wiki:UserGuide

Version 28 (modified by Fredrik Levander, 14 years ago) (diff)

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User Guide

Below you'll find a quick start for both administrators and users. We assume that you've installed proteios successfully. Also the proteios servlet and ftp service must be running. Follow the steps in the below quick start to get a feel for the application. When you want to learn more about specific features, click the links below.

For Administrators

  1. User account administration
    1. Login with the root account
    2. Click Users then New User
    3. Fill out all blue(required) fields
    4. Make sure the User role is checked and click Save
  2. Adding extensions
    1. Place your extension EXTENSION.ext.jar in /path/to/proteios/WEB-INF/lib/
    2. Restart tomcat

For Users

  1. Working with projects
    1. Login with a User account
    2. Click on My Projects then New Project
    3. Fill out the form and click Save
    4. Select the project as active and note the difference in the left frame
  2. Working with files
    1. Browse to a directory from Files
    2. Upload a file using Upload file
    3. Use an ftp client to upload your files
  3. Samples and activity tracking
    1. Select Samples and New sample
    2. Fill out the form and click Save
    3. Switch to the annotations tab and add an annotation
    4. Switch to the properties tab and Make Extract
    5. Fill out the form and click Save
    6. Select New Separation Event.
    7. Select gel electrophoresis.
    8. Create a new gel.
  4. Protein identification reports
    1. Upload demo files from the Files menu.
    2. Select Hits report and Hits import wizard.
    • Step 1: Select spot picker results file
    • Step 2: Select peak lists files
    • Step 3: Select search results
    1. Filter the hits report by E-value
    2. Save the filtered report to file
  5. Browsing search results
    1. Select Imported Searches under Personal.
    2. Select a search results
    3. Click on an identified protein
    4. Go back and click on an identified peptide

Work in progress!!!

Activities

Most of the work in Proteios is performed by various plugins. These are executed sequentially in a job queue. To follow the activities in the job queue, select Server->Jobs. Note that the status reported in the job table will not update automatically when the job status changes. To follow the execution of a job, press the 'Refresh' button in the right frame to update the displayed information.

Running plugins

There are several options on how to run plugins, depending on their input and output parameters. Many plugins are using a file as only input parameter. To execute such a plugin, click on the file, select 'Run plugin' and the name of the plugin.

Peak List Sets

Under Personal -> Peaklistsets you will find peak lists that have been imported into the Proteios database. In many cases it is not necessary to import the peak lists into the database, but it is enough to upload the peak list files to the Proteios server. However, some analyses require the files to be imported into the database, and then the peak lists will be listed here. To import a peaklist into the database you should run the appropriate import plugin on the file (see Running plugins)

Specific tools

DIGE Analyzer Running dye effects analysis on a set of DiGE gels.