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The Functional Annotation and Correlation Tool allows the meta-analysis of data from high-throughput experiments (typically microarrays) by annotating (clones, genes, GeneOntology, location, etc) and correlating data sets to identify important patterns.

Download Now! FACT-1.1.0.tar.gz (5.7 MB) OR View all files

http://fact-analysis.sourceforge.net





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Release Date:

2008-06-27

Topics:

Bio-Informatics, Chemistry, Information Analysis

License:

GNU General Public License (GPL)

Operating System:

All POSIX (Linux/BSD/UNIX-like OSes)

Translations:

English

Intended Audience:

Science/Research

User Interface:

Web-based

Database Environment:

MySQL, Perl DBI/DBD

Programming Language:

Perl

Registered:

2007-05-09

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  • fact-analysis FACT-1.1.0 file released: FACT-1.1.0.tar.gz

    <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html> <head> <META http-equiv="Content-Type" content="text/html; charset=UTF-8"/> <title>FACT - flexible annotation & correlation tool</title> <link href="../style/factStyle.css" type="text/css" rel="stylesheet"/> </head> <body> <div class="topmenu"> <h2>Changes since last version</h2> </div> <div class="pagecontent"> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-08-16T18:08:15+0200</span> <br/> Message: <span><b>Last step for packaging</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-08-16T18:27:54+0200</span> <br/> Message: <span><b>new FACT version 1.0.0</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-08-16T18:38:08+0200</span> <br/> Message: <span><b>Changed the SQL to use EnsEMBL version 46...</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-08-16T18:42:19+0200</span> <br/> Message: <span><b>corrected the archive to use EnsEMBL v.46</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-09-24T16:10:15+0200</span> <br/> Message: <span><b>Added a new clean function to the daemon starter</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-09-27T20:23:45+0200</span> <br/> Message: <span><b>Fixed an issue when there are no illumina IDs to be retrieved from a gene. Ensure as well that the highThroughputmethod dies properly</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-09-28T19:14:04+0200</span> <br/> Message: <span><b>Corrected several interface bugs when using the admin view. Fixed the IlluminaAnnotation module to ensure that unproper character retrieved from the EnsEMBL description are removed.</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-10-09T16:50:46+0200</span> <br/> Message: <span><b>Added a Doc/Todo directory. Extended the install script to add the fact daemon to the default boot on gentoo.</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-10-11T16:32:10+0200</span> <br/> Message: <span><b>added a cron job to restart the server</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-10-11T16:45:18+0200</span> <br/> Message: <span><b>end of line problem...</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-10-11T17:15:41+0200</span> <br/> Message: <span><b>Corrected the sh scripts...</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-10-11T17:22:12+0200</span> <br/> Message: <span><b>a final warning</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-11-23T17:34:15+0100</span> <br/> Message: <span><b>Created a module to retrieve basic Entrez information using Entrez IDs</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-11-23T17:49:50+0100</span> <br/> Message: <span><b>Corrected the use statements for two modules.</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-11-27T14:29:24+0100</span> <br/> Message: <span><b>Extracted a method to format the description properly to avoid unwanted characters in the SQL query strings</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-11-27T14:40:06+0100</span> <br/> Message: <span><b>Deal with the case where no annotations are found...</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-11-27T14:45:55+0100</span> <br/> Message: <span><b>Just inverted the job and admin menu for admins only.</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-12-18T12:06:21+0100</span> <br/> Message: <span><b>Deal with the csv delimitor programatically</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-12-18T12:31:55+0100</span> <br/> Message: <span><b>Die properly when no tuples are created. It used to stay as a zombie job.</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-12-18T14:06:49+0100</span> <br/> Message: <span><b>Corrected a typo while passing the args for the DBD::CSV dbh creation</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-12-19T15:11:56+0100</span> <br/> Message: <span><b>Removed the port argument when getting the EnsEMBL registry. They have changed the port for the version above v48 and they select the right one programatically</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-12-21T16:55:13+0100</span> <br/> Message: <span><b>Implemented the high throughput upload in the one column parser to speed up things...</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2007-12-21T17:04:15+0100</span> <br/> Message: <span><b>Corrected some bugs introduced while speeding up the one column import</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-01-07T15:45:03+0100</span> <br/> Message: <span><b>Updated the user preferences so that a message is printed if the user update his password or email</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-01-07T16:49:59+0100</span> <br/> Message: <span><b>Fixed a bug submitting the wrong parameter in the Preferences form.</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-01-07T17:04:30+0100</span> <br/> Message: <span><b>Forgot to close the form tag...</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-03T18:11:56+0200</span> <br/> Message: <span><b>Updated the affy annotations </b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-03T18:15:11+0200</span> <br/> Message: <span><b>just a tiny line got forgotten...</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-03T18:36:21+0200</span> <br/> Message: <span><b>corrected minor issues</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-07T14:11:06+0200</span> <br/> Message: <span><b>Just to have .txt and not .text exported files.</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-08T13:23:47+0200</span> <br/> Message: <span><b>Implemented the possibility to updated flatfile databases.</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-08T13:26:54+0200</span> <br/> Message: <span><b>Corrected a typo.</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-08T13:39:54+0200</span> <br/> Message: <span><b>corrected the web browser display</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-08T16:53:37+0200</span> <br/> Message: <span><b>Added bioperl as a dependancy. And extended the config to have a directory to store the flatfile databases.</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-09T14:09:48+0200</span> <br/> Message: <span><b>Finished the implementation of the OMIM annotation tool. Testing is still required.</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-09T16:05:39+0200</span> <br/> Message: <span><b>corrected typos</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-09T18:40:43+0200</span> <br/> Message: <span><b>Modified the update implementation to make it more genric. Added the version info for OMIM in the config</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-09T18:42:03+0200</span> <br/> Message: <span><b>Ensure that all version info get displayed. Modified the updated mechanism to make it more generic.</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-11T16:11:12+0200</span> <br/> Message: <span><b>Corrected some issues with the flatfile update. Some modules did not work as understtod from the docu</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-11T21:04:57+0200</span> <br/> Message: <span><b>Corrected some more issues with the OMIM annotation</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-11T21:08:18+0200</span> <br/> Message: <span><b>Prepared the fact release 1.1.0</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-15T16:59:12+0200</span> <br/> Message: <span><b>final OMIM corrections</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-22T16:18:47+0200</span> <br/> Message: <span><b>Ensure that all the OMIM ID are retrieved (three different db name in EnsEMBL) and the gene symbol as well</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-22T16:29:08+0200</span> <br/> Message: <span><b>Corrected some other xref dbnames...</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-22T16:50:54+0200</span> <br/> Message: <span><b>Just to escape some sql killing chars...</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-22T16:52:44+0200</span> <br/> Message: <span><b>corrected a minor mistake</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-04-22T17:34:18+0200</span> <br/> Message: <span><b>OMIM: corrected the alt_title and chapters content to be able to export them easily. Makes it a little less human readable.</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-05-05T19:01:43+0200</span> <br/> Message: <span><b>Removed a useless import.</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-06-26T20:40:15+0200</span> <br/> Message: <span><b>new database dump</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-06-26T20:46:41+0200</span> <br/> Message: <span><b>Fixed a cmd line change of wget btw version 1.10 and 1.11</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-06-26T21:26:29+0200</span> <br/> Message: <span><b>Changed the URL for the gene ontology download</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-06-26T21:52:03+0200</span> <br/> Message: <span><b>another URL for downloading geneontology </b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-06-27T10:22:31+0200</span> <br/> Message: <span><b>typo in the properties file</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-06-27T18:19:57+0200</span> <br/> Message: <span><b>Just changed the xsl file to convert the xml change log. We are using the newest svnant jar. No more need for personalized jars.</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-06-27T18:21:29+0200</span> <br/> Message: <span><b>Using the new svnant jar. Deprecated the personalized jar.</b></span> <br/> </p> <p> Author: <span style="color:#c00000">delhomme</span> <br/> Date: <span style="color:#8040ff">2008-06-27T18:38:29+0200</span> <br/> Message: <span><b>just convert the last change log xml file into html</b></span> <br/> </p> </div> </body> </html>

    posted 505 days ago

  • File released: /fact-analysis/FACT-1.1.0/FACT-1.1.0.tar.gz

    posted 505 days ago

  • fact-analysis FACT-1.0.0 file released: FACT-1.0.0.tar.gz

    posted 815 days ago

  • File released: /fact-analysis/FACT-1.0.0/FACT-1.0.0.tar.gz

    posted 815 days ago

  • fact-analysis FACT-1.0_Beta_03 file released: FACT-1.0_Beta_03.tar.gz

    posted 918 days ago

  • File released: /fact-analysis/FACT-1.0_Beta_03/FACT-1.0_Beta_03.tar.gz

    posted 918 days ago

  • Code repository

    We now keep the source code for FACT on SourceForge for people to use, as we can't maintain the installation at the DKFZ easily. We hope you will find it useful for your data analysis or your onw analysis software projects.

    posted by fkokocinski 918 days ago

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