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Getting Started GuidePhoenix™ WinNonlin® 6.1Phoenix™ Connect 1.1Phoenix™ NLME 1.0

PhoenixGetting Started Guide41Supported Pharsight software*When used in conjunction with PKS 4.0. Phoenix does not interact directly with PKS Reporter

InstallationInstalling Phoenix51Phoenix can coexist with all current Pharsight software, including WinNonlin 5.2.1 with or without the IVIVC Toolkit.H

PhoenixGetting Started Guide61» If Phoenix is being installed on a computer that uses Windows 2003 Citrix Server, see “Windows 2003 Citrix Server inst

InstallationInstalling Phoenix71If the computer reboots, start the installation process again by double-clicking Setup.exe after the operating system

PhoenixGetting Started Guide813. Read the license agreement. To accept its terms and proceed with the installa-tion, select the I AGREE option button

InstallationInstalling Phoenix914. Enter the appropriate user information and click Next.5. The Destination Folder screen is displayed. Accept the def

PhoenixGetting Started Guide1016. Select an installation type and click Next.» Typical is the default installation type. MPICH2 is not installed when

InstallationInstalling Phoenix111• To change the passphrase from the default, click the Set button.• In the Property Value field, enter a new passphra

PhoenixGetting Started Guide1217. Use the Back button to return to the previous screens to make any changes to the installation. 8. Click Next to cont

InstallationInstalling Phoenix131If they are not already installed, the LegacyWNL components and Microsoft Visual C++ 2005 Redistributable are install

Phoenix™Phoenix™ WinNonlin® 6.1, Connect 1.1, and NLME 1.0 copyright ©2005-2009, Tripos, L.P. All rights reserved. This software and the accompanying

PhoenixGetting Started Guide141Windows Vista installationThe Vista installation process is similar to the XP installation process with the following e

InstallationConfiguring Phoenix for international use151• Select a maintenance operation and click Next.» Modify is the default selection type. Modify

PhoenixGetting Started Guide161CAUTION: If the settings are not changed then Phoenix cannot correctly run projects that are created in the English (Un

InstallationOpening TCP ports for MPICH2171» Users can restrict MPICH2 to use a range of ports, and open those ports in a firewall to avoid the multip

PhoenixGetting Started Guide181The batch file then presents three options that allow users to open ports, close ports, or quit.• Press 1 to add the po

19Chapter 2LicensingInstallation and renewal of Phoenix software licensesThe chapter contains the following topics:» “Phoenix Licensing Service” on pa

PhoenixGetting Started Guide202License key code typesPhoenix requires the installation of a license key code. There are three types of license key cod

LicensingPhoenix Licensing Service212When Phoenix is purchased, customers are sent an email with the five things nec-essary to use Phoenix:– The appli

PhoenixGetting Started Guide222BQL XXXColumn Properties XXXColumn Transformation XXXCrossproduct Worksheets XXXFilter Worksheet XXXJoin Worksheets XXX

LicensingPhoenix Licensing Service232Indirect Response Model XLinear Model XMichaelis-Menten Model XPD Model XPK Model XPK/PD Model XWNL5 ASCII Format

of SAS Institute Inc. in the USA and other countries. Sentinel RMS is a trademark of SafeNet, Inc. Microsoft, MS, the Internet Explorer logo, MS-DOS,

PhoenixGetting Started Guide242WinNonlin 5.2.1 license holdersUsers who have WinNonlin 5.2.1 licenses can use Phoenix with no intervention from Pharsi

LicensingLicense Activation252WinNonlin 5.2.1 floating license serversWinNonlin license servers are not detected during the installation process on Wi

PhoenixGetting Started Guide262On-line activation:On-line activation allows users to activate Phoenix by connecting to Pharsight’s licensing server fr

LicensingLicense Activation272Online license activation1. Select the On-line option button.2. Enter the authorization code in the Authorization Code f

PhoenixGetting Started Guide282» In Windows XP, the default location C:\Program Files\Phar-sight\Phoenix\application\Services\Licensing.» In Windows V

LicensingLicense Activation292The purchased license is displayed in the Licenses list.Offline license activation1. Select the Off-line option button.2

PhoenixGetting Started Guide302» In Windows Vista, the default location C:\Users\username>\App-Data\Local\VirtualStore\Program Files\Phar-sight\Pho

LicensingLicense Management312The license server provided for Phoenix is Sentinel RMS server 8.x. It is avail-able for download when Phoenix is purcha

PhoenixGetting Started Guide322Phoenix license managerThe License Management dialog has five fields:Use the License Management dialog:1. In the Edit m

LicensingLicense Server Management3322. Select Licensing>License Management in the Preferences dialog menu tree.Node licensesThere are no options f

Pharsight Corporation1699 S. Hanley Road, St. Louis, MO 63144 USAhttp://www.pharsight.com • [email protected] in binary form must

PhoenixGetting Started Guide342Use the License Server Management screen:1. To add a license server, enter the IP address of the server in the IP Addre

35Chapter 3Testing the InstallationConfirming proper installation of the main Phoenix functionsThe following instructions test the installation of Pho

PhoenixGetting Started Guide363Confirm license installationThe ability to execute different Phoenix plug-ins depends on the license type installed. Us

Testing the InstallationStart Phoenix and create a new project373Confirm plug-in startupThe Phoenix architecture is based on a series of plug-ins that

PhoenixGetting Started Guide383Create a plot1. Select the workflow object in the Object Browser. In the Insert menu select Plotting>XY Plot.• The

Testing the InstallationStart Phoenix and create a new project3934. Click the Execute button. The Results are displayed on the Results tab.XY Plot re

PhoenixGetting Started Guide403• Click the (+) signs beside Install Test>Data to expand the menu tree. • Select Bguide1 and click Select.The Bguide

Testing the InstallationStart Phoenix and create a new project413The results are presented as three HTML tables. Compare the tables in the Results tab

PhoenixGetting Started Guide423Table 3

Testing the InstallationConfirm model functions433Confirm model functionsThis section tests examples of noncompartmental analysis, pharmacokinetic mod

vContentsChapter 1 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1Pharsight contact informati

PhoenixGetting Started Guide4439. Select items in the NCA model object’s Setup tab list to explore the model’s data mappings and option settings.10.Cl

Testing the InstallationConfirm model functions453Core output text fileSubject=1,Form=Capsule Date:

PhoenixGetting Started Guide463The Settings file lists all the settings used to specify the noncompartmental anal-ysis.Settings text file/************

Testing the InstallationConfirm model functions473Output DataThe NCA object creates seven results worksheets: Dosing Used, Exclusions, Final Parameter

PhoenixGetting Started Guide483Summary Table worksheet

Testing the InstallationConfirm model functions493PlotsA total of 12 plots are generated; one for each of two formulations, for each of the six subjec

PhoenixGetting Started Guide503Pharmacokinetic modeling1. In the File menu select Import or click the Import button. The Open File(s) dialog is displ

Testing the InstallationConfirm model functions513eters, and Summary Table. The Final Parameters, Secondary Parameters, and Summary Table worksheets a

PhoenixGetting Started Guide523Text OutputThe Core output text results include all model settings and iterations, including the output from the worksh

Testing the InstallationConfirm model functions533The Settings file lists all the settings used to specify the noncompartmental anal-ysis.Settings tex

PhoenixGetting Started GuideviConfirm model functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43Noncompartmenta

PhoenixGetting Started Guide543Some plot results are shown below.Observed Y and Predicted Y vs XPredicted Y vs Observed Y

Testing the InstallationConfirm model functions553Residual Y vs XWeighted Residual Y vs Weighted Predicted YBioequivalenceImport the data:1. In the Fi

PhoenixGetting Started Guide5633. In the Files of type menu select ASCII Data (*.csv;*.dat).4. Select the file Seq2Per4.csv and click Open.The Workshe

Testing the InstallationConfirm model functions573Use the Model tab to specify settings for Bioequivalence model options. The Model tab is located und

PhoenixGetting Started Guide583Parameters, Least Squares Means, and Sequential Tests. The Diagnostics, Final Variance Parameters, and Sequential Tests

Testing the InstallationConfirm model functions593The Worksheet Import Options dialog is displayed. The dialog is used to assign options for how the d

PhoenixGetting Started Guide603Use the Model tab to specify settings for Bioequivalence model options. The Model tab is located underneath the Setup t

Testing the InstallationConfirm model functions613The output includes analysis settings and results, and three worksheets. The first two worksheets ar

PhoenixGetting Started Guide623

63Chapter 4The Phoenix User InterfaceNavigating the Phoenix applicationThis chapter presents an overview of the Phoenix user interface (UI). The diffe

1Chapter 1InstallationInstalling the Phoenix PlatformThe Getting Started Guide contains installation and licensing instructions for both Phoenix WinNo

PhoenixGetting Started Guide644Phoenix main interfacePhoenix Menu OptionsThe Phoenix main menu allows users to create and save projects, import data s

The Phoenix User InterfacePhoenix Menu Options654Note: All menu options are not always active. Inactive options are unavailable. Some options are only

PhoenixGetting Started Guide664– Ascii model (*.lib)– BQL Rule Set (*.phxruleset)– Excel Files (*.xls)– Image File (*.bmp;*.gif;*.jpeg;*.jpg;*.png)– L

The Phoenix User InterfacePhoenix Panels and Tabs674» Verify - checks if an executable object can be run.» Execute - executes an object or workflow, d

PhoenixGetting Started Guide684» Documents folder - contains any binary objects that do not belong in the other folders.» Workflow object - an object

The Phoenix User InterfacePhoenix Panels and Tabs694» Contains the operational objects in a workflow.» Contains the Object Toolbox, which allows users

PhoenixGetting Started Guide704» The Setup tab is the default view of any newly inserted operational object.» The Setup tab gives users access options

The Phoenix User InterfacePhoenix Panels and Tabs714» The Results tab displays the results of an executed object.» Results are automatically grouped b

PhoenixGetting Started Guide724» The Verification tab displays operational object status and execution error messages.Information tabNCA Information t

The Phoenix User InterfacePhoenix Panels and Tabs734» The Information tab displays information about a selected object. The name, date created, last d

PhoenixGetting Started Guide21Contact Pharsight sales for purchases, license renewals and product upgrades.For licensing issues, including sales and t

PhoenixGetting Started Guide744

75Chapter 5Phoenix ConceptsAn introduction to the Phoenix platformIntroductionThis chapter provides an overview of the Phoenix architecture, definitio

PhoenixGetting Started Guide765» This type of architecture is called a plug-in architecture because compo-nents or plug-ins, which are discrete functi

Phoenix ConceptsPhoenix Terminology775context associations include sort, concentration, time, formulation, X-axis, Y-axis, etc.» Data folder - contain

PhoenixGetting Started Guide785objects in a project or workflow. The Diagram tab also shows the flow of the operational procedures.» Documents folder

Phoenix ConceptsPhoenix Terminology795license. System functions include drug modeling, statistical calculations, and data manipulation.» Project - a p

PhoenixGetting Started Guide805are created in an operational object and can be published to the Data folder.Phoenix Work ConceptsWork in Phoenix invol

Phoenix ConceptsPhoenix Work Concepts815» Phoenix projects are designed to be easily updated and shared, which allows for better data management. Phoe

PhoenixGetting Started Guide825PK analysis, and any other models that Phoenix supports are added to the work-flow object.Root workflow with a sub-work

Phoenix ConceptsPhoenix Work Concepts835» Workflow objects allow users to put together as many types of operational objects as needed to complete an a

InstallationSystem and hardware requirements31Supported operating systemsThe following operating systems have been tested to ensure they are compatibl

PhoenixGetting Started Guide845What are the types of operational objects?Examples of operational objects include data manipulation objects such as Col

Phoenix ConceptsPhoenix Work Concepts855TemplatesA template in Phoenix works like a template in Microsoft® Word - it allows users to recreate the same

PhoenixGetting Started Guide865How are templates different from workflows and objects?» Templates do not store pointers to non-results data, such as i

Phoenix ConceptsPhoenix Work Concepts875» User-created worksheets and workbooks.» Worksheets that are the results of operational objects.How is data u

PhoenixGetting Started Guide885

89IndexNumerics10019, server error, 28CCreate Template button, 68Customer support, 1licensing, 1DDiagram tab, 69HHistory tab, 73IInformation tab, 72In

PhoenixGetting Started Guide90RResults tab, 71SSetup tab, 69Show Dependents button, 68Show Sources button, 68TTechnical support, 1licensing, 1ToolbarC