag
        -noontologychecking:     The MGED ontology terms will be checked
        -I:      Info logging level
        -D:      Debug logging level
        -update resourcename:    update the resourcename (Internet connection re
quired)
        -updateall:      update all available resources. (Internet connection re
quired)
        -resources:      list of available resources for update.

For treating an ADF file, the path to the ADH file or simply the path without file extension is given as parameter.

ADF file must be in the new ADF format composed of three parts/files.

Example

Start a checking, conversion

adfconverter.bat -I examples/ADF-conversion-test1-correct.adh

Update a resource.

adfconverter.bat -update approveddb

Graphical User Interface (G.U.I)

Calling

A script is called to launch the tool. The script sets the ADFCONVERTERHOME variable and calls the tool.

• Under Microsoft Windows O.S.:

  adfSimpleGUI.bat

• Under Unix - GNU/Linux O.S.:

  adfSimpleGUI.sh

Prior to call the script, please set the ADFCONVERTERHOME variable to the path of the directory containing tool files.

Thanks to the ADFCONVERTERHOME variable, the script can be called from anywhere.

Options

ADF MAGE-ML Tool - EBI Tue, 23 Aug 2005
European Bioinformatics Institute - MicroArray Informatics Team
Home Page: http://adfconverter.sourceforge.net/
Developed by: Pierre MARGUERITE
Version  1.0
ADF MAGE-ML Tool [options] file
parameters:
file :  file or directory to convert

Options
        -h || --helptext :      for this help
        -lf || --lookandfeel look and feel name :       for setting the UI look
and feel
        --availablelookandfeel lookAndFeelname :        Retrieve list of availab
le UI look and feels
        -l || --lang :  for setting the UI locale/language

Example

Simply start the GUI

adfSimpleGUI.sh

Set UI language

adfSimple.sh -l fr

Once GUI launch, select a file and check needed options, then click on the "launch" button. You can have additional information on the tool by clicking on the "About" button. From the about window, you can modify tool configuration/default options and update resources.

File given in parameter:

ADF

For ADF, the file given in parameter can be:

• the .adh, header data
• the workbook,
• or the ADF name (file name without extension).

The three ADF text file have to have the adh, adr ,adc extension. After treatment, there are one log file per ADF file (adh,adr,adc if present) and a global one (ADF name with .log extension).

MAGE-ML file

For MAGE-ML file, the allowed file extension is ".xml" (case insensitive).

Archive Files

Path to archive file can be provided to the application. Files are uncompressed by the application in a directory called by the name of the archive file. Uncompressed files are erased at the end of treatment. Once uncompressed, the whole newly created directory is treated by the tool.

Supported file extension are:

• .zip
• .rar
• .gz

The ".tar.gz" support is not fully functional. (should be available fix in the next release)

Log

Several information are provided to the tool.

There is currently two type of log:

General/Global

It is unique. It contains general information about the tool(Initialisation, execution,...). By default, this log is in the adfconverter.log, in the directory where has been called the tool. But, it can be modified in the tool configuration. For the command line mode, the log is also displayed in the console.

Treated File specific:

There is a log file per treated file. The log file name is the treated file name with "e;.log""" extension. This log contains specific information about file treatment - error, warning, info,...

The log is powered bu the Log4J API.

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Support

Please contact Pierre Marguerite or send a message to the General Mailing List -adfconverter-general@lists.sourceforge.net- (Archive, Subscribe) for more information or use of the ADF MAGE-ML Tool.

Feedback

Feedbacks are welcome for upcoming version of the tool. Please use needed trackers:

• Bugs trackers
• Support request
• Patches
• Feature Requests

Resources

• Tool development atom feed
• Project News RSS
• Project file Releases RSS
• Project releases
• Log4j Project
• IzPack Project
• Java Web Services Developer Pack (Java WSDP)
• MIAME - The formulation of the minimum information about a microarray experiment required to interpret and verify the results.
• MAGE - The establishment of a data exchange format (MAGE-ML) and object model (MAGE-OM) for microarray experiments.
• Ontologies (OWG) - The development of ontologies for microarray experiment description and biological material (biomaterial) annotation in particular.
• Transformations - The development of recommendations regarding microarray data transformations and normalization methods.
• RSBI WGs - Reporting Structure for Biological Investigations Working Groups (RSBI WGs) - A single point of focus for Toxicogenomics, Nutrigenomics and Environmental Genomics domains of application.
• MISFISHIE - The development of the Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments required to interpret and verify the results.

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Feedbacks are welcome.

You are welcome to use this documentation and scripts on this page, however, we do not take any responsibilities for their use.
Please read our license (OSI approved).

ADF MAGE-ML Tool is written in (and requires) Java, and should work on any platform that support Java 1.4.1 or later. Note however, that the tool have currently been compiled and tested on Microsoft Windows, and GNU/Linux (Debian Unstable). It should work on other platforms, but we have no way of testing this ourselves.

Last modified: Mon Oct 24 15:35:51 GMT Daylight Time 2005