Saga™ Administrator’s Guide For SagaGT and SagaMX Software Version 3.3 ii 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. iii 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 Setting 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 iv 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 1 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. 3 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