SAMSWiki/WebDocumentation/HowTo

• SAMS Menu

In the SAMS main window, on the left you can access the following options:

• /GeNeral
• /BasicActions
• /ClassiFication
• /TooLs

But first please have a look at the following information:

• 1) Requirements for using the SAMS web frontend

To run SAMS, please use one of the following browser:

• Mozilla
• Netscape 7 and higher
• Firefox
• Konqueror

Please also enable Javascript, Cookies and Popup-windows for this site.

• 2) How to get an account, login and password for using SAMS?

The GPMS system is an online management tool responsible for controlled access of SAMS software:

• Account
• Login/password
• Restricted access etc..

Once you get a login and password, you can also check which projects you can access under thislink.

• 3) Logging in

Start the web frontend of SAMS by entering the following URL.

Log in (username and password received by email from the GPMS system). Once you have logged in, you will be able to select one of the projects you have access to. After the selection the SAMS main window is launched. A search tool allows you to search within the different fields of the system such as:

• Data import
• Clustering ESTs or running the default function prediction pipeline
• Browsing your sequence datasets
• Annotating sequence data
• Other options (Gene Ontology, KEGG pathway, COG)

A guided tour introduces you to the basic functions the SAMS system has to offer. Have a look at the following URL.

• 4) View permissions, Rights and Roles

Access control in SAMS is provided for each individual object. Here you can check other member's rights on this object. If you have the appropriate permissions you can also change these permissions.

For each project, there is a "chief" who has all the privileges and can give access or not to other users for this project. He also decides what kind of tasks you can perform or not on this project.

Here are some type of members you can have on a project and their corresponding privileges.

• Chief: user who is responsible for a project, can do everything (e.g. configure project) except modifying the database.
• Developer: user who is responsible for the database and for the solution of bugs and problems.
• Guest: user with read only permissions and almost completely restricted access.