OpenSource

GETTING STARTED

• GETTING STARTED
  • Web interface
    • GEPETTO web page
    • How to use it?
  • Command line
  • Downloads
  • Sources
    • License
    • Source code

Web interface

GEPETTO web page

The SM2PH-Central website integrates [GEPETTO]. It can be accessed either directly or through the menu bar :

This leads us to the gene prioritization web page which is pretty simple :

There are 5 components :

1. The training set as a gene symbols (or Uniprot accessions) list
2. The test set as a gene symbols (or Uniprot accessions) list
3. The list of [GEPETTO] modules that will be used (if checked)
4. The button to run prioritization
5. The reset button that reinitializes the page with default parameters (clear set fields and checked all boxes).

How to use it?

Use [GEPETTO] is very easy :

• Provide the training set
• Provide the test set
• Select data sources that will be used ([GEPETTO] modules)
• Click on the Prioritize button to start the prioritization

Currently, when the prioritization is done, [GEPETTO] return results like this :

The first results are provided by local prioritization from all modules. At the end, there is the overall result from global prioritization.

Reminder : the identifier of genes must be characterized by gene symbols.

You can also set up the training set from a KEGG Pathway :

or from serach results using full text :

using the button.

Command line

Warning : Only GNU/Linux operating system (OS) based on Debian or Red Hat Enterprise Linux can support [GEPETTO] due to dependencies.

Downloads

All releases can be downloaded from SourceForge. Select the version you want to download and select the distribution you want to :

• installer-full : containing all (sources, data, modules,...)

Sources

License

The [GEPETTO] code itself is using the LGPL-2.1 License.

Some other components we integrate with have their own license :

• BLAST is a "United States Government Work" under the terms of the United States Copyright Act.
• R as a package is licensed under GPL-2 | GPL-3.
• RJava as a package is licensed under GPL-2.
• Spring Framework is licensed under Apache License
• jBPM is licensed under GNU LGPL
• Apache Commons liraries is licensed under Apache License

For all the Java libraries, please check it individually.

Source code

[GEPETTO] now uses SVN for its source code version control system. The sources of the [GEPETTO] project can be founded here :

• svn+ssh://svn.code.sf.net/p/gepetto/code/GEPETTO
• svn+ssh://svn.code.sf.net/p/gepetto/code/GEPETTOModel

The source of local prioritization modules we integrate with can be found here :

• svn+ssh://svn.code.sf.net/p/gepetto/code/Alignment
• svn+ssh://svn.code.sf.net/p/gepetto/code/Evolucode
• svn+ssh://svn.code.sf.net/p/gepetto/code/Geco
• svn+ssh://svn.code.sf.net/p/gepetto/code/GxDb
• svn+ssh://svn.code.sf.net/p/gepetto/code/IDGP
• svn+ssh://svn.code.sf.net/p/gepetto/code/Pubmed
• svn+ssh://svn.code.sf.net/p/gepetto/code/String