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This page contains a list of Proteios wiki pages.

• A wiki page is normally listed under the first wiki page linking to it, but exceptions may occur, in order to keep wiki pages with related contents listed together.
• Not all wiki pages are guaranteed to be included in the list.
• Some wiki pages may occur more than once in the list.
• Some links to non-wiki pages are included, if the links were included on a wiki page in a list with wiki links.

Links to Proteios Wiki Pages

1. Proteios Wiki Start Page
   1. About Proteios Software Environment
   2. List of Proteios Wiki Pages
   3. Proteios Software Environment releases
   4. Download
   5. Known Issues
      1. Known problems
   6. Proteios SE Manual
      1. Some Concepts in Proteios SE
      2. User Guide
         1. Working With Accounts
         2. Working With Extensions
            1. Extension Manual
               1. Implement Action
               2. Implement Plugin
         3. Plugin handling
         4. Working With Projects
         5. Working With Files
            1. Sharing information
            2. Proteios FTP Server Usage
         6. Samples and sample tracking
            1. Batch Import of BioMaterial Items
         7. Working With Hits Reports
            1. Generating a report for a gel-based project
               1. ExQuest import
            2. Hits Report Table Features
               1. Filters
            3. PRIDE 2.1 XML Export
               1. Overview of the Generated PRIDE XML Export File
         8. Search results
         9. Sharing information
         10. Label-free quantitative analysis
         11. Feature Detection
         12. Hits Comparison Report
             1. Non-Quantitative Hits Comparison Report
             2. Quantitative Hits Comparison Report
         13. Following a Job
         14. DIGE Analyzer
         15. ExQuest import
      3. Webservice
      4. X!Tandem Search Engine Interface
      5. Proteios 2 Installation
         1. Build Proteios from Source Code
            1. Detailed Build Instructions
               1. Setting up Eclipse
         2. How to grant rights for remote access to a MySQL server
      6. Update
      7. Proteios SE server administration
         1. Tomcat/Apache Web Server/SSL Configuration Hints
      8. Proteios FTP Server
         1. Proteios FTP Server Usage
         2. Third Party Licenses
   7. Information for Developers
      1. Some Concepts in Proteios SE
      2. Database Schema (Non-wiki page)
      3. Extension Manual
         1. Implement Action
         2. Implement Plugin
      4. Setting up Eclipse
      5. Build Proteios from Source Code
         1. Detailed Build Instructions
            1. Setting up Eclipse
      6. JavaDoc
      7. Ticket Manual
      8. Subversion usage
      9. Testing
         1. Unit Tests and JUnit - Background
         2. JUnit 4 Issues and Alternatives
         3. jWebUnit Package Dependencies for Latest Releases
         4. jWebUnit Compile Test for Used Packages
         5. Test Package Alternatives
      10. TableFactory Use
      11. Naming Conventions
      12. Logging Guidelines
      13. Useful Links
      14. Third Party Licenses
      15. Tomcat/Apache Web Server/SSL Configuration Hints
      16. Release Procedure
   8. Specification
      1. User management
         1. UseCase Create New Account
         2. Use Case Remove Account
      2. Role based permissions
      3. Data sharing
         1. Use Case Sharing Directory
      4. Uploading a set of files
      5. Data import of different formats, e.g. mzData, PKL
      6. Data searching/filtering
      7. Sample Management
         1. Use Case Create New Sample
      8. Project management
         1. Use Case Create New Project
      9. Report generation
      10. Data annotation
      11. Notification management
          1. Use Case Create New Account
      12. 2D Gel-based proteomics workflow
          1. Different mass spectrometry modes to handle
          2. File Naming
          3. Gel Report
      13. Quantitative LC-MS use case
      14. Different mass spectrometry modes to handle
      15. Dep of Biochemistrys broad view of aim with Proteios
      16. Biochemistry 2DGel-based workflow
      17. How to write a Use Case
          1. Login to Proteios wiki
      18. Mass Spectrometry part of the Proteios database
      19. General Activity Diagrams