wiki:UserGuide

Version 14 (modified by olle, 14 years ago) (diff)

Added link to Hits Report Table Features under Hits Report.

User Guide

The first thing you will need is a user account. User accounts can be created by the site administrator. See the site administration? help page if you are a site adminstrator. If you just want to have a look at Proteios you can use the demo account (if it has been enabled by the site administrator). Once you have a user account, you need to log into Proteios and create a project. Users can have multiple projects, and all work has to bee done within a project. However, data can be shared also to other projects.

Activating a project

When logged in as an User you have permissions to create projects. Click on Personal/My? Projects/New? Project. When you have saved the project you have to activate it. Do this by clicking on your project name under Personal/My? Projects. You'll see that the menu is updated with the selected project.

Uploading files

Most types of analysis in Proteios require that you upload the files that are the basis of the work. Each user has a file directory on the server, and right under the root directory projects will have their own directory structures. The complete file structure can be reached by selecting Personal->My Files. When you have an active project - select Files in the left frame below the project name.

If you just want to test Proteios you can try the provided demo files. To add the demo files, activate a project and click Files in the left frame. In the right frame click 'Upload demo files'. (You have to be online for this to work). If all went fine you should now see three new folders in the right frame.

It is recommended that you generate a directory structure for the projects such that peak lists are in one folder, search results in another etcetera.

For normal file upload you can choose to upload files via the web interface or using ftp. The limitation of the web interface is that you have to upload files one by one which is not very practical for most projects. To upload a file via the web interface you should descend into the directory where you want the file to end up and select 'Upload file'

If you have many files to upload it is usually best to use the ftp (instructions)

Deleting files

To delete files, check the checkbox to the left of the files and press the 'Delete' button. The files will then end up in the trashcan. You will not be able to upload another file with the same name to the direcory until the trashcan has been emptied. To empty the trashcan select Personal->Home and press the 'Empty trashcan' button.

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.

Hits Report

Much of the work in Proteios is centered around protein identification. The 'Hits report' for a project is a table which contain protein identifications for a project. To generate the complete report for a gel-based project follow these instructions. For a description on how to simplify inspection of the Hits table, see Hits Report Table Features.

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)