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Saga™ Administrator’s Guide

For SagaGT and SagaMX Software

Version 3.3

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Notice The information contained in this document is subject to change without notice. LI-COR MAKES NO WARRANTY OF ANY KIND WITH REGARD TO THIS MATERIAL, INCLUDING, BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. LI-COR shall not be liable for errors contained herein or for incidental or consequential damages in connection with the furnishing, performance, or use of this material. This document contains proprietary information which is protected by copyright. All rights are reserved. No part of this document may be photocopied, reproduced, or translated to another language without prior written consent of LI-COR, Inc. Copyright 2000-2005 LI-COR, Inc.

Publication Number 984-07946 June, 2005

AFLP is a registered trademark of Keygene N.V. Saga, IRDye, and LI-COR are trademarks or registered trade- marks of LI-COR, Inc. NEN is a registered trademark of Perkin-Elmer Inc. Windows and Microsoft are regis- tered trademarks of Microsoft Corporation. Oracle is a registered trademark of Oracle Corporation.

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Table Of Contents

Chapter 1: NEN® 4300 Database...... 20 Computer Requirements ...... 20 Hardware Installation Installation ...... 21 Installation...... 1 Installing the Saga Application Server ...... 28 Firewall Recommendations ...... 3 Installation ...... 28 Adding a Scanner Account ...... 3 Installing the USB Security Device...... 32 Adding the First Users to the Saga Chapter 2: NEN® 4200 Application Server ...... 32 Hardware Installation Starting the Application Server as a Desktop Application ...... 34 Typical Server Edition Network Starting the Application Server as a Configuration ...... 7 Service...... 34 Gathering the Network Information...... 7 the Backup Directory...... 35 Firewall recommendations ...... 9 Completing Client Installation...... 36 Connecting Communication Cables ...... 9 Installing Saga Clients On Other Power Connections ...... 10 Computers ...... 37 Modifying Addresses in the Model 4200... 11 Windows® 95/98/XP/NT/2000 Personal Edition Network Configuration ... 11 Installation ...... 37 Personal Edition Stand-Alone Adding Scanners in Saga...... 41 Configuration ...... 12 Upgrading from Saga Version 3.x...... 46 Network Address Information...... 12 Installation...... 46 Connecting the Parallel Cable ...... 12 New Features in Saga Version 3.3...... 47 Power Connections ...... 12 Where to Go from Here ...... 50 Connecting Cat. 5 RJ-45 Cables...... 14 Applying Power to the Network Switch...... 14 Chapter 4: Saga Application Server Entering Addresses in the Model 4200.... 14 Administration Managing Global Controller Accounts...... 15 Opening the Application Server Window ....51 Opening the Administrator’s Page ...... 16 Status and Activity Messages...... 51 Adding a User Account to the Global Logging in to the Saga Application Controller ...... 17 Server...... 51 Logging Out of the Saga Application Chapter 3. Software Installation Server ...... 52 Installation Overview ...... 19 Managing Saga User Accounts...... 53 Installing the Oracle 9i Personal Edition Overview of User Accounts ...... 53 Adding, Deleting, and Changing User

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Accounts ...... 54 Displaying A List Of Current Users ...... 57 Logging Users Out...... 57 Shutting Down the Saga Application Server ...... 58 Registering the Saga Application Service.... 59 System Setup ...... 59 General Tab ...... 59 E-mail Tab...... 60 Home DirectoryTab ...... 61 Data Directory Tab...... 62 Incoming Directory Tab ...... 62 Backup Directory Tab ...... 63 Database Tab ...... 64 Analysis Settings ...... 65 Assigning Analysis Settings ...... 66 Creating or Changing Settings Files...... 66 Saga MX Scoring Tab ...... 67 Saga GT Scoring Tab ...... 69 Backing Up the Oracle Database...... 72 Restoring the Oracle Database...... 72 Migrating a Saga Database...... 74 Displaying a List of Saga Databases ...... 75 Re-initializing the Saga Database...... 75 Deleting a Saga Database ...... 76

Chapter 5. Appendices Upgrading to Saga Version 3.3 From Version 2.1...... 77 Installation ...... 77 New Features ...... 79 Installing Oracle 8i Personal Edition Database ...... 79 Computer Requirements...... 79 Installation ...... 80

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Chapter 1: NEN® 4300 Hardware Installation

This chapter discusses the configuration and operation of Saga™ with the NEN® Model 4300 DNA Analyzer. If you are installing an NEN Model 4200 Global IR2 System, refer to Chapter 2 for instal- lation instructions.

Installation

The Model 4300 Installation Manual for the NEN Model 4300 DNA Analyzer has complete instructions for a typical hardware installation. This section includes a few additional instructions that are specific to Model 4300 installations for use with Saga analysis software. For a non-network installation, the Model 4300 and computer can be installed exactly as described in Chapter 3 of the Installation Manual. The Oracle® database software, Saga Application Server, and Saga Client Software should all be installed on the computer as described in Chapter 3 of this manual. If the Model 4300 is being installed on a network, installation is as described in Chapter 2 of the Model 4300 Installation Manual with a few minor exceptions. Figure 1-1 shows a typical Saga hardware configuration for network operation. If you are using only one computer in the network configuration, the Oracle database software, Saga Application Server, and Saga Client Software should all be installed on the computer as described in Chapter 3 of this manual. If you have additional computers running Saga Client Software, they can be connected to the network switch or any other network wall port.

2 CHAPTER 1 NEN 4300 Hardware Installation

Saga Application Connections to Server and Oracle existing network database running on Windows XP/NT/2000 Multiple Saga Clients Cat. 5 RJ-45 operating system running on Windows cable to operating systems network port (optional).

Cat. 5 RJ-45 Cat. 5 RJ-45 cable Cable To to a numbered port Uplink Port

Power Dual speed switch 123 45Uplink

Port Disabled NOTE: Network switch is optional. Cat. 5 RJ-45 cable Computers and Model 4300 can to a numbered port be connected directly to network wall ports.

4300 back panel

4300

MOTOR OPERATE TRANSPORT LOCK EMI filter

Figure 1-1. Typical network configuration with a network switch for Saga Server Edition.

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Firewall Recommendations For networks connected to the Internet, the safest way to protect your research and data is to put all computers (client and server) and all Model 4300 DNA analyzers on a subnet that is behind a firewall. Inexpensive firewall appliances can perform this function. Contact your local IT department for help in selection and configuration if your organization does not already provide you with firewall protection. Legitimate, safe, remote access to Saga can still be achieved when the server is protected by a firewall. Failure to adequately protect the Model 4300 or its computer from attack can have very serious consequences that are not covered by LI-COR's express or implied warranty.

Adding a Scanner Account

When a user starts a gel, Saga automatically logs on to the Model 4300 using a user account in the server software. The user account is desig- nated when the scanner is added to Saga using Saga’s Scanner Manager. Before you install Saga software for the first time (Chapter 3), you should create a user account that will be used to connect to the Model 4300. Chapter 5 in the Model 4300 Operator’s Manual describes how to log on to the Model 4300 server using an Internet browser. Chapter 6 in the Operator’s Manual describes how to add user accounts to the Model 4300. These instructions are repeated in abbreviated form below. Follow the following steps to log on using an Internet browser: 1) Open an Internet browser application on your computer (requires Netscape Navigator 4.7 or above, or Internet Explorer 5.0 or above).

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Note: When the browser opens, you may get an error message that implies a connection failure or that the browser cannot find a certain server. This message is not related to the 4300 and can be dismissed. 2) In the Location/URL field of your browser, enter http:// plus the IP address assigned to the Model 4300.

The Model 4300 “home page” is displayed

3) Click Utilities to open the Utilities page. 4) If you are logging on for the first time, enter admin for the User Name and Password in the password window. You can also use any other account with Administrator rights. (User Name and Password are case sensitive.)

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5) Click the Manage User Accounts link on the Utilities page.

6) Click the Add Account link.

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7) Set the Account Rights for the new user to Control.

8) Enter a new user name (case sensitive) in the User Name field. User names and passwords can be 1 to 32 characters long. Alphabetic or numeric characters, as well as dashes and underscores, are acceptable. Do not use any other characters. Always start names with an alphabetic or numeric . 9) Type the password for the new user in the Password field. Type the password again in the Confirm field for verification. 10)Click Create User Account. Go back to the Manage User Accounts page and verify that the new account is in the account list. During Saga software installation (Chapter 3), one of the steps will be to add your scanner to Saga using Saga’s Scanner Manager. When prompted for the account, enter the user account and password that you created in the steps above.

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Chapter 2: NEN® 4200 Hardware Installation

This chapter should only be used to configure the NEN® Global IR2 System (model 4200) for use with Saga.

Typical Server Edition Network Configuration

Typical connections are shown in Figure 2-1. Refer to this diagram while performing the configuration procedure in this section.

Gathering the Network Information Before beginning, the requisite network addresses should be assigned. Table 2-1 lists the required addresses and others that may also be necessary. Table 2-1. Network addresses needed for installation. Description Example

IP Address (required) 123.45.67.190

Gateway/Router Address (required) 123.45.67.185

Subnet Mask (required) 255.255.255.0

Host Name (not required) my_system

Domain Name (not required) unlv.edu

Domain Name Server (may be one or more) 122.3.44.155

Dynamic Addressing (DHCP) is not supported by the Global System.

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Saga Client Software running on Windows operating system Connections To Existing Network

Saga Application Server and Oracle database running on Windows XP/NT/2000 operating system Cat. 5 RJ-45 Cat. 5 RJ-45 Cable To Cables To Uplink Port Numbered Ports Network Switch Network Switch Back Panel: Power Computers and Global Controller can also be connected directly to 123 45Uplink the network if there are enough network wall ports.

Port Disabled Cat. 5 RJ-45 Cable To A Numbered Port

Do Not Use The Global Controller 10/100 Base-T Port Global Controller Back Panel

LINE SERIAL PHONE 10/100 BASE-T PARALLEL ® VIDEO

G lob al E dit ion POWER Stereo Hand Stereo KEYBD IN OUT MONITOR C MOUSE ontr 10 BASE-T oller IN Set OUT

Model 4200 Parallel Cable (supplied)

PARALLEL Parallel Connector On Model 4200 Back Panel

Figure 2-1. Typical network configuration with a network switch for Saga Server Edition.

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Firewall Recommendations For networks connected to the Internet, the safest way to protect your research and data is to put all computers (client and server) and all Model 4200 instruments on a subnet that is behind a firewall. Inexpensive firewall appliances can perform this function. Contact your local IT department for help in selection and configuration if your organization does not already provide you with firewall protection. Legitimate, safe, remote access to Saga can still be achieved when the server is protected by a firewall. Failure to adequately protect the Model 4200 or its computer from attack can have very serious consequences that are not covered by LI-COR's express or implied warranty.

Connecting Communication Cables For direct connection to a network, connect the 10 Base-T port on the Global Controller and any computers to network wall ports using Cat. 5 RJ-45 cables. If you need to use a network switch to conserve network ports, follow the instructions below. 1) Connect the parallel port of the Global Controller (Figure 2-1) to the parallel connector on the back panel of the Model 4200 using the supplied 25-pin parallel cable. 2) Connect the supplied Cat. 5 RJ-45 cable to the port labeled 10 Base-T on the Global Controller (Figure 2-1). Do not use the port labeled 10/100 Base-T. 3) Connect the other end of the Cat. 5 RJ-45 cable to any port on the network switch except the Uplink port or the port next to the Uplink port. (The port next to the Uplink port is inactive when the Uplink port is in use.) 4) Connect the Uplink port on network switch to a network wall port using a second Cat. 5 RJ-45 cable.

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5) Connect the Saga Application Server and other computers running Saga Client Software to any of the numbered ports on the network switch, or directly to network wall ports.

Power Connections Since all devices in the Global IR2 System are network devices, it is important to apply power in proper order so that each device estab- lishes communication at the right time. 6) Connect the battery on the uninterruptible power supply (UPS) according to the manufacturers instructions. Connect the UPS to a supply outlet and turn on the UPS. 7) Connect the power cord to the Power port on the network switch and apply power to the switch by plugging the power cord into the UPS. There is no ON/OFF switch. 8) Plug the power cord into the Model 4200 and then plug the power cord into the uninterruptible power supply (UPS). 9) Close the front door on the Model 4200 and switch the power switch (instrument back panel) to the ON position. 10)Connect the power cord to the Power port on the back of the Global Controller and apply power to the Global Controller by plugging the power cord into the UPS (there is no ON/OFF switch). 11)The computer can be started at any time. Start it now, if necessary. During normal power up, system start-up is done after the IP address is sent from the Global Controller to the scanner and is shown on the Model 4200 display.

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Modifying Addresses in the Model 4200 Network addresses are entered during installation and usually don’t need to be entered again unless the addresses have changed. If the correct IP address is shown on the Model 4200 display after system start-up (step 10), the following steps do not need to be performed. 12)Flip open the covered keypad on the front of the Model 4200 and press Up Arrow key. 13)At the prompt for Host IP address, use the keypad to enter the IP address assigned to the Global Controller. Remember to enter the decimal points between each group of numbers. Use the Left Arrow key as a delete key to correct any mistakes. 14)Press the Enter button to store the IP address. 15)Enter the Gateway address at the prompt and press Enter. 16)Enter the Subnet Mask at the prompt and press Enter. The Global Controller will reboot. After a little more than 2 minutes, the new IP address is displayed on the display of the Model 4200. Hardware setup for the Model 4200 is now complete. Complete information on the Model 4200 can be found in the Model 4200 System Administrator’s Guide and Operator’s Manual.

Saga Personal Edition Network Configuration

For Saga Personal Edition, a computer running Windows XP/NT/2000 is used for both the Saga Application Server and to run a single copy of the client software. Both stand-alone and network configurations are possible. Network configurations are similar to Figure 2-1, except the client software is run on the Saga Application Server and there are no additional computers running Saga clients.

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Saga Personal Edition Stand-Alone Configuration

A non-network configuration of Saga Personal Edition using a network switch is shown in Figure 2-2 and described below. Later in this section, a configuration that does not require a network switch is also discussed.

Network Address Information Stand-alone configurations use fixed IP addresses for the Global Controller and Windows XP/NT/2000 computer. The addresses below are recommended: Windows Computer: 192.168.0.1 Global Controller: 192.168.0.2 Gateway Address: 192.168.0.1 Subnet Mask: 255.255.0.0 If other addresses are used, the Windows XP/NT/2000 computer and Global Controller should differ only in the last octet.

Connecting the Parallel Cable 1) Connect the parallel port of the Global Controller (Figure 2-2) to the parallel connector on the back panel of the Model 4200 using the supplied 25-pin parallel cable.

Power Connections 2) Connect the battery on the uninterruptible power supply (UPS) according to the manufacturers instructions. Connect the UPS to a supply outlet and turn on the UPS.

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SAGA Application Server, Oracle database and SAGA Client Software running on Windows XP/NT/2000 operating system

Cat 5 RJ-45 192.168.0.1 Cable Connected 255.255.0.0 To Any Port Except Uplink

Network Switch Power Network Switch Back Panel 123 45Uplink

Cat 5 RJ-45 Cable Connected To Any Port Except Uplink Global Controller Do Not Use The 10/100 Base-T Port Global Controller Back Panel

® LINE SERIAL PHONE 10/100 BASE-T PARALLEL VIDEO G lob al E dit ion

Controller POWER Stereo Stereo Hand KEYBD MOUSE IN OUT MONITOR IN Set OUT 10 BASE-T

Host IP: 192.168.0.2 Gateway: 192.168.0.1 Subnet Mask: 255.255.0.0

Model 4200 Parallel Cable (supplied)

PARALLEL Parallel Connector On Model 4200 Back Panel Figure 2-2. A stand-alone configuration of Saga Personal Edition configuration using a network switch.

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3) Plug the power cord into the Model 4200 and then plug the power cord into the UPS. 4) Make sure the front door on the Model 4200 is closed, and then switch the power switch on the back panel of the instrument to the ON position. 5) Connect the power cord to the Power port on the back of the Global Controller and apply power to the Global Controller by plugging the power cord into the UPS (there is no ON/OFF switch). 6) Turn on the computer.

Connecting Cat. 5 RJ-45 Cables 7) Connect the supplied Cat. 5 RJ-45 cable to the port labeled 10 Base-T on the Global Controller (Figure 2-2). Do not use the port labeled 10/100 Base-T. 8) Connect the other end of the Cat. 5 RJ-45 cable to any of the numbered ports on the network switch (not the Uplink port). 9) Connect the Windows XP/NT/2000 computer to any of the numbered ports on the switch (not the Uplink port) using a Cat. 5 RJ-45 cable.

Applying Power to the Network Switch 10)Connect the power cord to the Power port on the switch and then apply power to the switch by plugging the power cord into the UPS (there is no ON/OFF switch).

Entering Addresses in the Model 4200 11)Flip open the covered keypad on the front of the Model 4200 and press Up Arrow key.

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12)At the prompt for IP address, use the keypad to enter 192.168.0.2 Remember to enter the decimal points between each group of numbers. Use the Left Arrow key as a delete key to correct any mistakes that are made. 13)Press the Enter button. 14)At the Gateway prompt, enter 192.168.0.1 and press Enter. 15)Enter 255.255.0.0 as the Subnet Mask and press Enter. The Global Controller will reboot and after about 2 minutes, the IP address is displayed on the display of the Model 4200. 16)Assign the Host IP address (192.168.0.1) to the computer. The Host IP address and other TCP/IP parameters can be entered using the Networking Control Panel (found by opening the Control Panels in the My Computer folder). Hardware setup is complete and accounts can now be established in the Global Controller for users.

Managing Global Controller Accounts

It is important to realize that Saga and the Global IR2 Instrument have user account names and passwords in three different places. In addition, the Windows XP/NT/2000 computer has its own account names and passwords that are unrelated to Saga. First, the Global Controller must have at least one administrator and one user account. Second, there are numerous user accounts in the Saga Application Server. Third, users must be assigned to the access list for a Saga project using Saga’s User Manager. 16 CHAPTER 2 NEN 4200 Hardware Installation

Managing user accounts in the Global Controller is discussed in Chapter 1 of the System Administrator’s Guide for the Global IR2 System. A portion of that discussion is repeated below to illustrate how to create the user account that will be needed during Saga software installation. Adding accounts in the Saga Application Server is discussed in Chapter 4 of this manual. Chapter 6 of the Saga User Guide discusses managing users in projects with Saga User Manager. If you also use the Global IR2 instrument for sequencing, it is important to understand that Saga uses Global Controller accounts differently than e-Seq DNA Sequencing Software. In Saga, Global IR2 instruments are made available to everyone using the Saga Appli- cation Server through one account that is assigned in Saga’s Scanner Manager. When a scanner is added in Scanner Manager, one Global Controller account name and password must be entered. Any user who starts a gel in Saga using the new scanner accesses the Global Controller using the account in the Global Controller. For this reason, only one Global Controller user account is needed, though users may want to have their own accounts in order to access the Global Controller through the browser interface.

Opening the Administrator’s Page Accounts in the Global Controller are managed using an Internet browser to connect to the Global Controller and open an HTML System Administrator’s page. Follow the steps below to log on to the Administrator’s page in the Global Controller. 1) In the location/URL field of your browser, enter http:// plus the IP address of the Global Controller, plus /admin. 17

2) In the password window, enter the User Name and Password of a current account with Administrator level access. If you are setting up Saga for the first time, the default administrator name and password are both admin. The User Name and Password are case sensitive. The Global Controller sends an Admin “home page” that shows a Table of Contents with user functions, as well as administration functions.

Adding a User Account to the Global Controller 3) Click the Accounts link on the Administrator’s page.

Note: If you would like to review a list of current accounts before making a new account, click the Current Accounts button at the bottom of the page. A list of accounts divided by access privileges will be displayed. 4) Enter the new user name (case sensitive) in the User Name field. 18 CHAPTER 2 NEN 4200 Hardware Installation

User names are case sensitive and must begin with an alphabetic character (not a numeric character). Name length can be 1 to 32 characters. After the first character, characters can be alphabetic, numeric, a dash or underscore. Do not use any other characters like slashes, periods, dashes, etc. 5) Set the access level for the new user to Control. 6) Type the password for the new user in the Password field. Type it again in the Retype Password field for verification. Passwords are case sensitive and must be at least 6 characters long. If more than 8 characters are entered, only the first 8 are used to verify the password when a user logs in. 7) Click Update Account. 8) Click the Back button on your browser. 9) Click Current Accounts and verify that the new user account is listed. 10)Close the browser to log off. During Saga software installation (Chapter 3), one of the steps will be to add your scanner to Saga using Saga’s Scanner Manager. When prompted for the account, enter the user account and password that you created in the steps above.

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Chapter 3: Software Installation

Installation Overview

A broad overview of Saga and NEN® DNA analyzers can be found in either the SagaGT or SagaMX Tutorial Manual. Reading the overview before software installation will increase your under- standing of Saga and make installation easier. You should also have the computer(s) and DNA analyzer configured as described in chapters 1 or 2 of this manual. Saga has four main components: Saga Client Software for Windows® 95/98/XP/NT/2000; Saga Application Server and Oracle® database on a computer with Windows XP, NT, or 2000 operating system; and finally, the DNA analyzer. The security device provided with Saga determines whether the Saga Application Server will function as an analysis platform for microsatellites (SagaGT), AFLP® projects (SagaMX), or both. This chapter focuses on installation of the Oracle database, Saga Application Server, and Saga Client Software. If you are installing Saga for the first time, start with the next section that describes installing the Oracle 9i database. If you are upgrading from version 3.0, 3.1, or 3.2 start with the upgrade instructions at the end of the chapter. Instructions for upgrading from version 2.1 are given in Chapter 5.

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Installing the Oracle 9i Personal Edition Database

Warning: Do not install Oracle 9i if you are upgrading from a previous version of Saga and Oracle 8i is already installed on your computer. The primary advantage of Oracle 9i is support for Windows XP. Saga version 3.3 is designed to operate with either version of the Oracle database.

Computer Requirements The computer that will run the Oracle Personal Edition Database and Saga Application Server should meet or exceed the following minimum specifications: Saga Personal Edition (client & server on same computer): Operating System: Windows XP, NT v.4, or 2000 Workstation. Microprocessor: 1.56 GHz Pentium recommended. RAM: 512 MB minimum (more RAM improves performance). Hard Disk: 30 GB, minimum. Parallel Port: Required for security device (a USB security device is available on request). Saga Server Edition: Operating System: Windows XP, NT v.4, or 2000 Workstation or Server. Microprocessor: 1.56 GHz Pentium recommended. RAM: 512 MB minimum (more RAM improves performance). Hard Disk: 30 GB, minimum. Parallel Port: Required for security device (a USB security device is available on request). Network: TCP/IP (10/100 Mbps recommended).

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Installation Note: If you would like to use Saga with an existing Oracle database server, contact LI-COR Technical Support rather than following this installation procedure. If you need to re-install Oracle 8i, rather than install Oracle 9i, instructions are given in Chapter 5. 1) Log on to Windows® XP/NT/2000 as a user with local Adminis- trative privileges. If you get your credentials from a network server rather than locally on your computer, you will not have sufficient access privileges to install Saga. 2) Important: Close all other programs and disable any virus protection programs. 3) Insert Disk 1 of the three Oracle installation CDs. The Oracle installer should start automatically when the CD is inserted. If not, choose Run on the Start menu, browse for the CD, select the Setup.exe program and click OK in the Run dialog. Note: The Oracle database installer is an adaptive program that determines what your computer needs to run the database and adapts accordingly. For that reason, installation will vary on different computers and on different operating systems. The remainder of the installation procedure below is a typical procedure for Windows XP. You may see other windows when you install Oracle 9i on your computer, but use this procedure as a guide. 4) Click Install Oracle to proceed with installation.

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5) A message is displayed that lists two passwords that you will need later in the installation. Record the account names and passwords or refer back to this page when the installer prompts for the passwords. Click OK to continue.

6) Check the file destinations and make sure the Oracle Home Name is set to OraHome92 and the Path is C:\Oracle\Ora92. Then click Next.

Even though a Browse button for the path is provided, the path should not be changed.

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7) Leave the port number set to the default value and click Next.

8) Enter saga.world as the Global Database Name. “saga” should appear as the Oracle System Identifier (SID). Click Next.

24 CHAPTER 3 Software Installation

9) Leave the database file location set to the default path and click Next.

10)Make sure Use Default Character Set is selected and click Next.

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11)Review the summary of what will be installed and click Install.

12)Installation begins and progress is shown in the Install window. During the lengthy process, you will be prompted to install Disk 2 and Disk 3 of the Oracle installation CDs.

26 CHAPTER 3 Software Installation

13)When the Database Configuration Assistant is displayed, enter “sysmanager” in the SYS Password field and enter it again in the Confirm SYS Password field. Enter “systemmanager” in the SYSTEM Password field and enter it again in the Confirm SYSTEM Password field. Both passwords are case-sensitive (all lowercase). Click OK to continue the installation.

Progress is indicated as the database is cloned.

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After installation is complete, the installer displays an “End of Installation” message.

14)Click Exit to finish installation.

28 CHAPTER 3 Software Installation

Installing the Saga Application Server

Unless you are using an existing Oracle Database Server, the Saga Application Server must be installed on the same computer as the Oracle database. During installation, you will also be given the choice of installing the Saga Client Software on the same computer. IMPORTANT: You must be logged on to Windows® XP/NT/2000 as a user with local Administrative privileges to complete this installation. If you get your credentials from a network server rather than locally on your computer, you will not have sufficient access privileges to install Saga.

Installation 1) Important: Close all other programs and disable any virus protection programs. 2) Insert the CD for the Saga Application Server and Client Software. 3) On the Windows Start menu, choose Run. 4) Click the Browse button in the Run dialog. 5) In the file selection dialog, switch to the CD-ROM drive, select the file named SagaGeneration2.exe, and click the Open button. 6) Click OK in the Run dialog. 7) Click Next and read the license information. If you accept the terms of the license, click Yes to continue with installation.

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8) Select the components to install, as described below, and click Next.

The first two check boxes give you the option of installing the Saga Application Server as a Desktop Application or a Service. Choose only one of the two options. If you choose the Desktop option, the Saga Application Server will behave like any normal application on the desktop. Installation as a Desktop application works well when the computer is being used for Saga Personal Edition. As a desktop application, when the user who started the Saga Application Server logs out, Saga Application Server will shutdown also. Images cannot be analyzed automati- cally until Saga is started again. When installed as a Service, the Saga Application Server will run continuously in the background until the computer is shut off or the service for the Saga Application Server is explicitly stopped. Commu- nication with the service is accomplished using Saga’s Application Controller program (Chapter 4). The Saga Service has to be started manually anytime the computer is restarted. The Service option is generally preferred for Saga Server Edition where multiple users may be using Saga on a server that runs continuously. 30 CHAPTER 3 Software Installation

Important: If you install Saga as a service, the desktop version is also installed. Saga should be run as a desktop application until all initial configuration options, etc., are complete and clients have success- fully logged in. After successful operation as a desktop application, you can exit the desktop application and start Saga as a service (see Starting The Application Server As A Service below). The desktop application and Saga Service cannot run at the same time. If you are unsure whether to use the Desktop or Service option, use the Desktop option. The Saga Generation 2 Client check box determines whether the Saga Client Software is installed. If you are installing the Saga Personal Edition configuration, make sure Saga Generation 2 Client is selected. For Saga Server Edition, client software installation is optional on the computer running Saga Application Server. However, note that the client does not count as one of your licenses unless it is running, and that the Saga Client Software takes only a modest amount of disk space when installed. Under Saga Generation 2 Client, it is generally desirable to have both check boxes selected for first-time installations. The Client is required to run the client software. The Example Files are used in the Saga Tutorial Manual. 31

9) Click Next to accept the default program folder name for Saga Generation 2.

10)Click OK to start installation of the dongle driver.

11)Click OK to continue installing the dongle driver.

12)If you have the parallel port version of the Saga security device (called a dongle), connect it to the parallel port on the computer and click OK. If you have a USB security device, click OK without installing the security device. Instructions for installing the USB security device are given after step 14 below. 32 CHAPTER 3 Software Installation

13)Click OK to complete dongle setup.

14)Click Finish in the window for the installation program to complete installation of the Saga Application Server.

Installing the USB Security Device Use these instructions only if you have the USB version of the security device. 1) If necessary, insert the Saga installation CD in CD-ROM drive. 2) Insert the security device into an empty USB port on the computer. Windows will detect the new USB hardware and search for a matching device driver. None will be found, so you will be prompted to locate the device driver. 3) Use the file window to identify the USB_key directory on the CD as the location of the device driver for the security key.

Adding the First User to the Saga Application Server When the Saga Application Server is initialized, there are no users in the database. A utility program called KeyGen.exe must be used to add a user with Administrator access. (Users are normally added as described in Chapter 4.) 33

1) Double-click the KeyGen.exe program located in the Saga Appli- cation Server directory (usually C:\Program Files\Saga2\Applica- tionServer).

2) Choose File > Open Key File. 3) Select the file named Saga.Key in the C:\Program Files\Saga2\ApplicationServer directory.

4) In the User Administration window, select the Registered Users tab and click New.

5) Enter a User Name for the Administrator of the Saga Application Server. 34 CHAPTER 3 Software Installation

6) Enter a Password and confirm it by entering it again in the Password Confirmation field. 7) Give the new Administrator all rights by selecting the following check boxes: Multiple Login, Read, Write/Delete, Scanner Control, Group Leader, and System Administrator. 8) Click Save to add the new Administrator to the database. 9) Click OK to close the User Administration window. 10)Choose File > Exit to close the KeyGen program. Note: For highest security, the KeyGen program can be deleted after initial use to prevent users from making unauthorized changes to the Application Server.

Starting the Application Server as a Desktop Application Do the following steps only if you installed the Saga Application Server as a desktop application. Skip to Starting Saga As A Service if you installed the Application Server as a service. 1) Double click the icon named Saga Generation 2 Application Server (Desktop) located in the Saga Generation 2 folder on the desktop. The Application Server window opens and displays a variety of messages as the server is initialized.

Starting the Application Server as a Service Do the next six steps only if you have installed the Saga Application Server as a Service. 1) If you are starting the Application Server for the first time, double click the icon named Saga Generation 2 Application Server (Desktop) located in the Saga Generation 2 folder on the 35

desktop. This starts the Application Server as a desktop appli- cation. After the Application Server is running, log in with Saga Client Software to make sure communication is successful. Log out and exit the client software. Next choose File > Exit in the Application Server window to close the Application Server. This step initializes the Application Server and is only necessary the first time it is started as a service. 2) Start the Application Controller program by double clicking the icon named Saga Generation 2 Application Server (NT Service Controller) located in the Saga Generation 2 folder on the desktop. 3) Choose Administration > Verify and log in using the Adminis- trator account created with the Keygen program. 4) Choose Administration > Service > Install in the Application Controller window. 5) Choose Service > Start Service. 6) Close the Application Controller program. (The Service will remain running.)

Setting the Backup Directory The default configuration of the Saga Application Server is to automatically backup the database (not images) once per day at 2:00 a.m. Backup files (*.dmp) are stored in the following directory: C:\Program Files\Saga2\ApplicationServer\Backup If you want to change the backup time, disable automatic backups, or use a different drive or directory to store the backup files, you can do this by choosing Administration > Setup in the Application Server window. Chapter 4 describes how to use the Backup Directory tab in the Setup window to change the backup time. 36 CHAPTER 3 Software Installation

Completing Client Installation If you installed the Saga Client Software on the same computer as the Saga Application Server, several more steps are needed to finish installing the client. 1) Start the client software by double-clicking the icon that was placed in the Saga Generation 2 desktop folder during installation.

2) In the Login window, click the Setup button. 37

3) Enter 127.0.0.1 in the IP Address field.

4) Leave the Port number set to the default value. 5) Click OK to complete setup. 6) Click Exit in the Login window to exit the Saga Client. The client setup is now complete.

Installing Saga Clients on Other Computers

Use this procedure to install the client software on a computer other than the computer used for the Saga Application Server.

Windows 95/98/XP/NT/2000 Installation

Computer Requirements Operating System: Windows 95/98/XP/NT/2000. Microprocessor: 800 MHz Pentium, minimum. RAM: 256 MB minimum. (Adding more RAM improves performance). Network: TCP/IP (100 Mbps recommended). 38 CHAPTER 3 Software Installation

Installation 1) Close all other programs and disable any virus protection programs. 2) Insert the CD for the Saga Application Server and Client Software. 3) On the Windows Start menu, choose Run. 4) Click the Browse button in the Run dialog. 5) In the file selection dialog, switch to the CD-ROM drive, select the file named SagaGeneration2.exe, and click the Open button. 6) Click OK in the Run dialog. 7) Click Next and read the license information. Click Yes to continue, if you accept the terms of the license. 8) Examine the directory. It should be set to C:\Program Files\Saga2. Click Next to continue. 9) Make sure both check boxes under Saga Generation 2 Client Components are selected if you are installing for the first time. (The Example Files are used in the Saga Tutorial Manual.) Deselect both check boxes for the Saga Application Server.

10)Click Next to continue. 39

11)Click Next to accept Saga Generation 2 as the name of a program folder for the Saga client software. The folder name can be changed, if desired. 12)Click Finish when installation of the Saga Client Software is complete. 13)Start the client software by double-clicking the icon placed in the Saga Generation 2 desktop folder during installation.

14)In the Login window, click the Setup button. 40 CHAPTER 3 Software Installation

15)Enter the IP address of the computer running the Saga Application Server.

16)Leave the Port number set to the default value. 17)Click OK to complete setup. 18)Click Exit in the Login window to quit the client software. Repeat the client installation procedure on any other computer needing the Saga client installed. 41

Adding Scanners in Saga

The last installation step is to register the DNA analyzer with Saga’s Scanner Manager. In order to register an instrument with Saga’s Scanner Manager, the instrument must be turned on and accessible through the network or a stand-alone configuration. Before you start this procedure, create a user account with Control access rights in the DNA analyzer (or Global Controller for the Model 4200). Saga will use this account to connect to the DNA analyzer.

1) Double-click the icon for the Saga client software. 2) Enter the Administrator User Name and Password that you 3) Click Login. previously added with the KeyGen program.

4) Click New in Project Manager.

A project must exist before Scanner Manager can be accessed. 42 CHAPTER 3 Software Installation

5) Enter Temp in the Name field for the project name.

6) Click OK.

7) Select the Temp project in the project list.

8) Click OK to open the Temp project.

9) Click the Scanner Manager button in Experimental Procedures Manager to open Scanner Manager. 43

10)Click New on the Scanner Manager button bar to add a new scanner.

11)Enter a name to identify the scanner.

12)Select the model of DNA analyzer you are using.

13)Select 1(800); 2(700) unless you are using a single-laser Model 4200 instrument.

14)Enter the IP address of the DNA analyzer (see your IT or IS administrator if your are unsure about this).

15)Use the Location and Comments fields to enter additional information that 16)Click OK to save the new identifies the scanner. scanner information. 44 CHAPTER 3 Software Installation

17)Enter the User Name and Password of a account in the DNA analyzer (or Global Controller on a Model 4200) with Control access rights. Do not use an Administrator account. Both fields are case sensitive.

18)Click OK.

After a few seconds, scanner status should be Idle. If the scanner status is Unreachable, the power is turned off or there is a network communication 19)Click Close. problem. 45

20)Choose Project > Close in the Experimental Procedures window.

21)Select the Temp project in Project Manager and click the Delete button in the button bar. (The Temp project was only needed for scanner setup. See the Chapter 3 of the User Guide for complete information on starting projects.)

22)Click OK and Yes in response to the warnings about deleting the project. 23)Choose Project > Log Out in Project Manager. 24)Click Exit in the Log In window. 46 CHAPTER 3 Software Installation

Upgrading from Saga Version 3.x

If your instrument is a Model 4200 Global IR2 System, Saga requires Global Controller software version 1.1.4, or higher. The Global Controller software version number is shown on the display of the Model 4200 when it is idle. If you see a version number like 1.0.0 or 1.1.2 on the display, contact LI-COR Technical Support to get an upgrade for the Global Controller software before proceeding.

Installation 1) Log on to Windows® XP/NT/2000 as a user with local Adminis- trative privileges. If you get your credentials from a network server rather than locally on your computer, you will not have sufficient access privileges to install Saga. 2) If you are running Saga as a desktop application, close the appli- cation by choosing File > Exit in the Application Server window. If you are running the Saga Application Server as a service rather than a desktop application, the Saga service must be stopped. Start the Application Controller program by double clicking the Saga Generation 2 Application Server (NT Service Controller) icon located in the Saga Generation 2 folder on the desktop. Choose Administration > Verify and enter an account name and password that has Administrator rights. Choose Service > Stop Service to stop the Saga service. Choose Administration > Unverify and close the Application Controller program. 3) Backup your Oracle database using the procedure described in Chapter 4. The Oracle database software does not need to be upgraded when you install version 3.3, but it is important to perform a backup for safety. 47

4) Run the Saga installation application on the Saga v3.3 Client and Application Server CD. The application will detect the presence of a prior version of Saga and prompt you to uninstall it. Important: Do not uninstall the Oracle database or existing data could be lost. 5) After you finish uninstalling Saga, run the installer again to install version 3.3. Start at the section titled Installing the Application Server earlier in this chapter and install the Saga Application Server and client software. For any additional computers running the Saga client software, uninstall the current version of the Saga client and install the new version.

New Features in Saga Version 3.3 The following changes were made in Saga version 3.3 compared to version 3.2. A log of changes in other versions can be found in the help system. Saga GT Changes: • Several new tests were added for pedigree and Mendelian errors. New tests include: multi-generation test for a child mistakenly declared its own ancestor, wrong sex for father or mother, and more than four alleles in a mother-father family unit (independent of declared family ID). These tests are performed automatically during image analysis, but the same tests can be started manually with new buttons added to DNA Source Manager (Check) and Gel Manager (Mendel). • Several new settings have been added to the Saga GT analysis settings (see General Changes for additional information). You can now designate the maximum number of stutter bands in a valid sample, call all alleles as homozygotes, and turn off automatic genotyping (image collection only). • The analysis software has numerous changes to improve molecular weight calibration accuracy. • Added a report that lists Mendelian errors only for individuals designated as fathers. 48 CHAPTER 3 Software Installation

• Important: Significant changes were made to the allele-calling algorithm in version 3.2. If you are upgrading from a version prior to 3.2, mixing alle- les called with version 3.3 and alleles called with versions prior to 3.2 in the same project may result in incorrect assignment of allele frequencies. If you are working on a project with a version prior to Saga 3.2, it is recom- mended that you complete the project before installing Saga version 3.3. Saga MX Changes: • Molecular weight calibration in the analysis software has been extensively changed to improve accuracy. Similar to the previous version, calibration begins by finding bands in molecular weight lanes and creating desmile lines for well qualified monomorphic bands. In version 3.3, a desmile line is also added at each molecular weight marker position. The shape of desmile lines at molecular weight markers is determined by interpolating between the desmile line above and below the molecular weight band. The molecular weight of the desmile line is, by definition, the same as the molecular weight band. These new desmile lines appear as magenta (default color) lines in desmile and cannot be edited. However, they can be changed by changing the shape of desmile lines above and below, and re-analyzing. After calibration is finished, all molecular weight values on the image are calculated using the magenta desmile lines at the molecular weight markers. The other yellow desmile lines do not further influence molecular weight calculations unless you change their shape and re-analyze the image. For increased accuracy, version 3.3 also performs all molecular weight calcula- tions using floating point numbers rather than integer numbers as in prior versions. • The bin detection parameters on the MX scoring tab of the analysis settings have been changed. The new analysis settings are described in the General Changes below. • When bins are edited, Bin Manager is now updated immediately after the changes are made. General Changes: • Saga version 3.3 is shipped with Oracle 9i. Existing Oracle 8i users SHOULD NOT UPGRADE ORACLE. The Oracle upgrade can be difficult and the benefits low. The most important difference between Oracle 8i and 9i for use with Saga is that Oracle 9i can be installed on computers run- ning Windows XP. If you have a reason to upgrade an existing Oracle installation, contact LI-COR Technical Support before proceeding. 49

• The gel status column in Gel Manager now displays the status of both 700 and 800 channel images. •A View button has been added to Gel Manager. After opening the first image using the Show button, you can select a second image in Gel Man- ager and click View to open the image in a new Gel Editor window (only two images can be open at once). • The Data Display window in both Saga GT and MX has been changed to allow samples to be moved up or down in the window. To move a sample, click the sample to select it and press Alt + Up Arrow or Alt + Down Arrow to move the sample up or down. • The database structure has been changed to allow each project to have its own analysis settings. A new Analysis Settings window has been created in the Saga Application Server software. The Analysis Settings window is opened by choosing Administration > Analysis Settings. The Analysis Set- tings window includes the GT and MX scoring tabs that were previously in the Setup window (Administration > Setup). The Analysis Settings window also includes controls for assigning an analysis settings file to individual projects as described in chapter 4 of this manual. • An image magnifier has been added to the Gel Editor window in both Saga GT and MX. The magnifier is opened by clicking the Magnify icon on the button bar. The magnifier can be moved by clicking and dragging the mag- nification box. The portion of the image under the center of the magnifier is the portion shown in the magnification box. Shift + left click increases the magnification and Shift + right click decreases magnification. • Insert and Delete buttons have been added to the Gel Constructor window in both Saga GT and MX. These buttons allow you to insert or delete a gel position (lane) in the sample map, making it easier to correct errors. • The columns displayed on the Source tab in Gel Constructor have been changed. The Genus and Species columns have been deleted and columns for Sex, Affection Status, and ID Family have been added. • The Data Display window in both Saga GT and MX has a new feature. In the past you could change multiple markers at once by dragging a selec- tion box around the markers you want to change. The selection box has been improved by displaying the beginning (left) and ending (right) molec- ular weights enclosed by the selection box. 50 CHAPTER 3 Software Installation

Where to Go from Here...

Installation is complete. If you have installed Saga for the first time, you will need to add an account in the Saga Application Server for each user that will be running gels with Saga. The first few sections in Chapter 4 describe how to log in and add new user accounts. The remainder of Chapter 4 describes the remaining operational functions of the Saga Application Server. To learn Saga, start by working through the Saga Tutorial Manual. The Saga User Guide is a reference manual for all Saga functions.

51

Chapter 4: Saga Application Server Administration

Opening the Application Server Window

Saga Application Server software is most frequently used to maintain user accounts. User account functions and a variety of other useful server functions are described throughout this chapter. These functions are accessed through the Application Server window that is automatically opened when the Application Server is running as a desktop application. If you are running the Saga Appli- cation Server as a service, the window described in this chapter must be opened by double clicking the Saga Generation 2 Appli- cation Server (NT Service Controller) icon located in the Saga Generation 2 folder on the desktop.

Status and Activity Messages

When the window for the Application Server is open, status and activity messages related to the Application Server are displayed.

Logging In to the Saga Application Server

The Administration menu in the window for the Application Server is used to access most of the functionality of the Saga Application Server. Initially, the Administration menu has only one menu choice named Verify that is used to log in and enter an Administrator account name and password. Once the account and password are

52 CHAPTER 4 SAGA Application Server Administration

verified, the Administration menu is expanded with additional menu choices as shown below. (You may also see a Service menu choice if Saga is running as a service, or a Mail Log File choice if e-mail has been setup as discussed in System Setup later in this chapter.)

The functions on the Administration menu and Service menu are discussed throughout the remainder of this chapter.

Logging Out of the Saga Application Server When you are through using the Application Server administrative functions, it is important to log out, but leave the Application Server running. To log out, choose Administration > Unverify. Logging out prevents unauthorized use of your administrator account. Note: If you are running the Application Server as a service, just close the Application Controller program and the Saga service will continue to function normally.

53

Managing Saga User Accounts

Overview of User Accounts It is important to realize that Saga and the DNA analyzer have user account names and passwords in three different places. First, the DNA analyzer (or Global Controller on a Model 4200) must have at least one account with Administrator access rights and one account with Control access rights. Second, there must be user accounts in the Saga Application Server for all users who access the server through Saga Client Software. In order to participate in a Saga project, users must also be assigned to the access list for the project. Third, the Windows computer has its own account names and passwords that are unrelated to Saga. User account management in the DNA analyzer is discussed in the Operator’s Manual (Model 4300) or Remote Connection Guide (Model 4200) for the instrument. The Saga User Guide shows how to use User Manager in Saga Client Software to add and delete users to and from projects. User accounts are an important part of Saga security. New users must first be added to the Application Server, then Saga’s User Manager can be used to add the new users to various projects. When the Saga Application Server was installed, an account with Administrator access rights was added using the Keygen program. The procedure below can be used to log in to the Application Server and add, delete, or change user accounts. Administrator level access is required.

54 CHAPTER 4 SAGA Application Server Administration

Adding, Deleting, and Changing User Accounts To add, delete, or change user accounts in the Saga Application Server, open the User Administration window by choosing Adminis- tration > User Administration.

If your e-mail is properly configured, you will see the message SMTP Server OK displayed beside the E-mail label.

Adding Users To add a user, click New User on the Registered Users tab and fill in the information fields for the new user. When you are through adding information, click Save to add the new user to the database. You must enter the User Name, Password, Password Confirmation, and Access Rules for each user. Additionally, if the user is to be a Saga Group Leader (can start new projects, add users to existing projects, add scanners, etc.) or System Administrator (complete access), those check boxes should be selected in the Administration Rights list. A

55

user with neither System Administrator nor Group Leader rights can perform only the tasks allowed by the Access Rules, which are normal daily operations like starting runs, viewing and editing data, etc. The Real Name, E-mail and Comments fields can be used to further distinguish users. The Access Rules check boxes are used to restrict the access of a given user. If a user has only Read access, the user can open and display data (images, allele calls, etc.) for any project they are a member of. A user who has Write/Delete access can edit or delete data. For a user to be able to start new runs, they must have Scanner Control access. A typical user will have all three check boxes selected. The Multiple Login check box allows a user to be simultaneously logged in from multiple Saga clients. This can be useful when working in both the lab and an office. However, each time a user logs in, one Saga license is used. A user logged in at three locations, for example, is using three of the available Saga licenses.

Changing User Information To change a user's name, password, or other information, open the User Administration window and select an existing user from the User Name drop-down list. Edit the account information and click Save to store any changes.

Deleting Users To delete a user, open the User Administration window and select an existing user from the User Name drop-down list. Click Delete to remove the user account. Note that clicking Delete only deletes an account in the Saga Application Server. Accounts in the DNA analyzer are unchanged.

56 CHAPTER 4 SAGA Application Server Administration

Available Administrator Types Tab The Available Administrators Type tab shows all users in a member list with check marks next to users of a particular type.

For example, with Type of Administrator set to Admin, the Members list will show all members, but only members that are Administrators will have check marks next to their name. Similarly, if you select Group Leader from the Type of Administrator drop- down list, only users with Group Leader access will have check marks next to their name in the Members list. The Available Administrator Types tab can also be used to change the administrator type. If you select or deselect the check box next to a user's name and click Save, administrative access will be enabled or disabled, respectively. For example, if Type of Administrator is set to

57

Group Leader and you deselect the check box next to a user name and click Save, that user will no longer have Group Leader access, though they may still have Administrator level access.

Displaying a List of Current Users

Choose Administration > Login List to view a list of all users who are currently logged in. The Login List also displays the Project ID of the project each user is working on.

Logging Users Out To log a user out, select the user from the list and click the Kill Login button. Close the window when finished.

58 CHAPTER 4 SAGA Application Server Administration

Shutting Down the Saga Application Server

If you run other applications besides Saga, you may need to shut down the Saga Application Server. If Saga is installed as a desktop application, choose File > Exit in the Application Server window to stop the service and shut down the Application Server. If Saga is installed as a service, either the Windows service utility or the Application Controller program (Saga Generation 2 Application Server (NT Service Controller) icon in the Saga Generation 2 desktop folder) can be used to stop the service. If you use the Application Controller program, the Saga service can be stopped by choosing Service > Stop Service.

Important! If Saga is shutdown in the middle of analyses or other processes, it will normally be able to resume those processes when the Application Server is started again. However, it is better to shutdown the Application Server during periods of inactivity, whenever possible. Users logged into the Application Server will be notified that the Application Server is shutting down. Restarting Saga: If you restart the Saga Application Server as a desktop application by double clicking the Saga Generation 2 Appli- cation Server (Desktop) icon in the Saga Generation 2 desktop folder, the Saga analysis service automatically starts. To restart the Saga Application Server as a service, start the Application Controller program by double clicking the Saga Generation 2 Application Server (NT Service Controller) icon in the Saga Generation 2 desktop 59

folder and then choose Service > Start Service. Any time the computer operating system is restarted, the Saga service must be restarted.

Registering the Saga Application Service

If Saga was installed as a service, the Saga Application Service was registered with the Windows Service Manager (Chapter 3). Regis- tration only needs to be done once, after installation. You should not need to unregister the Saga service, however, it can be unregistered by logging in, stopping the service (choose Service > Stop Service), and then choosing Administration > Service > Uninstall. (The Uninstall function changes the registration but has nothing to do with uninstalling the Saga software.)

System Setup

The Application Server setup can be changed by choosing Adminis- tration > Setup.

General Tab The port settings on the General tab are used when the client software communicates with the Saga Application Server. In the unlikely event that these numbers cause a conflict, contact LI-COR Technical Support for suggestions on alternate port numbers. The port numbers should not be changed and should appear as shown below. 60 CHAPTER 4 SAGA Application Server Administration

As Saga performs tasks, the information about the tasks is recorded in a log file. ”Verbose” log messages provide more operational details. If LI-COR Technical Support requests that you e-mail a log file to solve a problem, they may also request that you verify that Verbose Log Messages is selected in order to better characterize the problem.

E-mail Tab In order for e-mail to work correctly, information on your SMTP mail server must be entered on the E-mail tab. Enter the server address in the SMTP Mail Server field. If you need an account name and password to access the server, enter those in the appropriate fields. Your local IT department can provide this information for you. Internet Service Providers also routinely provide this information when an account is created. After entering the information, click Test Mail to find out if your e-mail is correctly configured. The word OK is displayed above the Test Mail button if the test is successful. 61

Home Directory Tab The Home Directory tab displays where the files for the Saga Appli- cation Server are stored. This directory should never need to be changed. 62 CHAPTER 4 SAGA Application Server Administration

Data Directory Tab Saga stores all image files in a single directory, rather than in the Oracle database. When Saga is installed, a Data directory is created in the path Program Files\Saga2\ApplicationServer\Data. This path should not be changed unless suggested by LI-COR Technical Support. The Data Directory tab should normally appear as shown below.

The data directory can be changed using the drive and directory lists, or by entering a path in the Data Dir field. Universal Naming Convention (UNC) paths can also be manually entered in the Data Dir field.

Gel image files (*.TIF) stored in the \Data directory should be period- ically backed up. Analyzed images can be deleted from the hard disk to reclaim space, however, you will not be able to view images in the Gel Editor if they have been deleted.

Incoming Directory Tab When Saga retrieves finished runs from the DNA analyzer, all files are initially stored in Saga's \Incoming directory until analysis starts. The path to the default \Incoming directory is C:\Program Files\Saga2\Application Server\Incoming 63

This path should never be changed unless suggested by LI-COR Technical Support. The Incoming Directory tab should normally appear as shown below.

The incoming directory can be changed using the drive and directory lists, or by entering a path in the Incoming Dir field. UNC paths can also be manually entered in the Incoming Dir field.

Backup Directory Tab The Backup Directory tab can be used to initiate an automatic backup that occurs once per day at a user designated time (the default is 2:00 a.m.). The backup includes the entire Saga database and all image files in the \Data directory. The drive and directory where the backup is stored can be specified. Automatic backup is turned on when Saga is installed. For safety, you should always set the backup directory to a disk drive or network volume other than the one where Saga is installed. Automatic backup can be disabled by deselecting the check box in the Time of Automatic Database Backups field. Database backup files for the last seven consecutive days are stored, giving you redundant backup files that can be restored. If there are already seven consecutive days stored when a new automatic backup is started, the oldest backup is deleted. 64 CHAPTER 4 SAGA Application Server Administration

The directory where backup files are stored can be changed using the drive and directory lists, or by entering a path in the Backup Dir field. UNC paths can also be manually entered in the Backup Dir field.

Note: The database can also be manually backed up or restored as described later in this chapter.

Database Tab Saga communicates with Oracle through a DBA account named "SYSTEM". The password assigned to this account when Oracle is installed is "systemmanager" for Oracle 9i and "manager" for Oracle 8i. The system account password is normally not changed from its default value. However, if Oracle tools have been used to change the password of the system account, the correct password must be entered in the DBA Account Password field on the Database tab. 65

In a typical Oracle Personal Edition installation that is not part of a larger Oracle database system, the Database Account is “SAGA”, the Database Password is “saga_magic_world” (case sensitive), and the Database Service field is blank, as shown below.

LI-COR Technical Support may ask for this Oracle version number when solving problems.

If you are using an existing Oracle database rather than Saga's Oracle Personal Edition, the database account, password, and service will need to be entered after the Saga Application Server is installed. Your Oracle System Administrator can provide the necessary information. If you have more than one Saga database account, you can switch between accounts using the Database Account drop-down list.

Analysis Settings

Gels in a given project are analyzed according to the analysis settings assigned to that project. Each project can have its own analysis settings, allowing user customization. Analysis settings can be assigned to a project by choosing Administration > Analysis Settings. 66 CHAPTER 4 SAGA Application Server Administration

Assigning Analysis Settings Initially, all projects are assigned the Default analysis settings file. The settings file for each individual project can be changed on the Projects tab in the Analysis Settings window. First, select the project and then select the settings file from Use Setting list. Click OK when you are finished making changes. The new settings file will be used for all subsequent gels analyzed in the selected project. Gels that were previously analyzed remain unchanged unless they are re- analyzed.

Creating or Changing Settings Files To change the Default settings file or to create your own settings file, start by clicking the Settings tab in the Analysis Settings window. To change an existing settings file, select the file in the Name list, make changes on the MX- and GT-Scoring tabs (described below), and 67

click Save. To create a settings file, enter a new file name in the Name of Setting field, make changes on the MX- and GT-Scoring tabs (described below), and click Save.

Saga MX Scoring Tab A complete description of how Saga MX scores bands can be found in the Saga MX User Guide. The MX Scoring tab is used to adjust the scoring software by changing the band detection and scoring param- eters. Each of these parameters is discussed below. Save Edited MX Alleles During Re-analysis: After an image is initially analyzed, if the image is analyzed again, any edits to band scoring are discarded before analysis starts. In some cases this may delete 68 CHAPTER 4 SAGA Application Server Administration

many time-consuming edits. If you would prefer to keep your edits when an image is re-analyzed, select the Save Edited MX Alleles During Analysis check box. Score (Bin) Detection Parameters: The score detection parameters determine how the gel is evaluated during analysis. The height on the gel, in base pairs, at which analysis starts is determined by the parameter named Start Scoring and BP Range At This Value. For example, if all bins are located above 100 bp, you can eliminate needless analysis by setting Start Scoring and BP Range At This Value to 100. Analysis starts at the value specified in the Start Scoring and BP Range At This Value parameter and the image is evaluated one section at a time. The width of a section is the width of the gel. The height of a section, in base pairs, is determined by the BP Range to Evaluate Over parameter. The number of bins that can be found in a given BP range (section) is determined by the Number of Possible Bins in Range parameter. The number of possible bins cannot exceed the base pair range. Band Scoring Parameters: The Band Scoring Parameters determine whether potential bands are scored as Present, Not Present or Unknown. When the scoring of potential bands at a base pair position starts, all gray scale values are normalized with respect to the largest gray scale value found in the bin. If the relative magnitude of a potential band is within the range of 0 to 15% of the largest gray scale value, the potential band is scored as Not Present (-). If the relative magnitude of a potential band is within the range of 15 to 25% of the largest gray scale value, the potential band is scored as Unknown (?). Finally, if the relative magnitude of a potential band is within the range of 25 to 100% of the largest gray scale value, the potential band is scored as Present (+). After this initial scoring, the bands with Unknown scores are analyzed again. If all the unknown bands are grouped at the top or bottom of the unknown range, the 69

scored is changed to Present (+) or Not Present (-), respectively. The range of each of the three scoring categories can be adjusted by changing the numbers in the Band Scoring Parameters fields. Bin Parameters: The Bin Parameter is typically set from 0 to ± 10 bp (maximum is ±65536 bp). This parameter is fully discussed in the Automatic Scoring Overview in Chapter 11 of the Saga MX User Guide. The purpose of the Bin Parameter is to promote more accurate scoring when there are small calibration differences between gels. A variance in a variety of gel conditions may cause slight calibration differences. Changing the Bin Parameter to a positive, non-zero number creates a region around each bin that will be searched for bands to score. Consult the User Guide for complete details.

Saga GT Scoring Tab The GT Scoring tab gives you several ways to control Saga GT during analysis. If you analyze an image a second time, any edited alleles are discarded before analysis starts. In some cases this may delete 70 CHAPTER 4 SAGA Application Server Administration

numerous time-consuming edits. If you would prefer to keep your edited allele calls when an image is re-analyzed, select the Save Edited GT Alleles During Re-Analysis check box.

When alleles are scored they are compared to an allele template, or fingerprint, which is a composite of similar alleles in the database. Creating the allele template can be time consuming when there are a large number of samples with the same allele in the database. The Max Number of Samples to Use in Template Creation field lets you control the maximum number of samples that will be used to create the allele template. For example, if you set the maximum number of samples to 500, only the 500 best alleles in the database will be used to generate the template. (When alleles are stored in the database, they are given an indicator of quality which is used to rank the alleles for template creation.) Lowering the maximum number of samples (e.g. from 500 to 200) generally results in very little statistical 71

difference on the template, but may improve analysis speed. The faster the microprocessor, the more templates can be used during template creation, while still maintaining adequate analysis speed. Samples will vary in the number of stutter bands that are produced during electrophoresis. The Maximum Number of Stutter Bands in Valid Sample field is used to set the maximum number of bands that Saga will identify as stutter bands for a given allele. Setting the maximum too low will cause Saga to call stutter bands as alleles and setting the maximum too high could cause Saga to treat alleles as stutter bands. When an image is analyzed, an allele grid is placed over the image to help identify where bands should be for specific alleles. However, when a project is first started there is no allele grid to analyze the first image since there are no data in the database to indicate allele positions. Suppose a molecular weight calibration error caused a certain allele to be placed 1 bp too high on the first image analyzed. Subsequent images would be analyzed using an allele grid based on the first image. If the bands for the allele were calibrated correctly on subsequent images, they would be 1 bp lower than the allele position on the allele grid and automatic scoring would not score the bands correctly. The Automatic Allele Shifting check box can be used to restore accurate, automatic scoring. When Automatic Allele Shifting is selected, Saga uses all allele profiles from all gels at a given locus to find the best fit for the grid, rather than just using allele profiles from the first gel. Care should be taken in using this function because the allele grid is changed to the best match for all allele positions on the grid. If you have an allele with numerous errors, the allele grid could be shifted away from the correct position for that allele. Examine data at all allele positions before using this function. If you prefer that all alleles be called as homozygotes, select the Call All Alleles as Homozygotes check box. 72 CHAPTER 4 SAGA Application Server Administration

If you want to use Saga to collect images without genotyping them, deselect the Automatically Genotype After Finding Lanes check box. This turns off genotyping for all subsequent gels until the check box is selected again.

Backing Up the Oracle Database

Saga has two backup procedures. An automatic backup procedure that backs up both the database and image files is automatically enabled when Saga is installed. This automatic backup can be disabled as described earlier in this chapter. A manual backup procedure is also included that lets you backup just the Saga database to a single file in a location that you choose. A backup is started by choosing Administration > Database > Backup in the Application Controller window. A standard file selection window is opened to let you choose where to store the backup file. A default backup file name is entered in the file name field. The format is ‘From_’, followed by the Saga database account name, followed by the date in ddmmyy format. It is generally best to accept the default file name, because the restore function will use the database account name to fill in part of the information needed to restore the database.

Restoring the Oracle Database

The Restore function in the Saga Application Server is used to restore databases that have been archived with the Database Backup command as described above. 73

Start the Restore function by choosing Administration > Database > Restore in the Application Server window.

Use the Browse button to browse for the Saga backup file you want to restore. Only Saga backup files with a *.dmp extension can be restored. The From Database Account name is entered automatically from the file name (middle section) of the file being restored. If you do not use the default file name during backup, you must manually enter the original database account name in the From Database Account field. For example, if you backup and restore a Saga version 2.1 database, the From Database Account field will always be ‘System’ because Saga version 2.1 stored all databases in the System User account. The Saga Database Account To Import To fields let you enter the name and password of the Saga account that you want to import the data into. Warning: If you enter the name and password of an existing account all the data in that account will be over written. 74 CHAPTER 4 SAGA Application Server Administration

If you enter the name and password of an account that does not exist, a new account will be created. All the data will be imported into the new account and the original account will be left unchanged. Click OK when you have specified the file to import and the database account. After the restore function has concluded, the new database you imported will be the active database account.

Migrating a Saga Database

If you upgraded from Saga version 2.1, the version 2.1 database account was automatically “migrated” to a version 3.x compatible database. In other words, all the data from the old Saga database account was copied into the appropriate places in the table structure of the new version 3.x Saga database account. Some users, however, may have additional Saga database accounts that are being used for different purposes. During installation, only one of the accounts will be migrated to version 3.x. If you have an additional version 2.1 account that needs to be migrated, you can do this by choosing Administration > Database > Migrate and specifying the database account that needs to be migrated. You will need temporary disk space equivalent to 2.5 times the size of your version 2.1 database in order to migrate the database. This is mostly temporary space that will be released when migration is complete. Do not try to migrate a Saga version 2.0 account with this function. Call LI-COR technical support if you need to use a Saga version 2.0 database with Saga version 3.x. 75

Displaying a List of Saga Databases

If you have more than one Saga database account, you can display a list of all available databases by choosing Administration > Database > Show Available...

Re-initializing the Saga Database

Use this function with EXTREME caution! Choose Administration > Database > Reinitialize to delete all data tables in the current Saga account and create new, empty tables. There is no undo for this function and data cannot be retrieved after re-initializing the database. Re-initialize the database only when you want to delete ALL data. Consult the Saga User Guide if you just want to delete projects, users, scanners, locus data, image files, etc. 76 CHAPTER 4 SAGA Application Server Administration

Deleting a Saga Database

Use this function with EXTREME caution! Choose Administration > Database > Delete if you want to completely delete a database account. All accounts for the current service are shown (this is the only window that lists all accounts). Select the database account to delete and click Delete.

Warning: This function deletes all data and the related database for the specified account.

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Chapter 5: Appendices

Upgrading to Saga Version 3.3 From Version 2.1

If you are upgrading from Saga version 2.0, rather than version 2.1, contact LI-COR Technical Support before starting the upgrade. If your instrument is a Model 4200 Global IR2 System, Saga requires Global Controller software version 1.1.4, or higher. The Global Controller software version number is shown on the display of the Model 4200 when it is idle. If you see a version number like 1.0.0 or 1.1.2 on the display, contact LI-COR Technical Support to get an upgrade for the Global Controller software before proceeding.

Installation 1) Log on to Windows® XP/NT/2000 as a user with local Adminis- trative privileges. If you get your credentials from a network server rather than locally on your computer, you will not have sufficient access privileges to install Saga. 2) If you are running Saga as a desktop application, close the appli- cation by choosing File > Exit in the Application Server window. If you are running the Saga Application Server as a service rather than a desktop application, the Saga service must be stopped. Run the Application Controller program by double clicking the Saga Generation 2 Application Server (NT Service Controller) icon in the Saga Generation 2 desktop folder. Choose Adminis- tration > Verify and enter an account name and password that

78 CHAPTER 5 Appendices

has Administrator rights. Choose Service > Stop Service to stop the Saga service. Choose Administration > Unverify and close the Application Controller program. 3) Run the Saga installation application on the Saga v3.3 Client and Application Server CD. The application will detect the presence of a prior version of Saga and prompt you to uninstall it. Important: Do not uninstall the Oracle database or existing data could be lost. 4) The Oracle database software does not need to be upgraded when you install version 3.3, but it is important to backup the data in your existing Oracle database using the procedure described in Chapter 4 of the version 2.1 Saga Administrator’s Guide. (New backup and restore functions replaced this procedure in Saga version 3.1.) The Oracle database used for version 2.1 of the Saga Application Server will be converted for use with a new table structure when the Application Server is started for the first time. Your data should be unchanged when the database is migrated from one version to the other, but the backup copy will keep your data safe if a problem occurs. Allow time for the database migration when you start the new Application Server for the first time. You should also check to make sure you have enough disk space. You will need temporary disk space equivalent to 2.5 times the size of your version 2.1 database in order to migrate the database. This is mostly temporary space that will be released when migration is complete. 5) Do not install the Oracle database. 6) Find the section in Chapter 3 titled Installing the Application Server and install the Saga v3.3 Application Server and client software. For any additional computers running the Saga client software, uninstall the current version of the Saga client and install the new version.

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New Features The Saga help system has a complete change list for the various ver- sions of Saga, including the most recent changes made in version 3.3.

Installing Oracle 8i Personal Edition Database

Oracle 8i was provided with versions of Saga prior to version 3.2. The instructions in this section are provided only for existing Saga users who may have a need to re-install Oracle 8i. See Chapter 3 to install Oracle 9i. Note, however, that Oracle 9i is not needed unless you need to run Oracle on Windows XP.

Computer Requirements The computer that will run the Oracle Personal Edition Database and Saga Application Server should meet or exceed the following minimum specifications: Saga Personal Edition (client & server on same computer): Operating System: Windows NT v.4 or Windows 2000 Workstation. Microprocessor: 500 MHz Pentium recommended. RAM: 256 MB minimum (more RAM improves performance). Hard Disk: 30 GB, minimum. Parallel Port: Required for security device (a USB security device is available on request). Saga Server Edition: Operating System: Windows NT v.4 or Windows 2000 Workstation or Server. Microprocessor: 500 MHz Pentium recommended. RAM: 256 MB minimum (more RAM improves performance). Hard Disk: 30 GB, minimum.

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Parallel Port: Required for security device (a USB security device is available on request). Network: TCP/IP (10/100 Mbps recommended).

Installation Note: If you would like to use Saga with an existing Oracle database server, contact LI-COR Technical Support rather that following this installation procedure. Warning: Do not perform this installation if you are upgrading from a previous version of Saga. 1) Log on to Windows® XP/NT/2000 as a user with Administrative privi- leges (e.g., as a user that is a member of the local Administrators group). 2) Important: Close all other programs and disable any virus protection programs. 3) Insert the Saga Database CD containing Oracle Personal Edition. The Oracle installer should start automatically when the CD is inserted. If not, choose Start > Run, browse for the CD, select the Setup.exe program and click OK in the Run dialog.

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4) At the Installer Welcome window, click Next to proceed with installation.

If you think there may be other Oracle products already installed on the computer, click Installed Products before clicking Next to see a list of all installed products.

5) Check the file destinations and make sure the Oracle Home Name is set to OraHome81 and the Path is C:\Oracle\Ora81. Then click Next.

Even though a Browse button for the path is provided, the path should not be changed.

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6) Select Oracle Personal Edition as the product to install and click Next.

If Oracle Personal Edition is not listed, the computer may not be running the Windows NT or 2000 operating system.

7) Select the Typical installation and click Next.

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8) Select to leave the Oracle documentation on CD-ROM (recom- mended) or install it on your hard disk. Then click Next.

The Oracle documen- tation requires over 130MB of disk space and is generally not needed for Saga.

9) Enter saga.world as the Global Database Name. “saga” should appear as the Oracle System Identifier (SID). Then click Next.

84 CHAPTER 5 Appendices

10)Review the summary of what will be installed and click Install.

11)Wait until all files are installed and click Next.

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12)Click Next to load the recommended database configuration tools.

The field at the bottom of the window lists some INTERNAL account names that Oracle and Saga will use to communicate. These are not needed by Saga users or admin- istrators.

A database is created and initialized.

12)Click OK when you are informed that database creation is complete.

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13)Read the message to make sure Oracle was successfully installed and click Exit.

The next step is to patch Oracle8i release 8.1.7 for use with Saga using the Patch CD-ROM (P/N 618-06953).

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14)Before installing the LI-COR patch to the Oracle database, Oracle services must be stopped. On the Windows Start menu, choose Control Panel or Settings > Control Panel. In the Control Panel window, open the Administrative Tools. In the list of tools, double-click Services. A list of all services is displayed.

15)Scroll down and find the various Oracle services. Stop any Oracle service that has a status of Started by right-clicking the service and selecting Stop from the popup menu. 16)Examine the Startup Type column in the Services window. The only Oracle services that should be set to Automatic are OracleOraHome81TNSListener and OracleServiceSaga. Any Oracle Service other than OracleOraHome81TNSListener and OracleServiceSaga that has a Startup Type of Automatic should be changed to Manual startup. To change the Startup Type of a 88 CHAPTER 5 Appendices

service to Manual, right-click the service and select Properties from the popup menu. In the Properties window, select Manual in the Startup Type drop-down list and click OK.

17)When you are finished, the only Oracle services set to Automatic startup should be OracleOraHome81TNSListener and OracleSer- viceSaga. Close the Services and Control Panel windows. 18)Insert the LI-COR Patch CD for the Oracle database into the CD-ROM drive. Choose Run on the Windows Start menu, browse for the installer application on the Patch CD, and run the installer. 19)Click Next on the Welcome screen to display the File Locations screen. 20)The default location for the Source... entry field should already be products.jar, which is the correct file for the patch set installation. Leave this field unchanged. 89

21)Select the Oracle Home in which you want to install the patch set from the drop-down list of Oracle Homes or Oracle Home Names. Normally there will be only one choice. Click the Next button. 22)In the Available Product Components window, click Next to use the preselected choices. 23)In the Summary window, verify the products listed and click Install. 24)When installation has completed successfully, the message “End of Installation” is displayed. Click Exit to exit the installer. 25)Restart the computer. The two Oracle services that are set to Automatic startup will be automatically started. There should be no other Oracle services running.

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