ProteinCenter User Manual
Table of Contents

Chapter 32. Administrative Settings

Table of Contents

32.1. License
32.1.1. Add or Upgrade License
32.1.2. License Information
32.2. Users
32.2.1. User State
32.2.2. Authentication method
32.2.3. Users and Roles
32.2.4. Add user
32.3. Communication
32.3.1. HTTP proxy server
32.4. Update
32.4.1. Field explanation

A number of system wide settings are configured in the Administration module in ProteinCenter™. This includes license management, user management, communication settings and software update. This chapter describes in details how to configure these application settings. The access to the various functions are devided between two roles, namely Manager and Administrator:

Manager

Administrator

To access the Administrative module:

  1. Open the ProteinCenter™ application from your web browser.

  2. Login as a user with administrative privileges, i.e. Manager and/or Administrator roles.

  3. Click on the Administration tab.

Figure 32.1. Administration pane

Administration pane

32.1. License

ProteinCenter™ requires a valid license to run. A license contains information about the owner of the license, the expire date and more. The License pane in Figure 32.1, “Administration pane” shows information about the currently installed license and offers the possibility of changing/upgrading this license. Note that the license can also be upgraded as described in Section 32.4, “Update”.

32.1.1. Add or Upgrade License

To change the license, paste the license key obtained from Thermo Fisher Scientific in the License key field and click Update.

32.1.2. License Information

The license key contains information on when the license expires, who the license belongs to, the key version and how many simultaneous users are allowed.

32.1.2.1. Owner

Name of the license owner. Usually the name of a person, a company, or an organization.

32.1.2.2. Users

The maximum number of simultaneous users using ProteinCenter™.

The total number of users is unlimited, but the number of users logged in at the same time is limited by this number.

32.1.2.3. Enabled optional features

Currently, only KEGG is available as an extra feature. This requires that you have your own valid license from Pathway Solutions.

32.1.2.4. Expire date

All licenses have an expire date. Please contact Thermo Fisher Scientific before the end of the license period to obtain a new license.

32.1.2.5. Key type and version

Each license key has a key type and a key version. The type can be Profession Edition, Enterprise Edtition and so on. The Key version must match the ProteinCenter™ version.

32.2. Users

ProteinCenter™ distinguishes between two types of user information:

  1. State – Contains information about what the user has selected in which view etc.

  2. Roles – Which permissions the user has to view and/or use different parts of the system.

The first kind of information is always kept within the ProteinCenter™ application, whereas the second can be configured in ProteinCenter and/or through an external authentication and authorization service, such as LDAP or ActiveDirectory.

Figure 32.2. Users pane

Users pane

32.2.1. User State

The user state section (top of the screenshot in Figure 32.2, “Users pane”) of the Users & Configuration page gives a simple overview of which users that are logged into ProteinCenter™. The list is not updated automatically; to do so, press Update. Users with the Manager role also have the option of logging out other users of the ProteinCenter server.

32.2.2. Authentication method

You can choose between two different authentication methods in ProteinCenter™. They are described in the next two subsections.

32.2.2.1. Built-in user management

We recommend this for easy configuration in smaller workgroups.

ProteinCenter™ is preconfigured with a custom login-module that authenticates users against an internal database. If you prefer to use the internal user management, please enable this feature by checking

Enable ProteinCenter's built-in user management.

When doing so, a “Users and Roles” part will be displayed along with an “Add User” part. See Section 32.2.3, “Users and Roles” for information on how to configure these.

32.2.2.2. External authentication

We recommend this for larger organizations with centralized authentication and authorization services.

ProteinCenter™ uses JAAS (Java Authentication and Authorization Service) to distinguish users and their rights. JAAS allows for using a modular authentication scheme and comes in many implementations. Some of the most widely used and known authentication and authorization services are LDAP and Active Directory.

32.2.3. Users and Roles

Users added through ProteinCenter’s internal user management are shown here. This information is only relevant when Built-in user management in enabled. The fields contained in the list present the following options.

Table 32.1. User values

ColumnFunction – Result of pressing “Save”
DeleteIf checked, this user will be deleted.
UserIdDisplays this user’s user id. This value is unique and cannot be changed.
NameAllows for changing this users name. This value is not used for identification.
PasswordIf text is entered here, the user’s password will be changed. Does not show current password.
WorkspaceIndicates if this user has the “Workspace” role. See below
LookupIndicates if this user has the “Lookup” role. See below
ManagerIndicates if this user has the “Manager” role. See below
AdminIndicates if this user has the “Admin” role. See below
GrantIndicates if this user has the “Grant” role. See below
UploaderIndicates if this user has the “Uploader” role. See below
CreatedDisplays the creation date of the user account
Last LoginDisplays the date of last login for the user account. Empty if this event has not been recorded.
ExpiresDisplays the expiry date of the user account, if one is set.

32.2.3.1. Roles

ProteinCenter™ operates with six user roles.

  • Workspace role - the typical user must be assigned with this role. It allows the user to access all the functionality in the workbench. The workspace role cannot see the Administration pane

  • Lookup role - users assigned with the lookup role can use the lookup functionality described in Chapter 7, The Lookup.

  • Manager role - the manager role is an extention to the workspace role. Managers have access to parts of the functionality of the Administration pane. Managers with the Workspace role will additionally be allowed to view and change permissions on every user's categories and datasets as shown in Section 22.2, “Permissions”.

  • Admin role - the administrator role is an extention to the manager role. Administrators have access to parts of the functionality of the Administration pane. Administrators with the Workspace role will additionally be allowed to view and change permissions on every user's categories and datasets as shown in Section 22.2, “Permissions”.

  • Grant role - a user with this role will be allowed to change permissions of his/hers categories and datasets as shown in Section 22.2, “Permissions”. The typical user should be assigned this role to allow the user to selectively give or deny other users' access to his/hers categories and datasets.

  • Uploader role - The uploader role gives access to upload data through the Import pane of the workbench. This role should be given to the typical user.

As shown on Figure 32.2, “Users pane”, users can have more that one role.

32.2.4. Add user

Creating new user accounts can be done by filling in the respective fields in the “Add User” part (identified by circle 4 on Figure 32.2, “Users pane”) . This information is only relevant when Built-in user management in enabled. For a short description of the values, see the table above.

Note

The UserId value must be unique, but is NOT case sensitive.

32.3. Communication

Most communication settings, which include links to external servers, have been preconfigured. However, there are a few settings that are unique for your installation. It is recommended to configure these communication settings, should they apply to your setup.

This section describes what the individual settings are used for and how they are typically configured.

Figure 32.3. Communications pane

Communications pane

32.3.1. HTTP proxy server

Database updates are retrieved from Thermo Fisher Scientific using the HTTP protocol. If your organisation is using a web proxy to control access to the internet, you should add an account (username and password) on your proxy server so that the database update program can authenticate itself to the proxy server.

Log into ProteinCenter as an administrator. On the Communication page enable the Proxy server, enter the host name and port of the proxy server and the account name and password you created earlier.

Table 32.2. HTTP proxy settings

SettingDescription
EnabledIf checked, database updates will be retrieved via your organisation's HTTP proxy server.
HostHost name of your organisation's HTTP proxy server.
PortPort number on your organisation's HTTP proxy server.
User nameUser name on the proxy server.
PasswordPassword on the proxy server.

32.4. Update

To avoid a complicated software update procedure, ProteinCenter has built-in update mechanisms for updating the software and updating the license.

As a new feature ProteinCenter will automatically update the software after a new version has been downloaded to the server. This ensures that the application is always up to data and that new data updates will not be prevented from being loaded into the database due to incompatibility between the schema of the database and the expected schema of the data release. When the update happens depends on whether the update will be quick to install (i.e., when there are no database schema changes or succeding data updates) or whether it it might take longer time (there are database schema changes or succeding data updates). In the former case the application will be updated immmediately if there are no users logged in. In the latter case the application update will happen at midnight between 00:00 and 02:00.

If a new license has been dowloaded to the server or if an application update has been downloaded but not yet automatically installed an information icon will be displayed in the upper right corner as shown in the screen shot below. When the cursor is held over the icon, a message is shown detailing what is available for update.

Figure 32.4. Update information icon

Update information icon

The screen shot below shows the typical layout of the update pane when a new software version is available.

Figure 32.5. Update pane

Update pane

32.4.1. Field explanation

The upper part of the view (Update application) shows which updates exist. They are explained in the table below.

The lower part (License Information) shows the contents of the new license key, if one is ready for download.

Table 32.3. Update information

SettingDescription
Current software versionThe ProteinCenter version you are currently using.
New software versionThe most recent ProteinCenter version available. It is possible that more updates have been released in between, but you will always get the most recent update.
Data updatesThe number of data updates that are required to be installed along with this update. Generally, data updates can take a long time to do, so if you don't want the down-time right away, wait with the update until the data updates have finished (typically done during the weekend).
Schema updatesThe number of database schema updates that will be performed during the update. These are typically fast to perform, but can take a while if it's a major change.
New license keyEither "YES" or "NO" depending on whether or not a new license key is to be installed. If "YES", a license information section is shown below with the information contained herein.