wiki:UserGuide

Version 24 (modified by Gregory Vincic, 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 and that proteios servlet is running aswell as the ftp service. 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. WorkingWithAccounts
    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. WorkingWithExtensions
    1. Place your extension EXTENSION.ext.jar in /path/to/proteios/WEB-INF/lib/
    2. Restart tomcat

For Users

  1. WorkingWithProjects
    1. Login with a User account
    2. Click on My Projects then New Project
    3. Fill out the form and click Save
  2. WorkingWithFiles
    1. Use an ftp client to upload your files.
  3. WorkingWithHitReports

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)