= User Guide =

Below you'll find a quick start for both administrators and users. We assume that you've [wiki:Installation installed] Proteios SE 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 optimal appearance of the web interface we recommend the [http://www.mozilla.com/firefox/ Firefox] web browser, even if other browsers also should work. 

=== Note on Menu System ===

The main method of navigation in Proteios is via the drop-down menu tool bar at the top. A menu is displayed
when the mouse pointer is placed on the menu title, and stays up as long as the mouse remains within the menu.
A hierarchical (cascade) menu item is indicated by a blue arrow to the right of the menu title; placing the mouse
pointer on the menu item makes the sub-menu appear, which might contain further hierarchical menu items.
Selecting menu item `Start Here` in menu `File` is indicated as `File -> Start Here` in this documentation.

The `Project` menu changes name to that of the active project, as soon as one has been selected, and its
menu items then refer to this project. The `Project` menu for an active project is indicated as
`<Active Project>` in this documentation. As an example, if the active project selected has name
"`Test Series 12`", you can inspect the files belonging to the project by selecting menu item `Files`
in the menu named `Test Series 12`, which will be indicated as `<Active Project> -> Files` in this
documentation.

To simplify navigation for often used tasks, the menu system contains shortcuts such as the
`File -> Select project` to change the active project, and `Files -> New` for creating new items.
In the examples below, only one way of how to perform the desired task is shown in these cases.

== For Administrators ==

 1. [wiki:WorkingWithAccounts User account administration] 
    1. Login with the `root` account
    1. Select `View -> Users` then click `New User`
    1. Fill out all blue (required) fields
    1. Make sure the `User` role is checked and click `Save`
 1. [wiki:WorkingWithExtensions Adding extensions]
    1. Place your extension EXTENSION.ext.jar in /path/to/proteios/WEB-INF/lib/
    1. Restart tomcat

== For Users ==

 1. [wiki:WorkingWithProjects Working with projects]
    1. Login with a `User` account
    1. Select `View -> My Projects` then click `New Project`
    1. Fill out the form and click `Save`
    1. Select the project as active by clicking on it and note that the name of the `Projects` menu changes to that of the project
 1. [wiki:WorkingWithFiles Working with files]
    1. Browse to a directory from `<Active Project> -> Files`
    1. Upload a file using `Upload file`
    1. Use an ftp client to upload your files
 1. [wiki:WorkingWithSamples Samples and activity tracking]
    1. Select `<Active Project> -> LIMS -> Samples` and click `New Sample`
    1. Fill out the form and click `Save`
    1. Switch to the annotations tab and add an annotation
    1. Switch to the properties tab and `Make Extract`
    1. Fill out the form and click `Save`
    1. Select `New Separation Event`.
    1. Select gel electrophoresis.
    1. Create a new gel.
 1. [wiki:WorkingWithHitReports Protein identification reports]
    1. Select `<Active Project> -> Files` and click `Upload demo files`
    1. Select `<Active Project> -> Hits -> Reports -> Hits` and click `Hits Import Wizard`
    - Step 1: Select spot picker results file 
    - Step 2: Select peak lists files
    - Step 3: Select search results
    3. [wiki:Filters Filter] the hits report by E-value
    1. Save the filtered report to file
 1. [wiki:WorkingWithSpectrumSearches Browsing search results]
    1. Select `View -> Imports -> Searches`
    1. Select a search result
    1. Click on an identified protein
    1. Go back and click on an identified peptide
 1. [wiki:SharingData Sharing information]
 1. Logging out
    1. Select `File -> Logout`

== 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 `View -> 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, click `Update`
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 `View -> Imports -> Peaklists` 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 ==

[wiki:DIGEAnalyzer DIGE Analyzer] Running dye effects analysis on a set of DiGE gels.[[BR]][[BR]] 
[wiki:ExQuest ExQuest spot cutter import] How to import spot mappings from ExQuest.[[BR]][[BR]]