OrthoInspector Files

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ORTHOINSPECTOR Suite v1.40 
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1. Overview
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The OrthoInspector suite is divided into three jar files.
- command-line to install database : oi_install_x.xx_.zip archive
- command-line to query database : oi_client_x.xx_.zip archive
- graphical interface to do both : orthoinspector_x.xx_.zip archive

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2. License
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The OrthoInspector suite is distributed under GNU GPL version 3.
You can freely modify and distribute it by crediting the authors.

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4. Pre-requisite
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Each zip file contains specific intructions to launch the software.

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5. Contacts
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For any questions or problems concerning the installation : linard@igbmc.fr

Tutorials, database, benchmarks : http://lbgi.igbmc.fr/orthoinspector
Sourceforge repository : http://sourforge.net/projects/orthoinspector
    
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6. Changelog
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ORTHOINSPECTOR V1.40 (21/11/2011)
    + veen/euler diagrams can now be generated in orthoinspector.
    + the OrthoXML format (http://orthoxml.org) in now included in the
      command-line and the graphical interface.
    * some minor bugfix in the client command-line.

ORTHOINSPECTOR V1.31 (28/07/2011)
    + best-hit density graph is now the default displayed graph. This graph 
      cannot be displayed if the Blast data tables were not created during
      the installation process.
    * correction of a bug in the graphical interface. The use of a fasta file as
      a query crashed the application if some special characters were used.
    * query blast searches are now faster

ORTHOINSPECTOR V1.30 (1/06/2011)
    + the graphical interface and the 2 command-line binaries share the same
      ./lib directory.
    + if OrthoInspector is connected to an empty database, it automatically
      creates the orthoinspector database schema (MySQL & PostgreSQL only).
    - previous 'direct' mode of data insertion is abandonned.
    + 'direct' mode is replaced by temporary database dumps that are written in
      a selected directory and are directly transfered to the database. Update
      operations are now really faster. This mode is currently only compatible
      with MySQL and PostgreSQL. For other database engines, first you need to
      create the OrthoInspector schema in your database, second transfer 
      manually the table dumps with your own SQL queries.
    + rename the 'direct' and 'dumps' options in the installation command-line
      to 'direct_insertion' and 'dumps_only'
    + installation steps are more verbose in the graphical interface by adding 
      new progress bars.
    + errors occuring during the installation process are better handled.
    + during the blast parsing step of the installation process, the user can 
      choose to produce (or not) blast and noHit table data. These data are 
      no longer compulsory for orthology inference. Here are the consequences if
      you avoid to produce these data:
         *no blast data: vastly reduce the database size.
                         blastoutputs cannot be browsed in the graphical interface.
         *no nohit data: the 'statistics' tool of the graphical interface will
                         produce less statistics about sequences without blast hits.
      To propose these options, a new menu has been implemented in the graphical
      interface and 2 new options exists in the installation command-line.
    + A graphical bug is corrected in the presence/absence tool of the graphical 
      interface.
    + A bug was introduce in version 1.21 for the presence/absence tool, it
      produced incomplete results files. This has been corrected.
    + Inclusive/exlusive modes have been renamed 'between all possible organism
      pairs' / 'between base organism pairs'. 
    + a simple FASTA output format has been added in the client command-line.
      These files can be directly loaded in multiple alignement programs.
    + several other minor bugfix
    

ORTHOINSPECTOR V1.21 (11/05/2011)
    + Bugfix to handle date formats in different database localization
      configurations. This bug occured during the first step of the installation.


ORTHOINSPECTOR V1.2     (21/01/2011)
    + Session systems to save/load analysis sessions. Sessions are saved in files
      with the *.ois (orthoinspecor session) extension.
    + Results are now displayed in a table, new queries using previous can be
      launched 
    + Pressence/absence tools now includes 2 algorithms : inclusive and exclusive
    
      	# Inclusive algorithm : use non-absolute intersection of the criteria
          
          ex : we want human proteins that have orthologs in mouse but not in rat
               human<->rat orthology is verified and must be rejected
               human<->mouse orthology is verified and must be validated
               rat<->mouse orthology is not verified
               
        # Exclusive algorithm : use absolute intersection of the criteria
          
          ex : we want human proteins that have orthologs in mouse but not in rat
               human<->rat orthology is verified and must be rejected
               human<->mouse orthology is verified and must be validated
               rat<->mouse orthology is verified and if one protein previously
               considered absent in rat and present in mouse show some
               rat<-> orthology, is it not considered as corresponding to 
               wanted criteria.
               
    + Administrators can now hide the 'installation menu' by modifying the
      'menu.installation' property in the 'GeneralProperties.properties' file.
    * All database schema upper-case letters are know removed, for a best MySQL
      compatibility (MySQL naming is case-sensitive). Users of previous versions
      must set all tables/columns to lower case in their database. All files of
      the orthoinspector website are updated in this way (schema, scripts...).
    * Minor bug fix in the command-line for installation.

ORTHOINSPECTOR V1.11	(25/08/2010)
    * Correction of a bug in the presence/absence bilan that included organisms not asked by the user in the results.
    * Modification of the CSV output format (presence/absence  bilan)  for best readability.

ORTHOINSPECTOR V1.1	(20/07/2010)
    + Refactoring of the project packages
    + Fasta outputs in presence/absence bilan
    * Correction of a bug that restricted databases access
    * Multiple minor bug fix

ORTHOINSPECTOR V1.0	(06/2010)
    + first release