Thermo Fisher Scientific Foundation 1.1 Administrator User guide

Brand: Thermo Fisher Scientific

Model: Foundation 1.1 Administrator

Category: Software

Type: User guide

Thermo Foundation

Version 1.1

Administrator Guide

XCALI-97328 Revision A May 2011

Xcalibur, Surveyor, LTQ, and Accela are registered trademarks, and LCQ, BioWorks, and LCquan are

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The contents of this document are subject to change without notice. All technical information in this

document is for reference purposes only. System configurations and specifications in this document supersede

all previous information received by the purchaser.

Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-

free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might

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Sale shall govern all conflicting information between the two documents.

Release history: Revision A, May 2011

Software version: Thermo Foundation 1.1

For Research Use Only. Not for use in diagnostic procedures.

Thermo Scientific Thermo Foundation Administrator Guide iii

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

About This Guide. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

Relation Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii

Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii

Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii

Chapter 1 Using the Thermo Foundation Auditing Database Configuration Manager . . . . .1

Chapter 2 Establishing Secure File Operations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5

Turning Off Fast User Switching for Local Workstations . . . . . . . . . . . . . . . . . . 5

Confirming the Properties of Thermo Foundation DatabaseService . . . . . . . . . . 7

Configuring Security Settings for Folders and Files . . . . . . . . . . . . . . . . . . . . . . 10

Working with Accounts Set Up by the Foundation Application . . . . . . . . . . 11

Adding Users. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Removing Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Setting Permissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Setting Permissions for Foundation Application Folders . . . . . . . . . . . . . . . . 18

Sequential User Logon and Automatic Logoff . . . . . . . . . . . . . . . . . . . . . . . . 22

Configuring Security Settings for the Database Registry Key. . . . . . . . . . . . . . . 23

Removing and Archiving Files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Chapter 3 Defining Secure User Groups and Adding Users . . . . . . . . . . . . . . . . . . . . . . . . . .29

Planning User Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Using the Thermo Foundation Authorization Manager. . . . . . . . . . . . . . . . . . . 30

Defining User Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Editing User Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Setting Permissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Setting the Permission Levels for an Individual Feature . . . . . . . . . . . . . . . 34

Setting All Permissions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Inheriting Permissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Exporting and Importing Permissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Specifying Predefined Comments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Viewing the Authorization Manager History Log . . . . . . . . . . . . . . . . . . . . . . . 38

Printing the Security Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Saving the Security Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Contents

iv Thermo Foundation Administrator Guide Thermo Scientific

Chapter 4 Using the Thermo Foundation CRC Validator. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .39

Checking Files with the Thermo Foundation CRC Validator . . . . . . . . . . . . . . 40

Selecting Files Using Database Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Selecting Files Using a Pattern. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Chapter 5 Auditing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45

Accessing the Auditing and Workbook Databases . . . . . . . . . . . . . . . . . . . . . . . 45

Accessing the Global Auditing Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Accessing the Application Workbook Database . . . . . . . . . . . . . . . . . . . . . . . 46

Viewing Audit Viewer Pages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

Filtering Audit Viewer Entries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Sorting Audit Viewer Entries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Printing Audit Viewer Entries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

Printing the Audit Trail for the Global Auditing Database . . . . . . . . . . . . . . 51

Printing the Audit Trail for an Application Workbook Database. . . . . . . . . . 51

Appendix A Installing an Oracle Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53

Installing the Oracle Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Installing the Oracle Client . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Appendix B System Administration Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .71

Thermo Foundation Administrator Utilities . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Instrument Configuration Dialog Box. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

Out of Date Instrument Drivers Detected Dialog Box . . . . . . . . . . . . . . . . . 73

Thermo File Converter Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

Library Manager Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Convert Libraries Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

Manage Libraries Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

Thermo Foundation Audit Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

All Page, Audit Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

History Page, Audit Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83

Event Page, Audit Viewer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84

File Tracking Page, Audit Viewer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

Instrument Error Page, Audit Viewer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

Sort Entries Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

Print Options Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

Filter Entries Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

Thermo Foundation Auditing Database Configuration Manager . . . . . . . . . 89

Thermo Foundation Authorization Manager. . . . . . . . . . . . . . . . . . . . . . . . . 91

Choose Secure Group Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102

Create Private Group and Edit User List Of Private Group Dialog

Boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102

Comment List Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

Contents

Thermo Scientific Thermo Foundation Administrator Guide v

Users In Group Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

New Comment Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

Thermo Foundation CRC Validator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .107

Thermo Scientific Thermo Foundation Administrator Guide vii

Preface

The Thermo Foundation Administrator Guide describes how to provide system administration

for standard system operation using the Thermo Foundation™ mass spectrometry data system.

For information on how to use tools in the Foundation data system to support compliance

with the Electronic Records and Electronic Signatures Rule, published by the United States

Food and Drug Administration as 21 CFR Part 11, refer to the Thermo Xcalibur LCquan

Administrator Guide.

To provide us with comments about this document, click the link below. Thank you in

advance for your help.

About This Guide

This guide has the following topics:

•Using the Thermo Foundation Auditing Database Configuration Manager

•Establishing Secure File Operations

•Defining Secure User Groups and Adding Users

•Using the Thermo Foundation CRC Validator

•Auditing

•Installing an Oracle Database

•System Administration Reference

Contents

•About This Guide

•Relation Documentation

•Special Notices

•Contacting Us

Preface

Relation Documentation

viii Thermo Foundation Administrator Guide Thermo Scientific

Relation Documentation

You will also find the information covered in this user guide in a Help system that comes with

the Thermo Foundation software.

Thermo Foundation includes Help in HTML format and the Thermo Foundation

Administrator Guide as a PDF file.

To view product manuals

Go to Start > All Programs > Thermo Foundation 1.1 > Manuals.

Special Notices

Make sure you follow the precautionary statements presented in this guide. The special

notices appear in boxes.

Special notices include the following:

Contacting Us

There are several ways to contact Thermo Fisher Scientific for the information you need.

To contact Technical Support

Find software updates and utilities to download at mssupport.thermo.com.

IMPORTANT Highlights information necessary to prevent damage to software, loss of

data, or invalid test results; or might contain information that is critical for optimal

performance of the system.

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.

Phone 800-532-4752

Fax 561-688-8736

E-mail us.techsupport.analyze@thermofisher.com

Knowledge base www.thermokb.com

Preface

Contacting Us

Thermo Scientific Thermo Foundation Administrator Guide ix

To contact Customer Service for ordering information

To get local contact information for sales or service

Go to www.thermoscientific.com/wps/portal/ts/contactus.

To copy manuals from the Internet

Go to mssupport.thermo.com, agree to the Terms and Conditions, and then click

Customer Manuals in the left margin of the window.

To suggest changes to documentation or to Help

• Fill out a reader survey online at www.surveymonkey.com/s/PQM6P62.

• Send an e-mail message to the Technical Publications Editor at

techpubs-lcms@thermofisher.com.

Phone 800-532-4752

Fax 561-688-8731

E-mail us.customer-support.analyze@thermofisher.com

Web site www.thermo.com/ms

Thermo Scientific Thermo Foundation Administrator Guide 1

Using the Thermo Foundation Auditing Database

Configuration Manager

This chapter describes how to use the Thermo Foundation Auditing Database Configuration

Manager to configure your database. The database keeps a record of auditable events and

changes made to files that a Thermo Foundation application either creates or manages.

Use the Thermo Foundation Auditing Database Configuration Manager to configure either a

Microsoft Access™ database on your local computer or an Oracle database on a remote

computer. To use an Oracle database, confirm completion of these tasks:

• An Oracle database has been installed on an accessible remote server. Consult your Oracle

database administrator for more information, or see Appendix A, “Installing an Oracle

Database.”

• The Oracle client software has been installed on your local computer. Consult your

Oracle database administrator for more information, or see Appendix A, “Installing an

Oracle Database.”

• Make sure that you know the User Name, Password, and Oracle Net Service Name of

your Oracle database. Obtain this information from your Oracle database administrator.

1 Using the Thermo Foundation Auditing Database Configuration Manager

2Thermo Foundation Administrator Guide Thermo Scientific

To configure your auditing database using the Thermo Foundation Auditing Database

Configuration Manager

1. From the Windows taskbar, choose Start > All Programs > Thermo Foundation 1.1 >

Database Configuration. The Thermo Foundation Auditing Database Configuration

Manager wizard opens (see Figure 1).

Figure 1. Thermo Foundation Auditing Database Configuration Manager wizard

2. Select the database type in the Select Database Type area:

• When using a Microsoft Access database, select the Microsoft Access option and go

to step 4.

• When using an Oracle database, select the Oracle on Network Server option and go

to step 3.

3. To use an Oracle database, specify the Oracle database parameters:

a. Type the database user name in the User Name box.

b. Type the database password in the Password box.

c. Select the Oracle Net Service Name for your database in the Oracle Net Service

Name list.

IMPORTANT Be sure to use the Oracle user name and password provided by your Oracle

database administrator.

1 Using the Thermo Foundation Auditing Database Configuration Manager

Thermo Scientific Thermo Foundation Administrator Guide 3

4. Click Next. The DatabaseConfigManager dialog box opens (see Figure 2).

Figure 2. DatabaseConfigManager dialog box

5. Confirm that the settings are correct and click OK.

The Thermo Foundation Auditing Database Configuration Manager wizard, similar to

Figure 3, appears.

Figure 3. Thermo Foundation Auditing Database Configuration Manager wizard, showing

restart settings

1 Using the Thermo Foundation Auditing Database Configuration Manager

4Thermo Foundation Administrator Guide Thermo Scientific

6. Select a restart option:

• To have the computer restart automatically after you click Finish, select the Restart

Computer now option.

• To restart the computer manually at a later time, select the I will restart later option.

7. Click Finish to save your settings and close the Thermo Foundation Auditing Database

Configuration Manager wizard.

IMPORTANT The changes you make in the Thermo Foundation Auditing Database

Configuration Manager do not take effect until you restart the computer.

Thermo Scientific Thermo Foundation Administrator Guide 5

Establishing Secure File Operations

This chapter describes how to configure the required operating system security settings to

make sure the auditing database, Authorization Manager, and other security features of

applications installed on Thermo Foundation software operate correctly.

Turning Off Fast User Switching for Local Workstations

Depending on the operating system, you can switch between users without actually logging

off from the computer. This feature, called Fast User Switching, can be turned off so that the

current user must log off before another user logs on.

Turning off fast user switching is important because as the system administrator, if you do not

turn off fast user switching, two users could log in at the same time, which can cause strange

behavior when they try to control their mass spectrometer. The acquisition service can only

handle one user logged in at a time. We recommend all labs turn off fast user switching,

regardless of whether secure file operations are important to them or not.

To maintain secure file operations, turn off Fast User Switching on all computers that provide

this option.

• Windows 7 operating system provides Fast User Switching on all computers.

Contents

•Turning Off Fast User Switching for Local Workstations

•Confirming the Properties of Thermo Foundation DatabaseService

•Configuring Security Settings for Folders and Files

•Configuring Security Settings for the Database Registry Key

•Removing and Archiving Files

2 Establishing Secure File Operations

Turning Off Fast User Switching for Local Workstations

6Thermo Foundation Administrator Guide Thermo Scientific

To turn off Fast User Switching

1. From the Windows 7 taskbar, choose Start.

2. In the Run dialog box, type gpedit.msc and press ENTER.

3. In the Local Group Policy Editor window, navigate to the Local Computer

Policy\Computer Configuration\Administrative Templates\System\Logon folder (see

Figure 4).

Figure 4. Local Group Policy Editor window

4. Double-click Hide Entry Points for Fast User Switching.

5. In the Hide Entry Points for Fast User Switching dialog box, select the Enabled option

(see Figure 5).

2 Establishing Secure File Operations

Confirming the Properties of Thermo Foundation DatabaseService

Thermo Scientific Thermo Foundation Administrator Guide 7

Figure 5. Hide entry points for Fast User Switching dialog box

6. Click Apply, and then click OK.

When a user logs out, the computer automatically shuts down any programs that are running.

Confirming the Properties of Thermo Foundation DatabaseService

The authorization and auditing functions of an application installed on the Thermo

Foundation application rely on two system services: the Finnigan Security Server and the

Thermo Foundation DatabaseService. These services are installed when you install the

application software. They automatically start whenever a user restarts a workstation.

The main function of the Finnigan Security Server is user authentication. If certain events

require authentication, the Finnigan Security Server verifies the user names and passwords

entered.

With the Thermo Foundation DatabaseService, layered applications can access the auditing

database and make auditing entries.

Note The Finnigan Security Server is only installed with the Xcalibur application. For

information related to Finnigan Security Server, refer to the Thermo Xcalibur Getting

Started Guide.

2 Establishing Secure File Operations

Confirming the Properties of Thermo Foundation DatabaseService

8Thermo Foundation Administrator Guide Thermo Scientific

To confirm the properties of Thermo Foundation DatabaseService are set correctly

1. To open the Services window, choose Start > Control Panel > System and Security >

Administrative Tools from your computer taskbar, and double-click Services to open the

Services window.

2. Right-click Thermo Foundation DatabaseService and choose Properties from the

shortcut menu. The Thermo Foundation DatabaseService Properties dialog box opens to

the General page (see Figure 6).

Figure 6. General page

3. On the General page, in the Startup Type list, select Automatic.

4. Confirm that Service Status reads Started.

5. Click the Log On tab to display the Log On page (see Figure 7).

2 Establishing Secure File Operations

Confirming the Properties of Thermo Foundation DatabaseService

Thermo Scientific Thermo Foundation Administrator Guide 9

Figure 7. Log On page

6. Under Log On As, select the Local System Account option.

7. Clear the Allow Service to Interact with Desktop check box.

8. Click OK to close the dialog box.

9. Close the Services window and close the Administrative Tools window.

2 Establishing Secure File Operations

Configuring Security Settings for Folders and Files

10 Thermo Foundation Administrator Guide Thermo Scientific

Configuring Security Settings for Folders and Files

To confirm the security of your data, restrict access to the folder named INI (located by

default in C:\Documents and Settings\All Users\Application Data\Thermo Scientific\) that

contains the configuration files. Because the Thermo Foundation Authorization Manager

reads the controlled feature information from the configuration files, prohibit access to these

files by non-administrators.

Set up specific user group access to folders and files with the NTFS file system (an advanced

file system used within the computer operating system). When you set up permissions, specify

the level of access for user groups, for example:

• Permit members of one user group to read the contents of a file.

• Permit members of another user group to make changes to the file.

• Prevent members of all other user groups from accessing the file.

New subfolders and files inherit folder permissions automatically. After you set the

appropriate permissions, an unauthorized user cannot maliciously or accidentally alter the

contents of the folder with utilities such as Windows Explorer.

In the procedures that follow, add an administrative user (or administrative group) and the

Everyone group to the Security page Group or User Names list. Grant the administrator full

access to the security folder and read-only access to everyone else.

•Working with Accounts Set Up by the Foundation Application

•Adding Users

•Removing Users

•Setting Permissions for Foundation Application Folders

Note The Application Data folder containing the configuration files is hidden by default

in Windows. To make it appear, go to Start > Control Panel > Appearance and

Personalization > Folder Options > View > Hidden Files and Folders, and select Show

Hidden Files and Folders.

Tip When you require more restricted access to folders and files, grant access only to

specific user groups. Set up appropriate user groups. See Chapter 3, “Defining Secure User

Groups and Adding Users.” Complete the procedures that follow, but use your specific

user group, instead of the Everyone group.

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Thermo Fisher Scientific Foundation 1.1 Administrator User guide

Brand: Thermo Fisher Scientific

Model: Foundation 1.1 Administrator

Category: Software

Type: User guide

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