https://sourceforge.net/p/gepetto/wiki/OpenSource/Recent changes to OpenSourceenFri, 01 Mar 2013 13:59:54 -0000https://sourceforge.net/p/gepetto/wiki/OpenSource/<div class="markdown_content"><pre></pre> </div>Vincent WALTERFri, 01 Mar 2013 13:59:54 -0000https://sourceforge.net1c9b105e740a1cbfc4a469528b58c8a27a7786c3https://sourceforge.net/p/gepetto/wiki/OpenSource/<div class="markdown_content"><pre>--- v12 +++ v13 @@ -77,7 +77,7 @@ * jBPM is licensed under GNU LGPL * Apache Commons liraries is licensed under Apache License -For all the Java libraries, please check it individually +For all the Java libraries, please check it individually. ###Source code### </pre> </div>Vincent WALTERFri, 01 Mar 2013 12:40:38 -0000https://sourceforge.netf1725d7d0b0bcf893e038bda274e80003bd290b8https://sourceforge.net/p/gepetto/wiki/OpenSource/<div class="markdown_content"><pre>--- v11 +++ v12 @@ -73,6 +73,11 @@ * 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### </pre> </div>Vincent WALTERFri, 01 Mar 2013 12:40:22 -0000https://sourceforge.netcc18f154aceb458b8b7995a35f8ff28359f22938https://sourceforge.net/p/gepetto/wiki/OpenSource/<div class="markdown_content"><pre>--- v10 +++ v11 @@ -76,8 +76,17 @@ ###Source code### -[GEPETTO] now uses SVN for its source code version control system. The sources of the [GEPETTO] project can be founded here : +[GEPETTO] now uses SVN for its source code version control system. The sources of the [GEPETTO] project can be founded here : -The source of local prioritization mdoules we integrate with can be found 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 </pre> </div>Vincent WALTERFri, 01 Mar 2013 12:36:11 -0000https://sourceforge.net118e500a4010bf5b5b49b88ff5119b92f9d9ae18https://sourceforge.net/p/gepetto/wiki/OpenSource/<div class="markdown_content"><pre>--- v9 +++ v10 @@ -70,7 +70,9 @@ 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. ###Source code### </pre> </div>Vincent WALTERFri, 01 Mar 2013 00:16:44 -0000https://sourceforge.net39344c0ae469b180c8ce0630eae5e6bedabf04ffhttps://sourceforge.net/p/gepetto/wiki/OpenSource/<div class="markdown_content"><pre>--- v8 +++ v9 @@ -10,7 +10,7 @@ The [SM2PH-Central](http://decrypthon.igbmc.fr/smph SM2PH-Central) website integrates [GEPETTO]. It can be accessed either [directly](http://decrypthon.igbmc.fr/sm2ph/cgi-bin/gepetto GEPETTO) or through the menu bar : - + This leads us to the gene prioritization web page which is pretty simple : @@ -48,7 +48,7 @@ or from serach results using full text :  -using the  button. +using the  button. Command line ------------ </pre> </div>Vincent WALTERSat, 23 Feb 2013 00:13:58 -0000https://sourceforge.net0d9394c6a14db038a49f41ae20616e7693d5fa5dhttps://sourceforge.net/p/gepetto/wiki/OpenSource/<div class="markdown_content"><pre>--- v7 +++ v8 @@ -16,6 +16,8 @@ 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) @@ -33,15 +35,20 @@ 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 ===>> PICTURE <<==== button. +using the  button. Command line ------------ </pre> </div>Vincent WALTERSat, 23 Feb 2013 00:12:32 -0000https://sourceforge.netd2ff8cdbe037cad4a365519fe0b6ab22bb9a1b23https://sourceforge.net/p/gepetto/wiki/OpenSource/<div class="markdown_content"><pre>--- v6 +++ v7 @@ -11,8 +11,6 @@ The [SM2PH-Central](http://decrypthon.igbmc.fr/smph SM2PH-Central) website integrates [GEPETTO]. It can be accessed either [directly](http://decrypthon.igbmc.fr/sm2ph/cgi-bin/gepetto GEPETTO) or through the menu bar :  - -[[img src=http://lbgi.igbmc.fr/~walterv/gepetto/sourceforge/images/0001.png alt=foobar]] This leads us to the gene prioritization web page which is pretty simple : </pre> </div>Vincent WALTERSat, 23 Feb 2013 00:02:58 -0000https://sourceforge.net7db09141a48fc23fa94002eb88bfd3662369ee77https://sourceforge.net/p/gepetto/wiki/OpenSource/<div class="markdown_content"><pre>--- v5 +++ v6 @@ -10,7 +10,7 @@ The [SM2PH-Central](http://decrypthon.igbmc.fr/smph SM2PH-Central) website integrates [GEPETTO]. It can be accessed either [directly](http://decrypthon.igbmc.fr/sm2ph/cgi-bin/gepetto GEPETTO) or through the menu bar : - + [[img src=http://lbgi.igbmc.fr/~walterv/gepetto/sourceforge/images/0001.png alt=foobar]] </pre> </div>Vincent WALTERSat, 23 Feb 2013 00:00:20 -0000https://sourceforge.net18ff4c94fd0bf9662bfaf52f7fd20aa144fe0c76https://sourceforge.net/p/gepetto/wiki/OpenSource/<div class="markdown_content"><pre>--- v4 +++ v5 @@ -9,6 +9,10 @@ ###GEPETTO web page### The [SM2PH-Central](http://decrypthon.igbmc.fr/smph SM2PH-Central) website integrates [GEPETTO]. It can be accessed either [directly](http://decrypthon.igbmc.fr/sm2ph/cgi-bin/gepetto GEPETTO) or through the menu bar : + + + +[[img src=http://lbgi.igbmc.fr/~walterv/gepetto/sourceforge/images/0001.png alt=foobar]] This leads us to the gene prioritization web page which is pretty simple : </pre> </div>Vincent WALTERFri, 22 Feb 2013 23:59:59 -0000https://sourceforge.net9e6f628737bee370d95c12995004f4a1bdcc5be3