Getting Started Guide Phoenix™ WinNonlin® 6.1 Phoenix™ Connect 1.1 Phoenix™ NLME 1.
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 documentation are owned by Tripos, L.P. Pharsight is authorized to distribute and sublicense the material contained herein with the express written permission of Tripos, L.P. The software and the accompanying documentation may be used only as authorized in the license agreement controlling such use.
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, the Office logo, Microsoft Word, Microsoft Excel, Microsoft PowerPoint, Windows, Windows 2000, Windows XP, Windows Vista, the Windows logo, the Windows Start logo, and the XL design (the Microsoft Excel logo) are trademarks or registered trademarks of Microsoft Corporation. Pentium and Pentium III are trademarks or registered trademarks of Intel Corporation.
Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. Neither the name of Jaroslaw Kowalski nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
Contents Chapter 1 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1 Pharsight contact information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 System and hardware requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 Installing Phoenix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Modifying, updating, or removing a Phoenix installation . . . . . . .
Phoenix Getting Started Guide Confirm model functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 Noncompartmental analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 Pharmacokinetic modeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 Bioequivalence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 Chapter 4 The Phoenix User Interface . . . . . . . . . . . . . . . . . .
Chapter 1 Installation Installing the Phoenix Platform The Getting Started Guide contains installation and licensing instructions for both Phoenix WinNonlin and Phoenix Connect. The generic term Phoenix is used in this guide to simplify terminology.
1 Phoenix Getting Started Guide Customer support Post Pharsight Corporation 5625 Dillard Drive, Suite 205 Cary, North Carolina 27518 Contact Pharsight sales for purchases, license renewals and product upgrades. Sales Email sales@pharsight.com Phone +1-888-708-7444 (US only) +1-919-852-4685 (International) Fax +1-650-314-3811 For licensing issues, including sales and technical support, use the following contact information. Licensing sales and support Email licensing@pharsight.
Installation System and hardware requirements 1 Supported operating systems The following operating systems have been tested to ensure they are compatible the Phoenix platform: English language versions Japanese language versions Windows 2000 SP4 Windows 2000 SP4 Windows XP Pro SP3 Windows XP Pro SP3 Windows 2003 Citrix Server Windows 2003 Citrix Server Windows Vista 32 bit* *Phoenix is not officially supported on Windows Vista 64 bit.
1 Phoenix Getting Started Guide Phoenix Plug-in Supported software versions Tested operating systems NONMEM Shell NONMEM 5 Windows 2000 SP4 Windows XP Pro SP3 NONMEM 6 Windows Vista 32 bit SAS Shell SAS 9.1 Windows 2000 SP4 Windows XP Pro SP3 Windows Vista 32 bit SigmaPlot Shell SigmaPlot 9.0.1 Windows 2003 Citrix Server SigmaPlot 10 Windows XP Pro SP3 SigmaPlot 11.1 Windows Vista 32 bit Windows XP Pro SP3 Japanese version S-PLUS 6.2 Windows 2000 SP4 S-PLUS 7.
Installation Installing Phoenix 1 Phoenix can coexist with all current Pharsight software, including WinNonlin 5.2.1 with or without the IVIVC Toolkit. Hardware requirements Minimum Hardware requirements Item Requirement Processor Intel Pentium 4 2.8 Ghz. or a CPU of EQUIVALENT processing power RAM 1 gigabyte RAM Harddrive space 300 megabytes free Installing Phoenix The instructions for installing Phoenix WinNonlin, Phoenix Connect, and Phoenix NLME are the same.
1 Phoenix Getting Started Guide » If Phoenix is being installed on a computer that uses Windows 2003 Citrix Server, see “Windows 2003 Citrix Server installation” on page 14 for postinstallation instructions. » If Phoenix is being installed on a computer that does have any .NET framework or a .NET framework prior to 2.0 Service Pack 1, see “Systems without .NET 2.0 SP1 or higher” on page 6 for an important installation warning.
Installation Installing Phoenix 1 If the computer reboots, start the installation process again by double-clicking Setup.exe after the operating system restarts. Continue the installation: 1. The Phoenix Setup wizard is started. 2. Click Next. The Sublicense Agreement screen is displayed.
1 Phoenix Getting Started Guide 3. Read the license agreement. To accept its terms and proceed with the installation, select the I AGREE option button and click Next. Note: If there are any questions about the agreement, then contact Pharsight’s sales department at sales@pharsight.com. The User Information screen is displayed.
Installation Installing Phoenix 1 4. Enter the appropriate user information and click Next. 5. The Destination Folder screen is displayed. Accept the default installation directory or choose a directory in which to install Phoenix. Click Next. Vista only: If Phoenix is installed on a machine running Windows Vista 64 bit, then Phoenix is installed in the default directory for 32 bit applications. The Select Installation Type screen is displayed.
1 Phoenix Getting Started Guide 6. Select an installation type and click Next. » Typical is the default installation type. MPICH2 is not installed when Typical is selected. – If Typical is selected, the Ready to Install the Application screen is displayed. » Complete installs the MPICH2 software for multiple- CPU and CPU core processing. – If Complete is selected, the MPI passphrase dialog is displayed. » Custom allows users to make additional choices about what is installed.
Installation Installing Phoenix 1 • To change the passphrase from the default, click the Set button. • In the Property Value field, enter a new passphrase and click OK to close the dialog. • Click Next to continue the installation. The Ready to Install the Application screen is displayed.
1 Phoenix Getting Started Guide 7. Use the Back button to return to the previous screens to make any changes to the installation. 8. Click Next to continue the installation process. If a WinNonlin 5.2.1 license is already installed, the Phoenix installation process asks whether or not to use it. 9. Click Yes to use the WinNonlin license, or No to use a new license. CAUTION: Only click Yes if the WinNonlin license is current.
Installation Installing Phoenix 1 If they are not already installed, the LegacyWNL components and Microsoft Visual C++ 2005 Redistributable are installed. The installation finishes and the following screen is displayed: 10.Click the OK button to exit the Phoenix installation wizard The Phoenix has been successfully installed screen is displayed. 11. Click Finish to finish the installation. » Users are prompted to restart their computers. » The Phoenix installation process is finished.
1 Phoenix Getting Started Guide Windows Vista installation The Vista installation process is similar to the XP installation process with the following exceptions: » .NET Framework 2.0 Service Pack 1 must be installed before Phoenix can be used. » By default, Windows Vista comes with the .NET 3.0 framework already installed. .NET 3.0 includes the .NET Framework 2.0 Service Pack 1 components necessary to run Phoenix WinNonlin. » If the .NET Framework 2.
Installation Configuring Phoenix for international use 1 • Select a maintenance operation and click Next. » Modify is the default selection type. Modify allows users to make additional choices about what is installed. – If Modify is selected, the Select Features dialog is displayed. » Repair reinstalls parts of Phoenix that need to be corrected or updated – If Repair is selected, the Ready to Repair the Application screen is displayed. » Remove uninstalls Phoenix.
1 Phoenix Getting Started Guide CAUTION: If the settings are not changed then Phoenix cannot correctly run projects that are created in the English (United States) region. • In the Control Panel, open the Regional and Language Options dialog. • In the Regional and Language Options dialog, select English (United States) as the region. If the region information cannot be changed, then users must set the decimal symbol to a period (.) for numbers and currency, and the list separator symbol to a comma (,).
Installation Opening TCP ports for MPICH2 1 » Users can restrict MPICH2 to use a range of ports, and open those ports in a firewall to avoid the multiple warnings. » Users can also set a system environment variable named MPICH_PORT_RANGE with a value of :. This restricts MPICH2 to only use the given port range. » For example, use MPICH_PORT_RANGE=3000:3100 to restrict to the range to 3000-3100. Pharsight provides a batch file called mpiPortTool.
1 Phoenix Getting Started Guide The batch file then presents three options that allow users to open ports, close ports, or quit. • Press 1 to add the port numbers to Windows Firewall. – A second command prompt is opened and adds the selected port range. – The batch file also creates a system environment variable that includes the port numbers.
Chapter 2 Licensing Installation and renewal of Phoenix software licenses The chapter contains the following topics: » “Phoenix Licensing Service” on page 19 – “License key code types” on page 20 – “Plug-in licenses” on page 21 – “Product and authorization codes” on page 20 – “WinNonlin 5.2.
2 Phoenix Getting Started Guide License key code types Phoenix requires the installation of a license key code. There are three types of license key codes: 1. Node - a license key code that activates the software on the machine on which it is installed. The license agreement restricts installation of the software and license to a single personal computer (PC) per node license. 2.
Licensing Phoenix Licensing Service 2 When Phoenix is purchased, customers are sent an email with the five things necessary to use Phoenix: – The application download link. – The license server download link. – The authorization code. – The product code. – The license code generation Web site link. A CD can be ordered for users who want a physical medium. To purchase a CD, contact Pharsight's sales department at: E-mail: Telephone: sales@pharsight.
2 Phoenix Getting Started Guide Table 2-1.
Licensing Phoenix Licensing Service 2 Table 2-1.
2 Phoenix Getting Started Guide Table 2-1. Phoenix plug-in license matrix Feature/Plug-in Phoenix Connect Phoenix WinNonlin Phoenix NLME CDISC import and export X ODBC Connectivity X Word Export X X X Edit in Excel X X X Plug-in APIs X X X Phoenix Framework X X X WinNonlin 5.2.1 license holders Users who have WinNonlin 5.2.1 licenses can use Phoenix with no intervention from Pharsight as long as the WinNonlin license is current.
Licensing License Activation 2 WinNonlin 5.2.1 floating license servers WinNonlin license servers are not detected during the installation process on Windows Vista. The license server IP address must be entered manually in the License Server Management screen in the Preferences dialog. License Activation Phoenix must be installed before the license key code can be installed. See “Installing Phoenix” on page 5.
2 Phoenix Getting Started Guide On-line activation: On-line activation allows users to activate Phoenix by connecting to Pharsight’s licensing server from within Phoenix.
Licensing License Activation 2 Online license activation 1. Select the On-line option button. 2. Enter the authorization code in the Authorization Code field. The authorization code is contained in an email attachment named AuthorizationCode.txt that is sent by Pharsight's License Administrator. Users can copy and paste the code. 3. Enter the product code in the Product Code field. For example, PHX_WNL for Phoenix WinNonlin. 4. Click the Acquire License button.
2 Phoenix Getting Started Guide » In Windows XP, the default location C:\Program Files\Pharsight\Phoenix\application\Services\Licensing. » In Windows Vista, the default location C:\Users\username>\AppData\Local\VirtualStore\Program Files\Pharsight\Phoenix\application\Services\Licensing. If the license was not added, Phoenix displays different error messages depending on the problem.
Licensing License Activation 2 The purchased license is displayed in the Licenses list. Offline license activation 1. Select the Off-line option button. 2. Go to the following Web site: http://licensing.pharsight.com/requestlicense/ default.aspx. 3. Enter the authorization code you received from Pharsight into the Authorization Code field. 4. Enter the system Locking Code from the License Activation panel in the Preferences menu in the Locking Code field. 5.
2 Phoenix Getting Started Guide » In Windows Vista, the default location C:\Users\username>\AppData\Local\VirtualStore\Program Files\Pharsight\Phoenix\application\Services\Licensing. 8. In the License Code field, enter the License Code from the text file and click the Install License button. • To confirm license installation, select License Management in the preferences dialog. The purchased license is displayed in the Licenses list.
Licensing License Management 2 The license server provided for Phoenix is Sentinel RMS server 8.x. It is available for download when Phoenix is purchased. The download link for the license server is included in the email sent to new Phoenix customers. It is also located on the Phoenix installation CD in the directory Tools\Sentinel RMS License Manager Installer. Sentinel RMS server 8.x is backwards compatible with WinNonlin 5.2.1, and can be used to provide floating licenses for WinNonlin 5.2.
2 Phoenix Getting Started Guide Phoenix license manager The License Management dialog has five fields: Table 2-2. License Management fields Field Function Name Lists the names of available licenses. Type Lists whether the license is local (node) or network (floating or commuter). Commuter Lists floating licenses that are available to be commuted. Status Lists the status (Available, Acquired, etc.) of licenses Expires Lists the license expiration date. Use the License Management dialog: 1.
Licensing License Server Management 2 2. Select Licensing>License Management in the Preferences dialog menu tree. Node licenses There are no options for node licenses in the License Management screen. Floating licenses 1. To use a floating license, click a network license name in the Name column. The license status is changed to Acquired. 2. Click the license name again to return the license. The license status is now Available. Commuter licenses 1.
2 Phoenix Getting Started Guide Use the License Server Management screen: 1. To add a license server, enter the IP address of the server in the IP Address or Host Name field beside the Add button and click the Add button. 2. To remove a floating license server, enter the IP address of the server in the IP Address field and click the Remove button. • Click the Refresh button to update the list of available license servers.
Chapter 3 Testing the Installation Confirming proper installation of the main Phoenix functions The following instructions test the installation of Phoenix by using a number of the sample files provided with the software. This chapter is not intended as a full validation of the product. It is intended to test for proper installation of major components of the application. A complete validation kit is available from Pharsight Corporation. Contact the Pharsight sales department for more information.
3 Phoenix Getting Started Guide Confirm license installation The ability to execute different Phoenix plug-ins depends on the license type installed. Use the Preferences dialog to check the installed Phoenix license(s). 1. In the Edit menu select Preferences to access the Preferences dialog. 2. In the Preferences menu tree, select Licensing>License Management to access the list of available licenses. 3. Confirm that the purchased license or licenses are listed in the Licenses panel. 4.
Testing the Installation Start Phoenix and create a new project 3 Confirm plug-in startup The Phoenix architecture is based on a series of plug-ins that allow different features to be enabled or disabled. Phoenix initializes these plug-ins when the application starts. The default setting is for all plug-ins to initialize when Phoenix starts. The plug-in initialization is independent of the installed license(s). 1. In the Edit menu select Preferences. The Preferences dialog is displayed.
3 Phoenix Getting Started Guide Create a plot 1. Select the workflow object menu select Plotting>XY Plot. in the Object Browser. In the Insert • The XY Plot object can also be added by right-clicking the workflow object and selecting New>Plotting>XY Plot. Any object can be added by selecting New in the workflow menu. The XY Plot object is added to the workflow in the Object Browser. » Objects automatically open in the right viewing panel when they are inserted in a workflow.
Testing the Installation Start Phoenix and create a new project 4. Click the Execute 3 button. The Results are displayed on the Results tab. XY Plot results • Now use the Bguide1 data set to test the Table object and its summary statistics function. Create a table 1. Select the workflow object in the Object Browser. In the Insert menu select Reporting>Table. • The Table object can also be added by selecting the workflow in the Object Browser.
3 Phoenix Getting Started Guide • Click the (+) signs beside Install Test>Data to expand the menu tree. • Select Bguide1 and click Select. The Bguide1 data set is mapped to the Table object. Use the Options tab to specify which table type the Table object uses. The Options tab is located underneath the Setup tab. Table Options tab 3. In the Table Type menu, select Table 1 - Column Summary by Row Stratification. 4. Select the Page Break on Row Stratification check box. 5.
Testing the Installation Start Phoenix and create a new project 3 The results are presented as three HTML tables. Compare the tables in the Results tab to the tables pictured below.
3 Phoenix Getting Started Guide Table 3 42
Testing the Installation Confirm model functions 3 Confirm model functions This section tests examples of noncompartmental analysis, pharmacokinetic modeling, bioequivalence, and population modeling. Noncompartmental analysis 1. In the File menu select Import or click the Import File(s) dialog is displayed. button. The Open 2. Navigate to the Phoenix examples subdirectory, which by default is located at C:\Program Files\Pharsight\Phoenix\application\Examples. 3. Select the Legacy WinNonlin subdirectory.
3 Phoenix Getting Started Guide 9. Select items in the NCA model object’s Setup tab list to explore the model’s data mappings and option settings. 10.Click the Execute button. The Results are displayed on the Results tab. Text Output The Core output contains the model settings and the same data as the worksheets, but presented in plain ASCII text. If there were errors in the model they would be listed here.
Testing the Installation Confirm model functions 3 Core output text file Subject=1,Form=Capsule Date: 4/29/2009 Time: 13:39:21 WINNONLIN NONCOMPARTMENTAL ANALYSIS PROGRAM 1.0 Core Version 04Jun2007 Settings -------Model: Plasma Data, Extravascular Administration Number of nonmissing observations: 12 Dose time: 0.00 Dose amount: 100.
3 Phoenix Getting Started Guide The Settings file lists all the settings used to specify the noncompartmental analysis. Settings text file /********************************* Begin Mappings *********************************/ Main : install Test.Data.profiles.Sheet1 Sort : Subject, Form Carry : Time : Time Concentration : Conc Dosing : install Test.Data.Profiles_sources.Dosing Sort : Subject, Form Dose : Dose Time of Dose : Time Tau : Tau Slopes : (Internal) Partial Areas : install Test.Data.
Testing the Installation Confirm model functions 3 Output Data The NCA object creates seven results worksheets: Dosing Used, Exclusions, Final Parameters, Final Parameters Pivoted, Plot Titles, Summary Table, and Partial Area Labels. Selections from the Final Parameters and Summary Table worksheets are shown below.
3 Phoenix Getting Started Guide Summary Table worksheet 48
Testing the Installation Confirm model functions 3 Plots A total of 12 plots are generated; one for each of two formulations, for each of the six subjects. The first two charts for subject one are shown below.
3 Phoenix Getting Started Guide Pharmacokinetic modeling 1. In the File menu select Import or click the Import File(s) dialog is displayed. button. The Open 2. Navigate to the Phoenix examples subdirectory, which by default is located at C:\Program Files\Pharsight\Phoenix\application\Examples. 3. Select the Legacy WinNonlin subdirectory. 4. In the Files of type menu select WinNonlin Files (*.cmd;*.pco;*.pmo;*.pto;*.pwo). 5. Select Exp1.pmo and click Open. The Data Import Wizard is displayed.
Testing the Installation Confirm model functions 3 eters, and Summary Table. The Final Parameters, Secondary Parameters, and Summary Table worksheets are shown below.
3 Phoenix Getting Started Guide Text Output The Core output text results include all model settings and iterations, including the output from the worksheets. Any model errors would be listed here. Core output text file WinNonlin 6.0.0.1645, WnlPKCore Library: 1.0.5.
Testing the Installation Confirm model functions 3 The Settings file lists all the settings used to specify the noncompartmental analysis. Settings text file /********************************* Begin Mappings *********************************/ Main : install Test.Data.exp1.Sheet1 Sort : Time : Time Concentration : Conc Carry : Dosing : install Test.Data.Exp1_sources.Dosing Sort : Time : Time Dose : Dose Initial Estimates : (Internal) Units : (Internal) Stripping Dose : install Test.Data.Exp1_sources.
3 Phoenix Getting Started Guide Some plot results are shown below.
Testing the Installation Confirm model functions 3 Residual Y vs X Weighted Residual Y vs Weighted Predicted Y Bioequivalence Import the data: 1. In the File menu select Import or click the Import File(s) dialog is displayed. button. The Open 2. Navigate to the Phoenix examples subdirectory, which by default is located at C:\Program Files\Pharsight\Phoenix\application\Examples.
3 Phoenix Getting Started Guide 3. In the Files of type menu select ASCII Data (*.csv;*.dat). 4. Select the file Seq2Per4.csv and click Open. The Worksheet Import Options dialog is displayed. The dialog is used to assign options for how the data are imported and presented. 5. Click Finish. The data set is added to the project’s Data folder. Set up the average bioequivalence model: 1. Select the workflow in the Object Browser. In the Insert menu select NCA and Toolbox>Bioequivalence.
Testing the Installation Confirm model functions 3 Use the Model tab to specify settings for Bioequivalence model options. The Model tab is located underneath the Setup tab. 4. Ensure that Crossover is selected as the Type of study, Average is selected as the Type of Bioequivalence, and R is selected as the Reference Formulation. 5. Select the Fixed Effects tab, which is located underneath the Setup tab. • Ln(x) is automatically selected in the Dependent Variables Transformation menu.
3 Phoenix Getting Started Guide Parameters, Least Squares Means, and Sequential Tests. The Diagnostics, Final Variance Parameters, and Sequential Tests worksheets are shown below. Diagnostics Final Variance Parameters Sequential Tests Import the data: 1. In the File menu select Import or click the Import File(s) dialog is displayed. button. The Open 2. Navigate to the Phoenix examples subdirectory, which by default is located at C:\Program Files\Pharsight\Phoenix\application\Examples. 3.
Testing the Installation Confirm model functions 3 The Worksheet Import Options dialog is displayed. The dialog is used to assign options for how the data are imported and presented. 5. Click Finish. The data set is added to the project’s Data folder. Set up the population/individual bioequivalence model: 1. Select the workflow object in the Object Browser. In the Insert menu select NCA and Toolbox>Bioequivalence. The Bioequivalence object is added to the workflow in the Object Browser.
3 Phoenix Getting Started Guide Use the Model tab to specify settings for Bioequivalence model options. The Model tab is located underneath the Setup tab. 4. In the Model tab, select the Population/Individual option button. Note: Crossover is the only study type allowed for the Population/Individual Bioequivalence model. • R is automatically selected in the Reference Value menu. Do not change this setting. 5. Click the Execute 60 button. The Results are displayed on the Results tab.
Testing the Installation Confirm model functions 3 The output includes analysis settings and results, and three worksheets. The first two worksheets are shown below. Population/Individual worksheet Ratios Test=T This concludes the installation tests.
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Chapter 4 The Phoenix User Interface Navigating the Phoenix application This chapter presents an overview of the Phoenix user interface (UI). The different menu options, tabs, and panels that make up the Phoenix UI are described in the sections below. This chapter also discusses the arrangement of Phoenix functions and the location of data sources.
Phoenix Getting Started Guide 4 Phoenix main interface Main Menu Verification tab Results tab Setup tab Object Browser panel Diagram tab Object Toolbox Information tab History tab Phoenix Menu Options The Phoenix main menu allows users to create and save projects, import data sets, export operational objects and worksheets, and connect to databases.
The Phoenix User Interface Phoenix Menu Options Note: 4 All menu options are not always active. Inactive options are unavailable. Some options are only available when a user selects a certain part of the interface, such as a cell in a worksheet. For example, the Insert menu is only available when a project, workflow, or operational object is selected. The Send To menu is only available when a worksheet is selected.
4 Phoenix Getting Started Guide – Ascii model (*.lib) – BQL Rule Set (*.phxruleset) – Excel Files (*.xls) – Image File (*.bmp;*.gif;*.jpeg;*.jpg;*.png) – Legacy Settings (*.bql;*.tdf;*.xml) – Legacy Workspace (*.wsp) – LML File (*.lml) – Phoenix Projects (*.phxproj) – Phoenix Template (*.wnlt) – RTF File (*.rtf) – SAS Transport Files (*.xpt) – Text (*;*.;*.bat;*.cmd;*.mdl;*.sas;*.ssc;*.txt;*.vbs) – WinNonlin Files (*.cmd;*.map;*.pco;*.pmo;*.pto;*.pwo) – All Files (*.
The Phoenix User Interface Phoenix Panels and Tabs 4 » Verify - checks if an executable object can be run. » Execute - executes an object or workflow, depending on which is selected in the Object Browser. Phoenix Panels and Tabs Phoenix uses a series of panels and tabs that allow users to create and edit projects, and view results and project information. Object Browser panel The Object Browser displays all the operational objects inserted into a project or a workflow.
4 Phoenix Getting Started Guide » Documents folder - contains any binary objects that do not belong in the other folders. » Workflow object - an object that allows users to group operational object and nest workflows within a project. » Operational object - any object that receives input, performs an operation, and produces results. An example is the NCA (noncompartmental analysis) object.
The Phoenix User Interface Phoenix Panels and Tabs 4 » Contains the operational objects in a workflow. » Contains the Object Toolbox, which allows users to insert objects into a project by clicking the buttons in Object Toolbox. » The objects in the Object Toolbox are grouped in the same way as they are in the Insert menu.
4 Phoenix Getting Started Guide » The Setup tab is the default view of any newly inserted operational object. » The Setup tab gives users access options used to set up an operational object. » The Setup tab contains a list of the panels and options tabs that are used to set up an operational object. » The Setup tab allows users to map data sets and other worksheets to an operational object.
The Phoenix User Interface Phoenix Panels and Tabs 4 » The Results tab displays the results of an executed object. » Results are automatically grouped by type. Result types are text, worksheets, and graphs. Results tab toolbar buttons Results tab toolbar » Do not group - does not group results. » Group by type - groups results by type. » Group by executable - groups results by executable object. » Copy to Data Folder - copies results to the Data folder. » Export - exports the results.
4 Phoenix Getting Started Guide » The Verification tab displays operational object status and execution error messages. Information tab NCA Information tab » When a project is selected the tab displays information items in the project, including the name, type, creation date, and project status. » When a workflow is selected the Information tab lists all the objects that are contained in the workflow. It also displays information about the object type and creation time.
The Phoenix User Interface Phoenix Panels and Tabs 4 » The Information tab displays information about a selected object. The name, date created, last date modified, the version of Phoenix used to create the object, and the status are displayed for each object. » Imported data sets also have the Source Information displayed, which shows the location from where they were imported. History Tab NCA History tab » Displays the history of selected projects, worksheets, workflows, and objects.
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Chapter 5 Phoenix Concepts An introduction to the Phoenix platform Introduction This chapter provides an overview of the Phoenix architecture, definitions of Phoenix-specific terms, and concepts used to describe work in Phoenix. Phoenix presents several new concepts and functions that users must be aware of in order to successfully use Phoenix. This chapter covers concepts and terminology new to Phoenix, including projects, workflows, objects, and templates.
5 Phoenix Getting Started Guide » This type of architecture is called a plug-in architecture because components or plug-ins, which are discrete functional units in Phoenix, can be added and removed without affecting the core application. Each plug-in provides a specific function. Descriptive statistics, noncompartmental analysis, and linear mixed effects modeling are all plug-ins created for use with the Phoenix platform.
Phoenix Concepts Phoenix Terminology 5 context associations include sort, concentration, time, formulation, X-axis, Y-axis, etc. » Data folder - contains all imported data sets, user-created data sets, and copies of results from operational objects. Data sets in the Data folder can be contained in workbooks or worksheets. » Data Link - operational object that links one or more operational objects to the same data source. A Data Link is only accessible in the Diagram tab.
5 Phoenix Getting Started Guide objects in a project or workflow. The Diagram tab also shows the flow of the operational procedures. » Documents folder - contains Microsoft Word documents and templates, images, and other binary objects that do not belong in one of the other folders. » Global Contexts and Context Associations - Global Contexts are column mappings that users can configure for use throughout Phoenix. Context associations allow a user to define mappings at an operational object level.
Phoenix Concepts Phoenix Terminology 5 license. System functions include drug modeling, statistical calculations, and data manipulation. » Project - a project can contain multiple workflows which can include multiple operational objects and data sets. A project is similar to a workspace in WinNonlin and a scenario in PKS. » Right viewing panel - the main panel in Phoenix that shows the setup options for any item that is selected in the Object Browser.
5 Phoenix Getting Started Guide are created in an operational object and can be published to the Data folder. Phoenix Work Concepts Work in Phoenix involves five important organizational concepts: projects, workflows, operational objects, templates, and data. Each of these concepts are explained in the following sections. Projects Projects contain all imported binary objects and all operational objects that are used to perform an analysis.
Phoenix Concepts Phoenix Work Concepts 5 » Phoenix projects are designed to be easily updated and shared, which allows for better data management. Phoenix projects can be saved locally or to a database and transferred between multiple users. » A Phoenix project file contains all the data sets, such as study data, that were imported into a project. Project files can be exchanged between users without also having to exchange external data sources.
5 Phoenix Getting Started Guide PK analysis, and any other models that Phoenix supports are added to the workflow object. Root workflow with a sub-workflow What in Phoenix can be considered a workflow? » A project and all its data, models, and output, can be a workflow. – Project workflows contain the data, models, and other objects needed to complete an analysis, from data setup through reporting of results. » A workflow is an operational object that is used to group other operational objects.
Phoenix Concepts Phoenix Work Concepts 5 » Workflow objects allow users to put together as many types of operational objects as needed to complete an analysis. » Workflow objects allow users to execute only a certain group of operational objects in a project. » They allow users to access the Diagram tab, which can be used to add operational objects, map data, and execute objects.
5 Phoenix Getting Started Guide What are the types of operational objects? Examples of operational objects include data manipulation objects such as Column Transformation and Pivot Worksheet, models like Semicompartmental Modeling and PK Models, and plots like the XY Plot. What types of data do operational objects use? » Operational objects use two types of data: external and internal. » An external data source for an operational object points to an imported data set in the Data folder.
Phoenix Concepts Phoenix Work Concepts 5 Templates A template in Phoenix works like a template in Microsoft® Word - it allows users to recreate the same steps over and over, and gives users a form or fields that can be used to automatically recreate a workflow to use with a new data set. Workflow added from a template file Workflow added from template file Templates are files that contain the settings used with a workflow or operational object. Templates are saved as WinNonlin Template (*.wnlt) files.
5 Phoenix Getting Started Guide How are templates different from workflows and objects? » Templates do not store pointers to non-results data, such as imported worksheets. » Workflows and objects contain pointers to data sets, but templates do not. How are templates different from project files? » Project files save all parts of the project - all the data sets, code, rule sets, other information objects, and all workflows and operational objects.
Phoenix Concepts Phoenix Work Concepts 5 » User-created worksheets and workbooks. » Worksheets that are the results of operational objects. How is data used in Phoenix? » The Data folder contains all the imported or created data sets that are used in a project. » All data sets used in a workflow are contained internally within Phoenix. » Changes made to imported data sets do not change the original data set. » Data must be mapped to an operational object before it can be used.
5 88 Phoenix Getting Started Guide
Index Numerics M 10019, server error, 28 Main menu Edit, 65 File, 65 Help, 65 Insert, 65 PKS, 65 Send To, 65 Window, 65 C Create Template button, 68 Customer support, 1 licensing, 1 D Diagram tab, 69 H History tab, 73 I Information tab, 72 Installing WinNonlin, 5 L Licensing customer support, 1 O Object Browser, 67 BQL Rules folder, 67 Code folder, 67 Data folder, 67 Documents folder, 68 Operational object, 68 Project, 67 Tables folder, 67 Workflow object, 68 P Pharsight contact information, 1 Ph
Phoenix Getting Started Guide R Results tab, 71 S Setup tab, 69 Show Dependents button, 68 Show Sources button, 68 T Technical support, 1 licensing, 1 Toolbar Copy, 66 Cut, 66 Delete, 66 Execute, 67 Export, 66 Freeze panes, 66 Import, 65 Insert Column, 66 Insert Row, 66 Paste, 66 Verify, 67 U User interface, 63 V Verification tab, 72 W WinNonlin installing, 5 90
