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1. Remote Access to Database Engine Share BioNumerics databases with other users in the local network Security Group that will have full access to the Database Engine CN D omain Uu sers CN U sers DC applied maths D C lox a j M Restart SQL Server Service to apply changes Figure 3 9 The Database Engine Properties dialog 3 1 9 Database Engine properties The location of the Microsoft SQL Server 2008 R2 Express data files can be entered in the Database Engine Properties dialog see Figure 3 9 Please make sure to select a local path with sufficient at least 700MB free disk space Network drives and shares are not supported for storing the SQL data files In addition this dialog allows you to specify if remote access to the database engine should be enabled If the BioNumerics databases are shared with other users in the local network then the Microsoft SQL Server BioNumerics inbound Windows firewall rule will be enabled and TCP IP and Named Pipes connections to the database engine will be allowed All computers that will be used to access shared BioNumerics databases should be part of the same Active Directory domain This allows domain users that need to access the shared database engine to be added to an Active Directory security group and this group can be selected in the Database Engine Properties dialog Subsequently the selected security group will be added to the local BioNumerics Database Admin
2. lt The NetKey service should only be deployed to a single license server computer hence silent deployment of this feature usually is not desired gt 1 feature display name Install NetKey server program p Figure 3 36 Setup INI XML file format The root XML node of the Setup INI file is the setup node The attributes in the setup node are only used for information purposes for example to display which BioNumerics Setup version created the Setup INI file The setup node also contains property sub elements one for each property that is required to configure the Setup Setup properties typically contain Setup related configuration values which are not feature specific or which are shared by multiple features The start XML element contains a time stamp indicating when the file was created Each feature that was selected for installation has a corresponding feature element with the display name attribute The attribute value must match the feature name displayed in the Select Features dialog box The feature element may contain property sub elements one for each property that is required to configure the parent feature 40 3 Installation procedure Chapter 4 NetKey configuration 4 1 Introduction If a network license has been purchased the NetKey server program and the Sentinel drivers must be installed on a computer where the hardware security will be connected to 1 e the server computer see
3. Browse Transfer file output Browse Note the created transfer file should be transferred to the destination computer where it can be applied to complete the license transfer Step 3 Figure 3 31 Transfer activation The third and last step is to apply the protection key transfer file on the target computer 1 Copy the v2c transfer file from the source to the target computer 2 Start the NetKey configuration tool on the target computer 3 Select Licenses in the left pane select the license string 4 Click the lt Activate gt button 5 Select Transfer activation in the Activate Hasp license dialog see Figure 3 27 and click lt Next gt 6 In the top Computer section select NetKey is running on the destination computer 7 In the Step section select Step 3 Apply transfer file Destination computer 8 Click lt Browse gt and browse to path where the copied v2c transfer file is located and select the file 9 Click lt Finish gt to install the protection key on the local computer 3 5 Setup log All messages generated while the Setup is running are written to the Setup log XML file The name of each XML element indicates the message type e lt message gt This is an information message and can safely be ignored e lt warning gt This is a warning message usually indicating that some user action may be required to resolve the issue e lt error gt This indicates that
4. End 1 01 2011 12 24 1 01 2011 11 24 1 01 2011 11 22 1 01 2011 11 32 1 01 2011 11 03 2 01 2011 10 32 2 01 2011 12 11 3 01 2011 13 03 C Duration s Lic 10182 XYZQ 82XP 134N 2N9V WWHP UP99 6574 ABCD 82FP 234N 2N8V VVHP URSS 6473 XYZQ 82XP 134N 2N9V WWHP UP99 7064 ABCD 82FP 234N 2N8V VVHP UR99 5337 ABCD 82FP 234N 2N8V VVHP UR99 3476 ABCD 82FP 234N 2N3V VVHP UR99 9416 XYZQ 82XP 134N 2N9V WWHP UP99 12512 ABCD 82FP 234N 2N8V VVHP UR99 D E F IP User 192 168 001 026 Anna 192 168 001 031 Jane 192 168 001 016 Luke 192 168 001 020 Luke 192 168 001 032 Tim 192 168 001 010 PeterS 192 168 001 033 Sophie 192 168 001 029 Anna Figure 4 18 The parsed usage file in MS Excel G ID fbdbce11a39b 82473553507a 8e944d3e9c49 9ee0fc6cdb16 13ff03553f56 991bb33ad03f 39becb89b6a6 698505cefble H Lab LAB2 LAB2 LAB3 LAB3 LABI LABI LAB2 LAB2 10 3 Select the whole range that contains data and insert a PivotTable with PivotChart in Excel 10 4 Click lt OK gt 10 5 Choose Lic and Lab as Category fields Axis field and Duration s as the Values field Sum The result is depicted in Figure 4 19 Figure 4 19 Resulting PivotTable and PivotChart in MS Excel A B Row Labels Sum of Duration s ABCD 82FP 234N 2N8V VVHP UR99 1584066 LAB1 535214 LAB2 611973 LAB3 436879 EXYZQ 82XP 134N 2N9V WWHP UP99 673165 LABI 230766 LAB2 258230 LAB3 184169 Grand Total 2257231 E D Sum of D
5. NOTES SUPPORT BY APPLIED MATHS While the best efforts have been made in preparing this manuscript no liability is assumed by the authors with respect to the use of the information provided Applied Maths will provide support to research laboratories in developing new and highly specialized ap plications as well as to diagnostic laboratories where speed efficiency and continuity are of primary impor tance Our software thanks its current status for a part to the response of many customers worldwide Please contact us if you have any problems or questions concerning the use of BioNumerics or suggestions for improvement refinement or extension of the software to your specific applications Applied Maths NV Applied Maths Inc Keistraat 120 8834 N Capital of Texas Hwy Suite 280 9830 Sint Martens Latem Austin Texas 78759 Belgium U S A PHONE 32 9 2222 100 PHONE 1 512 482 9700 FAX 32 9 2222 102 FAX 1 512 482 9708 E MAIL info applied maths com E MAIL info US Oapplied maths com URL http www applied maths com LIMITATIONS ON USE The BioNumerics software its plugin tools and their accompanying guides are subject to the terms and conditions outlined in the License Agreement The support entitlement to upgrades and the right to use the software automatically terminate if the user fails to comply with any of the statements of the License Agreement No part of this guide may be reproduced by any means without prior wri
6. Starting from BioNumerics version 7 0 the NetKey server supports two types of SafeNet protection keys e SentinelSuperPro provider hardware based Sentinel SuperPro USB protection key The Sentinel USB dongle is used to protect standalone and network licenses of BioNumerics running on computers either equipped with a physical USB port or with a network attached USB hub The USB dongle has been tested with network attached USB hubs from Digi AnywhereUSB and Silex USB Device Servers e SentinelHasp provider software based Sentinel HASP protection keys The software based Sentinel HASP SL key is used to protect network licenses of BioNumerics more specific to provide a software protection key for the NetKey license server program running on a computer that is not equipped 3 4 Installing Protection Keys 29 with a free physical USB port This is particularly useful if the NetKey license service is running on a virtualized operating system and a network attached USB hub is not available 3 4 2 Install Protection Key Driver The BioNumerics Setup includes the latest version of the SafeNet drivers available at the time of the product release When installing older BioNumerics versions it is recommended to download and install the latest version of the SafeNet driver before attaching the USB dongle The drivers for the Sentinel USB dongle can be downloaded from the following web site http www applied maths com sentineldriver The Sent
7. 5 3 Setup processes 61 5 3 6 Save Setup Log The first time the XML_SaveLogFile function is called the Setup will generate a unique file name for the Setup log XML file Next the Setup will copy the following style sheet files to the Setup log folder processlogs xsl applied maths css amheader jpg and amlogo gif Finally the XML_SaveLogFile function will save the contents of the Setup log XML object from memory to the Setup log XML file 5 3 7 OnMoveData The OnMoveData function is the main Setup process that handles the file transfer First the function will display the progress bar dialog and create the uninstall information in the registry Next the function will call the CheckLicense function to check and save the license string to the HKEY LOCAL MACHINE hive of the registry if a valid license string was entered Subsequently the OnMoveData process will call the FeatureTransferData function to install or remove fea ture files The FeatureTransferData function will launch the lt feature gt Installing or lt feature gt _UnInstalling function before installing or removing a feature After a feature has been installed or removed the Setup will call the lt feature gt Installed or lt feature gt _UnInstalled function Finally the OnMoveData function will call the LaunchNetKey function to launch the NetKey server con figuration tool if the corresponding feature was selected for installation 5 3 8 Feature functions Each f
8. and that are invoked by the InstallShield engine and installation script see Table 5 1 This does not include the dialogs from the NetKey Configuration tool 5 3 Setup processes 5 3 1 Read command line options When the Setup executable is launched the Setup engine will first attempt to detect if a previous instance of the software is already installed If the same or another version of the software 1s already installed the Setup will initially display the Existing Installed Instances Detected dialog box Next the engine will launch the InstallShield installation script 60 5 Installation process Number Dialog name Dialog image Related section DI Existing Instances CN NS D2 DIg SdWelcome CM NM D3 Dlg_Start SdWelcomeMaint Figure 3 21 3 34 D4 DIg SdLicense2 D5 DIg SdSetLicense Figure 3 4 da D6 DIg_SdPathOptions Figure 3 6 LEF D7 DIg_SdFeatureTree Figure 3 7 3 1 8 D8 Dlg SdNetKey Figure 3 10 3 1 10 D9 Dlg_SdStartCopy2 D10 SdFinish SdFinishReboot Table 5 1 The Setup dialog list One of the first initialization steps in the installation script is to read the optional command line options used to launch the Setup executable Currently the Setup supports the ini and logdir command line parameters See 3 6 for more details 5 3 2 Read global variables After parsing the optional command line parameters the Setup will call the ReadGlobalVariables function This function will e Read database home directory from the regis
9. replaced by the newer version BioNumerics InstallShield Wizard Welcome to the InstallShield Wizard for BioNumerics The InstallShield Wizard vell update the installed version 6 0 0 of BioNumerics to version 7 0 1 To continue Next Figure 3 12 The Welcome dialog 3 2 1 2 Updating a 6 5 or later instance of BioNumerics If an instance of BioNumerics 6 5 or later is already installed then the Existing Installed Instances Detected dialog box will appear when launching the Setup executable see Figure 3 13 Choose the Maintain or update the instance of this application selected below option to perform an update of the BioNumerics application 3 2 2 Software End User License Agreement The next dialog will display the Software End User License Agreement EULA see Figure 3 14 Please read the EULA carefully and click the top I accept the terms of the license agreement radio button and the lt Next gt button to continue the installation Click lt Cancel gt if you do not agree with the license agreement this will abort the installation The Software End User License Agreement document can be printed to the 3 2 Updating a BioNumerics instance 21 fi Instances Detected NAATH S dpriate application instance to maintain or update Setup has detected one or more instances of this application already installed on your system You can maintain or update an existing instance or install a completely new instance C Install a
10. 3 After installation of these features on the server computer the NetKey service needs to be installed and started using the NetKey Configuration tool NetKey Config exe see 4 2 Once started the license s can be configured in the NetKey Configuration tool see 4 3 and the NetKey service can start distributing sessions to the requesting BioNumerics applications running on the client computers i e the computers with the application software installed see 4 4 4 2 Installing and starting the NetKey service on the server If a network license string has been entered in the Customer Information dialog box and the NetKey server program feature was selected for installation in the Select Features dialog box the Setup will ask if you want to run the NetKey Configuration tool see Figure 4 1 This tool allows you to install and subsequently start the NetKey service Question The NetKey Server program has been installed DY Please attach the hardware security key dongle to the NetKey Server computer Would you like to start the NetKey Server configuration tool now ae e Figure 4 1 Run the NetKey Configuration tool Click lt Yes gt to start the NetKey Configuration tool This will run the tool with Windows elevated privi leges Run as administrator and the Login window will be displayed see Figure 4 2 The NetKey Configuration tool can also be called by double clicking on
11. INI XML file lt path to Setup files gt Setup exe s ini lt path to Setup_x_ini XML file gt logdir lt path to log folder gt Example all command line parameters should be on a single line C Users Public Documents Applied Maths BioNumerics Setup exe s ini C Users Public Documents Applied Maths Setup_1_ini XML 3 6 Silent installation 39 logdir C Users Public Documents Applied Maths SetupLogs During silent installations no error or warning messages are displayed when the Setup is running The installation Administrator should check the Setup log XML file to verify that no errors have occurred and that no further action is required to complete the BioNumerics installation on the target computer The Microsoft NET Framework 2 0 SP2 or 3 5 SPI and Windows Installer 4 5 prerequisites described in 2 should be installed prior to launching the Setup in silent installation mode For example the silent installation will fail if the Setup is not able to download and install the Microsoft NET Framework 3 5 SPI 3 6 3 Setup INI XML file format The information recorded in the Setup_x_ini XML file has the format as displayed in Figure 3 36 lt xml version 1 0 encoding utf 8 standalone yes gt setup name BnSoftwareName version 7 0 1 date 2012 12 12 time 00 00 00 gt lt start date 12 12 2012 time 00 00 00 gt feature display name Install application software gt lt property netkey_
12. Read command line options Read global variables Write global variables Save Setup INI xml file Read requested features Save Setup Log OnMoveData Application_Installing Application_Installed Application_UnInstalling Application UnInstalled Sentinel Installing Sentinel Installed Sentinel UnInstalling Sentinel UnInstalled NetKey Installing NetKey Installed NetKey_UnInstalling NetKey_UnInstalled Database Installing Database Installed Database UnInstalling Database UnInstalled Sample Installing Sample Installed Sample UnInstalling Sample UnInstalled FeatureStart FeatureEnd DeleteOldFiles IsSentinelInstalled HasDongles CheckLicense LaunchNetKey IsOldNetKeyInstalled SetFilePermissions MSI InstallProduct WMI ServiceStart WMI ServiceStop Save Setup INI xml file CleanUp Table 5 2 The Setup process list 5 Installation process Related section number 5 3 1 Lia 5 3 3 5 3 4 252 5 3 6 dod 5 3 8 5 3 8 5 3 8 5 3 8 5 3 8 5 3 8 5 3 8 5 3 8 5 3 8 5 3 8 5 3 8 5 3 8 5 3 8 5 3 8 5 3 8 5 3 8 5 3 8 5 3 8 5 3 4 5 3 8 Chapter 6 Command line options 6 1 Running BioNumerics from the command line The BioNumerics software bn exe can be started from the command line This can be done by opening a command prompt navigating to the BioNumerics installation directory or opening the command prompt immediately in this directory and entering bn exe See Figure 6 1 for an example Em C Windows sy
13. The location of the data files can be specified in the next step 24 3 Installation procedure Install sample database and Install sample and tutorial data e The sample database and sample and tutorial data that are contained in the Setup package are used in the manual to illustrate the features of the software Selecting these features will install the sample database and sample and tutorial data in the database home directory that is specified in the Choose Destination Location dialog box see Figure 3 16 Install Sentinel drivers The Install Sentinel drivers feature will install version 7 5 7 of the Sentinel System Driver In addition this feature will also install the Sentinel Run time Environment previously known as HASP version 6 51 if the NetKey server program feature has been selected for installation The Sentinel Run time Environment will not be installed if a standalone license string was entered in the Customer Information dialog box e In case of a standalone license the Sentinel drivers need to be installed on each computer that you want to use to run the software e In case of an internet license you only need an internet connection to run the software The Install Sentinel drivers option does not need to be checked e In case of a network license the Sentinel drivers only need to be installed on the NetKey server computer in the network Install NetKey server program e The NetKey server program feature will
14. active internet connection on the computer running the NetKey configuration tool Click lt Next gt to display the Manual activation dialog Select the Create activation request file option in the Manual Activation dialog Click lt Browse gt to enter the path and file name for the activation request file Click lt Finish gt to save the customer to vendor c2v activation request file and include the file as an email attachment and send an email to activation O applied maths com If your email system does not allow sending c2v files you can change the file extension to txt 32 3 Installation procedure Activate Hasp license Manual activation Enter the file s required for manual activation Create activation request file The created activation request file c2v should be emailed to activation applied maths com You will then receive a confirmation file v2c that can be used to activate the license Activate with confirmation file Complete the manual activation of the license by applying the confirmation file Activation request output file Figure 3 26 The Manual activation dialog After receiving the vendor to customer v2c confirmation file from Applied Maths the activation process can be completed Select the Activate with confirmation file option in the Manual Activation dialog Click lt Browse gt to select the v2c confirmation file and click lt Finish gt to install the SentinelH
15. and any other possible documentation related thereto Documentation and v upgrades modified versions updates additions and copies of the Software if any licensed to Customer by Applied Maths under this Agreement License Conditioned upon compliance with the terms and conditions of this Agreement Applied Maths NV or its subsidiary limmmrino the Esfera inertas af Annlind Marthe MVS f Annmlind Mathe erante ta Cuctamer S neancwclicisim and C accept the terms of the license agreement o Bit o y EULA language Figure 3 3 The License Agreement dialog box 3 1 5 Customer information The Customer information dialog box allows you to enter the user and organization names and the BioNu merics license string see Figure 3 4 You must enter a valid license string to be able to continue with the installation In addition the user and organization names cannot be empty The license string is provided on the sleeve of the CD ROM or you may have obtained it electronically Please enter your name the name of the organization for which you work and the BioNumerics license string User Name My Name rganization N ame My Organization Name License Strin Please enter the License String Figure 3 4 The Customer Information dialog box 14 3 Installation procedure 3 1 6 Setup Type In the Setup Type dialog you can choose between a Default and a Custom setup configuration The Defau
16. data for all users CommonAppDataFolder The path of this folder depends on the operating system version e Windows Vista or later C ProgramData Applied Maths NetKey e Windows XP C Documents and Settings M11 Users Mpplication Data Applied Maths NetKey 4 2 Installing and starting the NetKey service on the server 43 Select Connection in the left panel to display the server connection settings Server connection panel and service status Service panel see Figure 4 3 The Refresh rate determines how often the information displayed in the NetKey Configuration tool is updated The default value 1s 30 seconds The Service status text box displays the current status of the NetKey windows service The status should be Not installed if this is the first time the BioNumerics Setup is running on the server computer uf NetKey Configuration administrator mode Local Sessions Server error Licenses Logging i Connection Server name 10 Server connection Server port 80 Server config port 30 Refresh rate sec 30 Change refresh rate Service status Not installed Refresh now Figure 4 3 The NetKey Configuration tool window Click the Install button in the lower Service panel to install the NetKey Windows service Next click the lt Start gt button to start the NetKey service The Change server password dialog will be displayed during a first time instal
17. epair iF Reinstall all program features installed by the previous setup C Remove E Remove all installed features Uninstall shared Database Engine feature This will cause the BioNumerics instance of Microsoft SQL Server 2008 R2 Express to be uninstalled Figure 3 21 The Welcome dialog box 2 The recommended method for uninstalling an instance of BioNumerics is to choose the Remove option in the Welcome dialog box see Figure 3 21 De selecting the BioNumerics application feature in the Modify maintenance mode will uninstall the application but will not delete any uninstall information from the registry and file system A message box will appear asking you to confirm that you want to uninstall the BioNumerics application Other features that remained selected like the sample database and NetKey server features will not be removed from the target system After pressing lt Next gt the NetKey connection settings dialog box will appear if a network license string was entered in the Customer Information dialog box and if the BioNumerics application feature was selected for installation in the Select Features dialog box Click lt Next gt to start applying the changes Files will be copied to the target system for new features that have been selected Any feature that was de selected will cause the corresponding files and shortcuts to be uninstalled The Maintenance Complete dialog box will appear after all changes have been
18. new instance of this application Maintain or update the instance of this application selected below Display Name Install Location x86 Applied Maths BioNumerics 6 6 4 Figure 3 13 The Existing Installed Instances Detected dialog box default printer by clicking the lt Print gt button The lt Save gt button allows you to browse to a folder where you want to save the Applied Maths EULA PDF Acrobat document VA M AT H S license agreement carefully Software End User License Agreement IMPORTANT PLEASE READ THIS END USER LICENSE AGREEMENT CAREFULLY DOWNLOADING INSTALLING OR USING APPLIED MATHS SOFTWARE CONSTITUTES ACCEPTANCE OF THIS AGREEMENT APPLIED MATHS IS WILLING TO LICENSE THE SOFTWARE TO YOU ONLY UPON THE CONDITION THAT YOU ACCEPT ALL OF THE TERMS CONTAINED IN THIS LICENSE AGREEMENT BY DOWNLOADING OR INSTALLING THE SOFTWARE YOU ARE BINDING YOURSELF AND THE BUSINESS ENTITY THAT YOU REPRESENT COLLECTIVELY CUSTOMER TO THIS AGREEMENT IF YOU DO NOT AGREE TO ALL OF THE TERMS OF THIS AGREEMENT THEN APPLIED MATHS IS UNWILLING TO LICENSE THE SOFTWARE TO YOU AND YOU SHOULD NOT DOWNLOAD INSTALL OR USE THE SOFTWARE The Software As used in this Agreement the term Software means collectively i the software product identified above ii all the contents of the disk s CD ROM s electronic mail and its file attachments or other media with which this Agreement is provided including the object code f
19. the NetKey Config exe application in the installation directory of BioNumerics Alternatively press the Settings button Lt in the startup window of BioNumerics if the application software has been installed and select NetKey configuration from the drop down list 42 4 NetKey configuration The configuration tool can be run as NetKey User or NetKey Administrator in combination with or without Windows elevated privileges An overview of all tools that are accessible in the NetKey Configuration program for the four different login options is given in 4 9 a To run a program with Windows elevated privileges in Windows Vista Windows 7 or Server 2008 right click on the application and select Run as administrator a NetKey Configuration Application mode User o Administrator Password Connect to Server Port Admin port Reset service Cancel Figure 4 2 The Login window Choose the Administrator mode in the Application mode panel This mode will allow you to install and start the NetKey service The first time the service will be started a password will be prompted for This Password is required the next time someone wants to access the configuration program in Administrator mode When the service has not been started yet the Password field can be left empty Enter the local computer name or localhost as the Server name in the Connect to panel to indicate that the Net
20. to BioNumerics databases During the installation of the BioNumerics application the Setup will create a Windows group named BioN umerics Database Administrators Figure 7 1 This local Windows group has Full control NTFS permis sions on the local Database home directory and if the BioNumerics Database Engine feature is installed members of this group have unrestricted access to the SQL Server databases db lusrmgr Local Users and Groups Local Groups S File Action View Help aa eE Mo Local Users and Groups Local Name Users Be Remote Desktop Users Groups He Replicator He Users a BioNumerics Database Administrators Si Figure 7 1 The BioNumerics Database Administrators Windows group By default the following users and groups are members of the local BioNumerics Database Administrators Windows group e User running the BioNumerics Setup e NT AUTHORITY Authenticated Users e Optional Active Directory Security Group selected in the Database Engine Properties dialog see 3 1 9 for example the Domain Users group Figure 7 2 The Local Users and Groups management console in Figure 7 1 can be started by running lusrmgr msc on a Windows Command Prompt Double click on the BioNumerics Database Administrators Windows group to view the current group members Figure 7 2 Click the lt Add gt or lt Remove gt button to change the group members If you do not want all authentic
21. w X 9 ROB DEUS ee bad AA S Running sessions on the clients LL Wh sessions i es o9 fa sea dea Pee ee A PI iui RR Oe X UR EOS how dos ewe oe Sg Resetting the NetKey settings eu p Rd EG OE u arar Repairing the NetKey Service Overview of configuration rights enn Usage ROIO ie eh ew Owe he 79 4 1 4 2 4 3 4 4 4 5 4 6 4 7 4 8 4 9 4 10 4 10 1 4 10 2 Usage information parse tool 2 2 llle E 22939 x hm RR ROUEN E S 4 809 9 SERA EGS Installation process 24 de VAS 5 4 UPON uxo uda x PH NEGEGSEXSS4 45 3 3 5 5 SONIDOS ouo xu o4 EROR osas aaa is ses MGR be Ree ARR e Ee T 5 3 1 Read command line options 22 2 e M Read global variables clle ee Write global variables lt osccocoo c 6 noob om ox a aa 5 3 4 Save sotup INI AML THIS uuu ok odo AR RR 2153 Read requested features cs nu 9 Rodeo E carnada A RR A 5 3 6 SAS OIDO ud on 6v ia a Rb kg xo iena xem oA 5 3 7 O a 5 4 95 m3 3 aa 5 3 8 Fegture functions gt lt LR hi we asee I oe ee ee E ee RHE ee ee Command line options Running BioNumerics from the command line Running the startup program from the command line 6 1 6 2 Granting access to BioNumerics databases 11 41 41 41 45 49 49 SI SI 52 53 53 53 55 59 59 59 59 59 60 60 60 60 61 61 61 64 67 67 68 69
22. 1 246 4 69 license3 applied maths com 71 42 72 154 license4 applied maths com 71 42 72 154 The BioNumerics application requires access to the above internet domain names and public IP addresses to be able to validate internet and evaluation licenses Note that the IP addresses of the license servers may change in the future hence firewall exception rules based on the internet domain name should be preferred In addition several BioNumerics plugins require access to specific internet domains to be able to download relevant data e applied maths com e pubmist org for the MLST online plugin e pasteur fr for the MLST online plugin e mlst ucc ie for the MLST online plugin e ridom de for the Spa typing plugin If applicable for your configuration you may need to grant the BioNumerics application internet access to the above domain names If internet access 1s only allowed through a proxy server the corresponding settings must be properly config ured for the Microsoft Internet Explorer browser see Figure 2 1 The BioNumerics application will use the same settings when connecting to the internet In other words if an automatic configuration script pac file or a static proxy server address has been configured for Internet Explorer BioNumerics will inherit these LAN settings to connect to the internet Local Area Network LAN Setti Automatic configuration Automatic configuration may override manual settings T
23. 15 Feature Install NetKey server program Feature installation start 12 12 2012 16 24 15 Feature installation End 12 12 2012 16 24 19 Figure 3 34 The BioNumerics setup log Allowing active content such as script and ActiveX controls can be useful However active content might also harm your computer Are you sure you want to let this file run active content Figure 3 35 Security warning refreshed The Setup log XML file is located in the SetupLogs sub folder of the BioNumerics program folder For example 38 3 Installation procedure e 32 bit platforms C Program Files Applied Maths BioNumerics SetupLogs Setup_1_log XML e 64 bit platforms C Program Files x86 Mpplied Maths BioNumerics SetupLogs Setup_1_log XML 3 6 Silent installation 3 6 1 Purpose Running the BioNumerics Setup in silent installation mode allows running the BioNumerics Setup pro gram without an end user interface No dialogs will be displayed in silent mode and all messages including errors will be logged to the Setup log file All information required to run the Setup needs to be recorded to a properly formatted Setup_x_ini XML file This file must subsequently be invoked through Setup exe command line parameters The silent installation mode can be helpful for mass deployment of BioNumerics for creating identical configurations and to automate repetitive behavior 3 6 2 Installation procedure Each installation o
24. Contents 1 Introduction 1 1 is LIRICA SOROR ee ee ee ee ee eee uS d 1 2 Toper i s mh eRe SESE ERE RE RBE ERE RES EE HES DE SS 1 3 RPE Gee Sew Ee Ree eae i System requirements Hardware Poe ce o secesi we autsa ake OR Sew A eH zd p dad 2 4 PA 2 6 dal 2 8 PAS ed 2 BP Minimum hardware requirements 22 ee et ee ee Recommended hardware configuration LL Operating Systemi ux e mro 9 4o A A RARA RUS Microsoft NET Framework 2 0 SP2 oaaae Microsoft NET Framework 3 5 SPL oaaae Microsoft Visual C 2010 Redistributable c Microsol AMLOUSPI uan oXom RR E Li Wandows Installer 4 3 uuu uuo ow aaa AAA A Permissi ns ox uoo ov ER e ATL 2 X03 4 X ok Ox3 3 Security SOWAT und uoo odo X AAA 29 1 232 MH Lu cu 4x Goes wee tae FOR es 9 9 99 x 4x 3 tae B S us Firewall and proxy SU uos xw 4 ox oe R3 9 ROO A94 O amp x CEES Installation procedure Sal da Installing a new BioNumerics instance o oo a 3 1 1 Pee escasa daa A S Be Existing instances detected kc cw he awe eee o 9 ww o9 OX oos 3 1 3 Vi TIOS a wR AAA AAA X3 3 1 4 Software End User License Agreement cles ms Customer information ke 9o wo Rose eee a 3 1 6 ee Lead rara AAA ddr Choose destination location uuu uuo o e 9 RR ERDAS SRE ERE xe 3 1 8 DUNAS escotes Gee ee 49 eS Be v XS lt a Database Engine properties oua dee bee wha ce a xk Yo X a 3 1 10 NetKey connection settings LL Lili Confirm inst
25. In My Documents C AUsers Mill APPLIED MAT entsiBioNumericsiD ata e will only b cessible to the current user CAUsersiPublic DocumentsBioNumericsD ata I Figure 3 6 The Choose Destination Location dialog box 3 1 8 Select features The BioNumerics features that you want to install on the local computer can be selected in the Select Features dialog box see Figure 3 7 Clicking on a feature in the left pane will display a short description in the right pane Tick the appropriate check boxes for the features you want to install BioNumerics InstallShield Wizard 4 Select the features you want to install and deselect the features you do not want to install Y Install application software Ii Install Database Engine Select this feature to install the Y Install sample database BioNumerics application Y Install sample and tutorial data software Install Sentinel drivers Y Install NetKey server program 724 63 MB of space required on the C drive 14061 05 MB of space available on the C drive Figure 3 7 The Select Features dialog box Install application software 16 3 Installation procedure e In case of a standalone license the Application software needs to be installed on each computer that you want to use to run the software Please note that only on the computer where the dongle is attached to you will be able to work with the software e In case of an internet license the Application software needs
26. IsGetObj dll file from memory and will delete the file from the temporary Setup folder 5 4 Setup Process list Table 5 2 shows the main processes and functions that are used in the installation script and that are dis played in the simplified Setup flow diagram see Figure 5 1 65 5 4 Setup Process list First Install Maintenance Existing Instances DI Read command line options P1 Read global variables P2 Silent Mode NO lt gt Update D2 SdWelcomeMaint D2 Dig_SdLicense2 D4 Dig_SdLicense2 D4 Dig_SdSetLicense Dig_SdSetLicense Dig_SdSetLicense D5 DS D5 Dlg_SdPathOptions D6 Dig_SdFeatureTree Dig_SdFeatureTree Dig_SdFeatureTree D7 D7 D7 mum Re um D8 D8 D8 em D9 Write global variables P3 Save Setup INI xml file P4 D6 S Read requested features z CE y TA TA A E E lr il Silent Mode NO Save Setup INI xml file P40 CleanUp P41 SdFinish Reboot D10 CleanUp P41 featureevents rul Sentinel Installing P12 Sentinel Installed P13 Sentinel Uninstalling P14 Sentinel Uninstalled P15 Sample Installed P25 Figure 5 1 The Setup flow diagram 66 Process number P1 PI P3 P4 P5 P6 P7 P8 P9 P10 P11 P12 P13 P14 P15 P16 P17 P18 P19 P20 P21 P22 P23 P24 P25 P26 P27 P28 P29 P30 P31 P32 P33 P34 P35 P36 P37 P38 P39 P40 P41 Process name
27. Key service will be installed on the computer where the tool is running The server Port number is an available TCP port number that will be used by the NetKey server and clients to exchange session information The Admin port is an available TCP port number that will be used to by the NetKey server and configuration tool to configure the service settings The default suggested TCP port number for both ports is 80 Any other port numbers can be specified An HTTP based protocol is used for the communication between the NetKey server the NetKey Configuration tool and the BioNumerics application Both TCP ports must be en abled on the Windows firewall or any other security tool that may block access to these ports both on the NetKey server computer and on each computer were BioNumerics is installed The NetKey server TCP ports may not be used by any other application or service For example no websites should be hosted on the IIS server using a NetKey TCP port number Clicking the lt Reset service gt button will stop the NetKey service on the server computer and will delete all current NetKey settings including the Administrator password see 4 7 for more information This operation is not applicable if the service is not already installed Clicking the lt Continue gt button will save the connection settings to the NetKey ini text file and to the NetKey _Config txt XML file These files are located in the folder containing application
28. Loggings Date 2011 11 03 12 53 57 2011 11 03 12 54 00 2011 11 03 12 54 00 2011 11 03 12 54 00 2011 11 03 12 54 00 2011 11 03 12 54 00 2011 11 03 12 54 00 2011 11 03 12 54 00 2011 11 03 12 54 00 2011 11 03 12 54 00 2011 11 03 12 54 00 2011 11 03 12 54 00 2011 11 03 12 54 00 2011 11 03 12 54 30 2011 11 03 12 54 30 2011 11 03 12 54 30 Message PORT 80 Http message processed in 0 0071388 secs ip 1 S PORT 80 Receiving http message PORT 80 Http message received body 196 bytes Processing GET SERVER 1 0 response RES SERVER 1 PORT 80 Http message processed in 0 0126343 secs ip 1 PORT 80 Receiving http message PORT 80 Http message received body 198 bytes Processing GET LICENSES 1 0 response RES LICENSES PORT 80 Http message processed in 0 010964 secs ip 12 PORT 80 Receiving http message PORT 80 Http message received body 197 bytes Processing GET LOGGING 1 0 response RES LOGGING PORT 80 Http message processed in 0 00776713 secs ip PORT 80 Receiving http message PORT 80 Http message received body 196 bytes Processing GET SERVER 1 0 response RES SERVER 1 2011 11 03 12 54 30 PORT 80 Http message processed in 0 011902 secs ip 12 d Mu Refresh Figure 4 15 Logging information Click the Reset service gt button in the Login window see Figure 4 2 Click lt Yes gt in the confirmation dialog see F
29. This operation will Stop the NetKey service on this computer Reset service ports to factory defaults Reset login data in this dialog Are you sure you want to continue Figure 4 16 Warning message 3 Select Connection in the left panel to display the Service settings Click the lt Remove gt button in the lower Service panel to uninstall the NetKey Windows service 4 Click Install to re install the NetKey service 5 Next click the lt Start gt button to start the NetKey service 6 Close the NetKey Configuration tool 4 9 Overview of configuration rights The NetKey Configuration program NetKey Config exe is available on the server computer and on all client computers that have the application software installed This configuration tool can be run as NetKey user or NetKey administrator in combination with or without Windows elevated rights An overview of all rights for the four different login options are shown in the table below 4 10 Usage statistics 4 10 1 Usage information parse tool The NetKey server program comes with a standalone command line tool called ParseUsage exe This tool will transform the NetKey log file see 4 6 to a tab delimited text file This text file can easily be imported in MS Excel which can be used to create usage statistics On the NetKey server computer open a command prompt or a Windows PowerShell window and navigate to the NetKey installation folder s
30. a severe error has occurred User action is required to resolve the issue Severe errors may cause the Setup to abort 36 3 Installation procedure Activate Hasp license Transfer activation Select the appropriate transfer step Computer O NetKey is running on the destination computer NetKey is running on the source computer Step Step 1 Create request file Destination computer Step 2 Create transfer file Source computer e Cies oem 1 Figure 3 32 Transfer activation Activate Hasp license Apply transfer file Apply a created transfer file on the destination computer to complete the license transfer Transfer file Figure 3 33 Transfer activation The Setup log XML file is best viewed with a recent version of the Microsoft Internet Explorer browser see Figure 3 34 This will allow you to expand and collapse specific message tables in the XML document Error and warning messages will be expanded by default and will be displayed at the top of the browser window Hence you do not need to scroll down to verify if an error has occurred A yellow information bar may appear in Internet Explorer with the following message To help protect your security Internet Explorer stopped this site from installing an ActiveX control on your computer Click here for options Right click the information bar and select Allow Blocked Content A Security Warning message box will appear Click lt Yes gt to c
31. allation uuu uou PRA da S142 NetK ey configuration lt gt 9 i ALARE i 3 113 IL XML le Lib o Pox o6 9 Orc bodes Eta Updating a BioNumerics instance llle dial Wee UID n hha ARRESE dd d Software End User License Agreement 000008 dud Customer information lt lt sedoso AAA 3 2 4 Choose destination location e Ja Mele ee ouis vo bou Koo ROGER A AUR A ORO NOR x PE X Ras m RC 3 2 6 NetKey connection settings e dud CARIOUS max REGE RO REOR E X ORO ESO ERA Eom o HERES 6 7 ENS 3 4 3 5 3 6 Maintenance installation 2 2 eel ens 3 3 1 Select instance to maintain sosa asas X o4 ch ROS SR ER SA E Maintenance options 2 2l e e eese 343 Modify maintenance mode leeren 3 3 4 Repair maintenance mode onoo d Remove maintenance mode oono 0 0 eee ee Installing Protection Keys iii oho Eom ER SAR 3 4 1 Prolec on key IUDAS ooo eek Rue xeEGEIE S4 43 3 Eu ee EES 3 4 2 Install Protection Key Driver 3 4 3 Activate Sentinel HASP SL key 2 2 2 oes e E Je x uu wx eee RRR ER ERE 2 x TTT TT eee Ree ee Silent installation uos oko ono o e E I ORE a a Ge 3 6 1 PU PROSE PE PI LO Installation procedure ia hd ah 3 6 3 Setup INI XML file format a e ua de eee a ee NetKey configuration ug ec a ee PRE ASAE EER eee ee ee GS eG E Installing and starting the NetKey service on the server 0 ONC licenses cuoco sow
32. allations of the selected BioNumerics instance see 3 3 5 If only one instance of the BioNumerics program is installed then the Uninstall shared Database Engine feature check box will be visible Selecting this option will cause the BioNumerics instance of Microsoft SQL Server 2008 R2 Express to be uninstalled 3 3 3 Modify maintenance mode The Customer Information dialog box will appear after selecting the Modify option and clicking lt Next gt in the Welcome dialog box see Figure 3 21 This dialog allows you to update the user and organization names and the BioNumerics license string You must enter a valid license string to be able to continue with the installation Next the Select Features dialog box will be displayed allowing you to choose which features to install or to uninstall u De selecting already installed features in the Select Features dialog box will cause these fea tures to be uninstalled during the update A message box will appear if you de select the main BioNumerics application feature Select lt No gt if you do not want to uninstall the BioNumerics application 3 3 Maintenance Installation 27 BioNumerics InstallShield Wizard Welcome Modify repair or remove the program Welcome to the BioNumerics Setup rat program This program lets you modify the current installation Click one of the options be q Select new program features to add or select currently installed features to remove CR
33. and admin ports The Setup will display the following message if the TCP port is already in use TCP port 80 is already in use Please choose an available TCP port BioNumerics InstallShield Wizard A NetKey connection settings Via Bm F Configure connection to NetKey license server i m a Dum The licenses for this software product are distributed by a central NetKey license server Please enter the required connection parameters NetKey Server name lt NETKEY SERVER NAME gt Server port number 1080 Server admin port number 1080 Note you can modify these parameters anytime later using the NetKey Config utility Figure 3 10 The NetKey connection settings dialog box After the BioNumerics application has been installed the Setup will save the server name and TCP port number to the NetKey ini text file on the client computer The NetKey ini file is located in the folder containing application data for all users CommonAppDataFolder The path of this folder depends on the operating system version e Windows Vista or later C ProgramData Applied Maths NetKey 3 1 Installing a new BioNumerics instance 19 e Windows XP C Documents and Settings All Users Mpplication Data Mpplied Maths NetKey 3 1 11 Confirm installation After clicking lt Next gt the Ready to install BioNumerics dialog box will appear Click Install to start the installation The lt Back gt button allows you to revi
34. asp soft lock key on the NetKey server Select Server in the left panel of the NetKey configuration tool If the manual activation was successful the software based protection key with SentinelHasp as the provider should appear within a minute or so in the list of available license keys 3 4 3 4 Transfer Sentinel HASP SL key To be able to transfer a software based protection key the NetKey server and the configuration tool must be installed on both the source and destination computers and the NetKey configuration tool must be started locally on both computers A license key with the SentinelHasp provider must be listed in the NetKey configuration tool on the source NetKey server to be able to transfer the key to another NetKey server computer Transferring the Sentinel HASP SL key is a three step process The first step 1s creating the protection key request file on the target computer 1 Start the NetKey configuration tool on the target computer 2 Select Licenses in the left pane select the license string 3 Click the lt Activate gt button 4 Select Transfer activation in the Activate Hasp license dialog see Figure 3 27 and click lt Next gt 5 In the top Computer section select NetKey is running on the destination computer 6 In the Step section select Step 1 Create request file Destination computer 7 Click the lt Browse gt button to enter the path and file name of the protection key request file 3 4 Ins
35. ated users to have full access to the BioNumerics Databases you can simply remove the NT AUTHORITY Authenticated Users group from the BioNumerics Database Administrators group and replace it with specific users or groups that require database access For example you could add all BioNumerics users to an Active Directory Security Group and add this group to the local BioNumerics Database Administrators Windows group to grant full access to the databases 70 7 Granting access to BioNumerics databases BioNumerics Database Administrators Properties a General BioNumerics Database Administrators Description Members of this group will have unrestricted access to the databases hosted on the BioNumerics Database Members H APPLIED MATHS Domain Users 88 NT AUTHORITY Authenticated Users S 1 5 11 88 NT AUTHORITY LOCAL SERVICE S 1 5 19 Changes to a user s group membership are not effective until the next time the user logs on OK Cancel Apply Help Figure 7 2 Properties of the BioNumerics Database Administrators Windows group If the Database Engine feature has been installed then the SQL Server BioNumerics service account will also be a member of the BioNumerics Database Administrators Windows group e NT AUTHORITY Local Service on Windows Vista Windows Server 2008 or later e NT AUTHORITY Local System on Windows XP or Windows Server 2003 The BioNumerics Database Administrators Window
36. ault value ProgramData Applied Maths netkey NetKey _LOG txt Example inp c Logfiles Netkey Netkey _LOG_2011 txt begin A begin date in the format Y Y Y Y MM DD optional Example begin 2011 01 01 end An end date in the format YY Y Y MM DD optional Example end 2011 03 31 Lic A filter on a specific license string optional Example Lic ABCD 82FP 234N 2N8V VVHP UR99 IP A filter on a specific client IP address 1Pv4 optional Example IP 192 168 001 010 User A filter on a specific user name optional Example User John Table 4 2 Options for ParseUsage exe e ID Session ID as generated by the NetKey server program 4 10 2 Example We will illustrate the use of ParseUsage exe with following hypothetical example In a research institute there are two types of BioNumerics network licenses one with all modules for 3 simultaneous users and another one with only the Fingerprint data module and the Tree and network inference module for 5 simultaneous users The institute has bought this for multiple users belonging to three different labs Since each lab has its own annual budget the institute would like to charge the labs for their usage of the different BioNumerics licenses Invoicing is done after the end of each quarter The financial department has calculated that the total cost of the 3 user network license is 500 euro per quarter and the cost of the 5 user network license 1s 350 euro
37. base Engine feature Microsoft SQL Server 2008 R2 Express Setup requires Microsoft Windows Installer 4 5 or a later version Windows Installer version 4 5 1s included with Windows Vista SP2 and Windows Server 2008 SP2 Win dows Installer version 5 0 1s included with Windows 7 Windows 8 Windows Server 2008 R2 and Windows Server 2012 Hence the BioNumerics Setup will not install Windows Installer on these operating systems 2 8 Permissions The user running the BioNumerics Setup package must have full Administrator privileges on the computer s where the Setup program will run In addition the user must have MODIFY NTFS folder permissions and FULL CONTROL share permissions if applicable on the database home directory for example when this folder will be located on a file server and will be accessed via a file share 2 9 Security software 2 9 1 Anti Virus To optimize the performance of the BioNumerics Setup program it 1s recommended to temporarily disable the real time protection or on access scanning features while running the installer More specifically anti virus software may considerably slow down the installation of the Database Engine feature Anti virus software may also affect the performance of the BioNumerics application If you notice a signif icant difference in responsiveness when the anti virus tool is enabled compared to when the tool 1s disabled it may be recommended to exclude the anti virus tool from scanning the BioNume
38. below Display Name Install Location BioNumerics 6 6 C Program Files x86 Applied Maths BioNumerics 6 6 4 Figure 3 2 The Existing Installed Instances Detected dialog This dialog allows you to choose between installing a new BioNumerics instance and changing an existing instance Choose the Install a new instance of this application option to install a new instance of the BioNumerics application 2 The above dialog will not appear if BioNumerics 6 1 or older versions are already installed since these applications were installed with a Setup program that was not yet multi instance aware In this case the welcome dialog will be displayed with an update message 3 1 3 Welcome dialog If no instance of BioNumerics is detected on the local computer the Welcome dialog box will display the version number of BioNumerics that is included with the Setup package when launching the Setup executable Please verify that you are installing the correct version and click lt Next gt to continue 3 1 4 Software End User License Agreement The next dialog will display the Software End User License Agreement EULA see Figure 3 3 Please read the EULA carefully and click the top I accept the terms of the license agreement radio button and the lt Next gt button to continue the installation Click lt Cancel gt if you do not agree with the license agreement this will abort the installation The Software End User License Agreement docu
39. by acrash network problems A session that exceeds the timeout time default 5 min Figure 4 8 is closed If a session is disconnected by the server e g due to idle time or maximum usage limit a warning box flashes warning the client that the session is removed from the list of connected sessions The session halts automatically after a few seconds To change the default suggested Usage time Idle time and Timeout values for a license select the license from the list in the left panel and press the lt Change gt button to call the License properties dialog box see Figure 4 8 4 4 Running sessions on the clients After the Setup has finished installing the BioNumerics application configured with a network license on the client computers see 3 the BioNumerics application should start on the client computers if the following conditions are met 1 The NetKey service 1s running on the NetKey server computer see 4 2 2 The correct NetKey server name and TCP port number have been specified on the client computer 3 If present the security software e g firewall has been configured to allow access to the NetKey TCP port 4 The TCP port is not in use by another application 5 There 1s a matching access rule that grants the client access to the license see 4 3 If a client is allowed access to the license but the session limit 1s reached see 4 3 the session is added to the waiting queue A message pops up o
40. cal Sessions E Server localhost Installed licenses TEE Licenses String State AMCM 4JFP BVC7 ANGV UVHP QV4N Active Figure 4 7 List of licenses License WWW 0000 0000 0000 0000 0000 P Note The new license will be configured to allow access for any dient To change this behaviour you need to configure the access rules after the license is added Figure 4 8 The License properties dialog box Change button The Remove button allows you to remove a string from the list of installed licenses Selecting the license string in the left panel below Licenses will display the matching license settings in the right panel see Figure 4 9 Click Change to edit the license properties Select AccessRules below the license string in the left panel to view and edit the access rules for the cor responding license Figure 4 10 The access rules are displayed in the right panel When a new license has been added to the list the Client filter will be set to No filter and any client can access the license by default If more than one rule is specified for a license the rule that appears on top of the list 1s the first rule that is checked when a client requests a new session If access is denied based on the first rule the second rule is checked and so on until a rule has granted access or until all rules have been processed Click Remove to delete a selected rule from the list Press the lt Add gt butto
41. cense is recorded by the server program The usage time is the total connection time for each connected Session or in case of a session present in the waiting queue the time the session has been put on hold In case there is a waiting list a connected session for which the usage time exceeds the maximum 4 4 Running sessions on the clients 49 usage time default 120 min see Figure 4 8 will be closed in favor of the first session in the waiting list The usage time of the session that was put on hold but now is launched by the software 1s reset A session that exceeds the maximum usage time limit will not be closed as long as there is no waiting list e Idle time The dle time of each connected session is also recorded by the server program The idle time starts running as soon as the session 1s running on a client computer The status of the session is checked each time a renew session request 1s sent to the server when the session 1s in use the idle time is reset if no user activity is recorded the idle time keeps running A session for which the idle time exceeds the maximum idle time default 60 min see Figure 4 8 will be closed in favor of the first session in the waiting list A session that exceeds the idle time limit will not be closed by the server as long as there is no waiting list e Timeout The Timeout of a connected session starts running when the server stops receiving renew session requests for the session e g caused
42. ct to the NetKey server Select Licenses under the Server option in the left panel see Figure 4 7 Click the lt Add gt button to add a new BioNumerics license string to the list of installed licenses In the License properties dialog box enter the 6 x 4 characters License String in the input fields see Figure 4 8 Alternatively use the lt P gt button to paste the contents of the clipboard in the License fields The license string 1s provided on the sleeve of the CD ROM or the string may have been delivered electronically An error message will pop up when attempting to add an invalid license string e g a standalone license string a second license string for the same key to the license list Press lt Add gt to insert the new license string into the list of installed licenses The added license string will be displayed in the String column see Figure 4 7 The number of concurrent sessions that are granted to the license is shown in the Allowed sessions column If the corresponding protection key is present in the Available license keys list see Figure 4 5 the state of the license is set to Active If the key is not detected on the server computer the state is set to Valid The last Sessions in use column displays the total number of sessions that are currently in use for this license The settings for a specific license can be modified by selecting the corresponding string and clicking the 46 4 NetKey configuration H Lo
43. d the path matches with the current BioNumerics program folder The SetFilePermissions function will use the xcacls vbs Microsoft Visual Basic script to grant NTFS folder permissions to a specific user The Setup will launch the xcacls vbs script using the cscript exe application in the 32 bit version of the Windows system folder The MSI InstallProduct function will use the msiexec exe Windows Installer tool to install an MSI package e g Sentinel System Driver Installer 7 5 1 msi The WMI ServiceStop function will first call the WMI ServiceExists function to verify that the service exists The function will attempt to stop the service if the service exists and is running The WMI ServiceStop function uses the built in InstallShield functions to control the service on a local computer The WMI ServiceStart function will first call the WMI_ServiceExists function to verify that the service exists The function will attempt to start the service if the service exists and is not running The WMI ServiceStart function uses the built in InstallShield functions to control the service on a local computer The CleanUp function will create the end time stamp element in the setup node of the Setup log XML file and close the progress bar dialog Next the CleanUp function will call the XML ShowLogFile function to 64 5 Installation process save and optionally display the Setup log file in Internet Explorer Finally the CleanUp function will unload the
44. e license string from the HKEY_LOCAL_MACHINE hive of the registry if the current string is empty If the license string 1s still empty the Setup will use the license string from the previous installation in maintenance mode If the license string has the correct length the Setup will launch the setlic exe tool to get the license type of the entered string The setlic exe license tool will return one of the following constants LIC_STANDALONE LIC_NETWORK LIC_INTERNET or LIC_INVALID If the CheckLicense function was called by the OnMoveData function and the license type is valid not LIC INVALID then the Setup will save the license string to the HKEY_LOCAL_MACHINE hive of the registry The LaunchNetKey function is called by the OnMoveData function to start the NetKey configuration tool after the NetKey server program feature has been installed repaired or updated The function will use the built in LaunchApp InstallShield function to start the NetKey Config exe executable The Setup will continue after the tool has been launched The IsOldNetKeylnstalled function will use Windows Management Instrumentation WMI queries to verify if other instances of the NetKey service are already installed Optionally this function can also be used to delete the service if the service name does not match or if the installation path does not match the current BioNumerics program folder The service will not be deleted if the service name is NetKey an
45. eature can be linked to four event handlers e The OnInstalling event handler responds to the Installing event that is generated just before the cor responding feature is installed This handler is linked to a lt feature gt Installing function e The OnUnInstalling event handler responds to the UnInstalling event generated just before the corre sponding feature is removed from the target system This handler is linked to a lt feature gt _UnInstalling function e The OnInstalled event handler responds to the Installed event that is generated just after the corre sponding feature has been installed This handler is linked to a lt feature gt _Installed function e The OnUnInstalled event handler responds to the UnInstalled event generated just after the corre sponding feature has been removed from the target system This handler is linked to a lt feature gt _UnInstalled function Each lt feature gt _Installing and lt feature gt _UnInstalling function will call the FeatureStart function to cre ate a feature node and a start time stamp element in the Setup log XML file In addition each lt feature gt Installed and lt feature gt _UnInstalled function will call the FeatureEnd function to create an end time stamp element in the Setup log XML file The feature event handler functions that call other function in addition to the FeatureStart and FeatureEnd function are described in the next sections The Application Installing event handl
46. ed dialog box will appear when launching the Setup executable see Figure 3 20 This dialog allows you to choose between installing a new BioNumerics instance or changing an existing instance Choose the Maintain or update the instance of this application selected below option to perform a maintenance of the BioNumerics application 26 3 Installation procedure BioNumerics InstallShield Wizard stalle d Instances Detected ppropriate application instance to maintain or update e hos O CL mora npenoss al Lon can maintain or update an existing instance or install a completely new Installa new instance of this application Maintain or update the instance of this application selected below Display Name Install Location BioNumerics 6 6 C Program Files x86 4pplied Maths BioNumencs 6 6 4 Figure 3 20 The Existing Installed Instances Detected dialog box 3 3 2 Maintenance options After selecting the BioNumerics instance that needs to be modified the Welcome dialog box will display the maintenance options see Figure 3 21 e Modify Select Modify to install a feature that was not installed during the previous installation see 3 3 3 e Repair Choose Repair to repeat the previous installation of the BioNumerics application The same features selected during the previous setup will be re installed see 3 3 4 e Remove Choose Remove to remove all BioNumerics files and shortcuts that were created during previous inst
47. ed on a computer running Windows Server 2008 or 2003 If a Windows Server computer is not available then the NetKey program can be installed on a Windows XP or later client operating system 2 3 Microsoft NET Framework 2 0 SP2 7 2 3 Microsoft NET Framework 2 0 SP2 The Microsoft NET Framework 2 0 Service Pack 2 is required to be able to run the BioNumerics Setup New installation functions have been added to the AppliedMaths SetupFramework dll NET assembly and this library requires the Microsoft NET Framework 2 0 runtime The Setup will install the Microsoft NET Framework 2 0 SP2 on Windows Vista Windows Server 2008 RTM and older Windows versions Note that the Setup will attempt to install the Microsoft NET Framework 3 5 Service Pack 1 Windows feature on Windows 7 Windows Server 2008 R2 and later versions instead of installing Microsoft NET Framework 2 0 SP2 2 4 Microsoft NET Framework 3 5 SP1 Microsoft NET Framework 3 5 Service Pack 1 is a cumulative update that contains many new features building incrementally upon NET Framework 2 0 3 0 3 5 and includes NET Framework 2 0 Service Pack 2 and NET Framework 3 0 Service Pack 2 cumulative updates The BioNumerics Database Engine feature is dependent on the Microsoft NET Framework 3 5 Service Pack 1 runtime The Database Engine feature installs a BioNumerics instance of Microsoft SQL Server 2008 R2 SPI Express Edition hence the corresponding prerequisites must be install
48. ed prior to installing this feature Note that the Setup will attempt to install the Microsoft NET Framework 3 5 Service Pack 1 Windows feature on Windows 7 Windows Server 2008 R2 and later versions even if the BioNumerics Database Engine feature was not selected for installation 2 5 Microsoft Visual C 2010 Redistributable The Setup will install the Microsoft Visual C 2010 Redistributable package on the target computer prior to installing any application files The redistributable is required to be able to run C applications like BioNumerics On 32 bit computers only the x86 version will be installed On 64 bit computers the x86 and x64 versions of the Microsoft Visual C 2010 Redistributable will be installed 2 6 Microsoft XML 6 0 SP1 The Microsoft Core XML Services MSXML 6 0 are required to be able to run the BioNumerics Setup This version has been included with Windows XP Service Pack 3 All other supported operating systems also include Microsoft XML 6 0 The BioNumerics Setup uses the MsxmI2 DOMDocument 6 0 COM object for reading and writing to the Setup INI and log files Hence MSXML 6 0 must be installed before running the BioNumerics Setup 2 Windows Installer 4 5 The BioNumerics Setup will install Windows Installer 4 5 on Windows XP SP2 Windows Server 2003 SPI and Windows Server 2008 or newer Windows versions 1f the required Windows Installer version 1s not 8 2 System requirements installed The Data
49. ee 3 1 7 Enter the command ParseUsage and press Enter to see how to use the ParseUsage exe tool The result is depicted in Figure 4 17 For Windows PowerShell start any command line with For example ParseUsage in a command prompt becomes ParseUsage in PowerShell Table 4 2 lists all available options for the ParseUsage exe command line tool For the ParseUsage exe tool to work at least the path for the output file should be specified e g ParseUsage out C LogFiles NetKey TXT In case a file path contains one or more spaces it should be enclosed with double quotes in the Windows command prompt or PowerShell The output of ParseUsage exe is a tab delimited text file with seven fields 54 4 NetKey configuration e Windows elevated rights Windows user rights NetKey admin password required Configure licenses passwords logging Monitor all sessions View log information Start stop service only when run on the server computer Configure ports NetKey user no password Limited user view Monitor own sessions Configure ports Full user view Monitor own sessions View ses sion information from other clients View log information Configure ports e Configure licenses passwords logging e Monitor all sessions e View log information e Limited user view Monitor own sessions e Full user view Monitor own sessions View session infor mation
50. er e Server admin port number TCP listening port number for configuring the NetKey server This can be the same number as for the Server port but to increase security a different TCP port number can be configured for administrating the NetKey license server This way the Windows firewall on the NetKey server can be configured to only allow remote NetKey administration from specific computers r BioNumerics InstallShield Wizard on to NetKey license server The licenses for this software product are distributed by a central NetKey license server Please enter the required connection parameters NetKey Server name lt NETKEY SERVER NAME gt Server port number 1080 Server admin port number 1080 Note you can modify these parameters anytime later using the NetKey Config utility Figure 3 19 The NetKey connection settings dialog box 3 2 7 Confirm update Click lt Next gt to start the update The Setup Status dialog box will be displayed Newer files will be copied to the target system for the selected features Any feature that was de selected will cause the corresponding files and shortcuts to be uninstalled The Update Complete dialog box will appear after the update has finished Click lt Finish gt to exit the Setup program 3 3 Maintenance installation 3 3 1 Select instance to maintain If an instance of BioNumerics 6 5 or later is already installed then the Existing Installed Instances Detect
51. er function is called by the Setup just before the main BioNumerics application feature is installed First this process will call the DeleteOldFiles function to delete legacy files from the BioNumerics program folder which are no longer included in the current Setup package Next the Application Installing function will run the vcredist_x86 exe executable to install the Microsoft Visual C 2008 Redistributable Package x86 62 5 Installation process The Application Installed event handler function is called by the Setup immediately after the application fea ture has been installed This function will write the database home directory to the HKEY_CURRENT_USER hive If a network license string was entered the Application Installed function will read the NetKey server properties from the Setup INI XML file and create or overwrite the NetKey ini file in the common applica tion data folder Finally the function will create the shortcuts in the Startup menu and desktop folder The Application_UnInstalled event handler function is called by the Setup just after the main BioNumerics application feature has been removed This function will call the DeleteOldFiles function to delete legacy files from the BioNumerics program folder which are no longer included in the current Setup package The Sentinel_Installed event handler function is called by the Setup after the Sentinel drivers place holder feature has been installed This process will
52. er reboot 3 4 3 Activate Sentinel HASP SL key 3 4 3 1 Introduction The first step in installing a software based Sentinel HASP SL key 1s adding the license string using the NetKey configuration tool If the added license string corresponds with a software lock protection key then the lt Activate gt button Figure 3 24 will be available which allows downloading and installing the SentinelHasp key on the NetKey server computer If the license key with the SentinelHasp provider is already listed in the NetKey configuration tool on the NetKey server then the software lock SL key 1s already activated Clicking the lt Activate gt button will display the Activate Hasp license dialog see Figure 3 24 It is recom mended to activate the software lock SL key using automatic activation This requires an active internet connection on the computer running the NetKey configuration tool This dialog enables an Administrator to perform an automatic or manual activation of a HASP software lock SL license string or to transfer an existing protection key to another computer Note that the NetKey Server never needs an active internet connection for the activation an active internet connection is recom mended for the NetKey configuration tool however 30 3 Installation procedure Activate Hasp license Activation Choose whether you want to activate a license or transfer an activation Automatic activation requires active internet connec
53. es control panel can be accessed from Control Panel gt System and Security gt Administrative Tools gt Services Select Server in the left panel see Figure 4 5 The ports displayed in the upper panel are the TCP listening ports on the NetKey server computer These port numbers must correspond with the port numbers saved in the NetKey ini file The next time the configuration tool is launched the program will read the port numbers from the NetKey ini file and au tomatically display the numbers in the Login window The Uptime value displays the amount of time the NetKey service has been up and running The hardware or software HASP security keys detected on the server computer are displayed in the lower Available license keys panel At least one key should be listed 1f not please check the dongle drivers Status Started Port 30 Config port 30 User view mode Limited Version NetKey 1 2 Uptime 28 sec Available license keys Provider Serial number SentinelSuperPro 779 975 411 Figure 4 5 The NetKey settings and available keys Click the lt Edit Settings gt button to display the Server properties window see Figure 4 6 and to change 4 3 Configuring licenses 45 the TCP port numbers E Server properties Port 80 Config port 80 User view mode Full Limited Figure 4 6 Edit the server properties If the NetKey Configuration tool or the BioNumerics application is unab
54. esponding soft lock key Hence the computer running the activation process must be able to access the 3 4 Installing Protection Keys 31 following web sites on the internet e https ssllicense applied maths com Secured License Server e https activate applied maths com Secured Activation Server Select Server in the left panel of the NetKey configuration tool If the automatic activation was successful the software based protection key with SentinelHasp as the provider should appear within a minute or so in the list of available license keys Note that the installed SentinelHasp soft lock key is only valid for a specific target computer and can by default only be activated once Afterwards the protection key can be moved to another NetKey server for example when installing a new NetKey server computer If an error message appears during the activation process you can look up the NetKeyConfigLog txt log file in your temp folder and send the file as an email attachment to activate applied maths com If receiv ing the vendor to customer v2c file from the Applied Maths activation server succeeded but applying it to the NetKey server failed a backup v2c file is created in the temp folder with a name formatted like NetKeyConfig autoActivate_backup_ v2c The activation can then be completed manually by using this file and the Activate with confirmation file option in the Manual Activation dialog e License Activation log file pat
55. ew the installation settings and clicking lt Cancel gt will cause the installation wizard to exit without modifying your system The Setup Status dialog box will be displayed after clicking the lt Install gt button This dialog will show the name of the feature that is being installed and the name of the file that is being copied The Install Complete dialog box will appear after the installation has finished Click lt Finish gt to exit the Setup program 3 1 12 NetKey configuration If a network license string has been entered in the Customer Information dialog box see Figure 3 4 and the NetKey server program feature was selected for installation see Figure 3 7 the Setup will ask if you want to run the NetKey Configuration tool see Figure 3 11 This tool allows you to install and subsequently start the NetKey service Click Yes if you want to start the NetKey Configuration tool Click lt No gt If you do not want to specify the NetKey settings at this time More information about the NetKey Configuration tool can be found in 4 Question The NetKey Server program has been installed DY Please attach the hardware security key dongle to the NetKey Server computer Would you like to start the NetKey Server configuration tool now e e Figure 3 11 Launch the NetKey Configuration tool 3 1 13 Setup INI XML file After the dialog sequence the Setup will record all settings
56. executed Click lt Finish gt to exit the Setup program 3 3 4 Repair maintenance mode After choosing the Repair option in the Welcome dialog box see Figure 3 21 and clicking lt Next gt the Setup program will re install all features that were selected during the previous installation All correspond ing files shortcuts and registry settings will be re created on the computer where the Setup 1s running If a network license string has been entered and the NetKey server program feature was selected for installation the Setup will ask if you want to run the NetKey Configuration tool This tool allows you to connect to the NetKey server to verify and update the license information In addition the tool allows you to repair the NetKey service see 4 7 and 4 8 Click lt Yes gt if you want to start the NetKey Configuration tool Click lt No gt if you do not want to change the NetKey settings at this time More information about the NetKey Configuration tool can be found in 4 28 3 Installation procedure The Maintenance Complete dialog box will appear after all changes have been executed Click lt Finish gt to close the Setup program 3 3 5 Remove maintenance mode The Remove option in the Welcome dialog box see Figure 3 21 allows you to completely uninstall the selected instance of BioNumerics All BioNumerics files and shortcuts that were created during previous installations of the selected BioNumerics instance will be de
57. f BioNumerics 6 5 or later not only creates a Setup log XML file but also a Setup INI XML file see 3 1 13 for more details This Setup INI XML file recorded during a manual install of BioNumerics can subsequently be used to perform silent installations The Setup INI XML file is located in the SetupLogs sub folder of the BioNumerics installation directory The file name is formatted like Setup_x_ini XML Check the file modification date to determine which INI XML file was created during the latest installation The BioNumerics 6 5 or later versions of the Setup program accept the following command line parameters to invoke the silent installation mode lt path to Setup files gt Setup exe s ini lt path to Setup_x_ini XML file gt e The s command line parameter instructs the InstallShield runtime engine to suppress the Existing Installed Instances Detected dialog box if BioNumerics version 6 5 or later is already installed e The ini parameter instructs the Setup script to read the installation settings from the INI XML file and to hide all dialogs e The double hyphen is required to differentiate between InstallShield runtime engine and custom In stallScript command line parameters e The slash parameters are used by the runtime engine e The double hyphen custom parameters are used by the installation script e Optionally the logdir command line parameter can be specified to override the log_dir path recorded in the Setup
58. file 7 In the Step section select Step 2 Create transfer file Source computer 8 Click the first lt Browse gt button to select the id protection key request file 9 Click the second lt Browse gt button to enter the path and file name of the v2c transfer file 10 Click lt Finish gt to remove the protection key from the local computer and to save the v2c transfer file Transfer activation Select the appropriate transfer step Computer O NetKey is running on the destination computer Step 1 Create request file Destination computer Step 2 Create transfer file Source computer Step 3 Apply transfer file Destination computer RETRO OTT Figure 3 30 Transfer activation u Upon completion of this step the software lock is effectively removed from the source computer This means that the license connected to this lock will be deactivated The software lock has not been transferred to the target computer yet however at this point the lock can be thought of as residing in the transfer file Until the transfer file has been applied on the target computer it is therefore crucial not to accidentally remove it As a back up measure a copy of the transfer file is stored in the temp folder with name e g NetKeyConfig_transferFile_backup_0 v2c 3 5 Setup log 35 Activate Hasp license Create transfer file Create a transfer file on the source computer based on the request file Request file input
59. first call the sSentinelInstalled function to check if the min imum required version of the Sentinel System Drivers is already installed If the required version is not installed or in repair maintenance mode the Sentinel_Installed function will call the HasDongles function to check if hardware security keys are connected to the target computer The appropriate warning messages will appear if existing hardware security keys were detected Next the function will call the MSI InstallProduct function to install the Sentinel System Driver Windows Installer package e g Sentinel System Driver Installer 7 5 1 msi The NetKey_Installing event handler function 1s called by the Setup just before the NetKey server program feature 1s installed First this function will stop the NetKey service if it already exists on the target system This will make sure that existing files are no longer in use and will allow the Setup to overwrite these files if needed Next the NetKey Installing process will call the sOldNetKeyInstalled function to delete conflicting versions of the NetKey service Finally the function will grant full NTFS permissions to the built in NT AUTHORITY SYSTEM account for the Applied Maths common application data folder This way the NetKey service running with the SYSTEM account will have sufficient privileges to create and modify files in the NetKey sub folder The NetKey_Installed handler function is called by the Setup ju
60. from other clients View log information Table 4 1 Running the NetKey configuration tool with different rights i Em C Windows system32 cmd exe Please provide argument out ense string gt IP lt ip address gt User lt user out output text file etKey _LOG txt Lic optional filter on specific license string 1P optional filter on specific ip address User optional filter on specific user C Program Files x86 gt Applied Maths BioNumerics66hbeta gt _ C Program Files x86 gt Applied Mathsx BioNumerics66beta gt ParseUsage exe ParseUsage out lt filename gt inp lt filename gt begin lt date gt end lt date gt Lic lt lic optional input file name default ProgramDatazxApplied Maths netkey N begin optional begin date in output file format YYYY MM DD EE end optional end date in output file format YYYY MM DD Figure 4 17 Windows command prompt with ParseUsage executed Start Time stamp for the start of a session End Time stamp for the end of a session Duration s Total time that the session lasted in seconds Lic License string used IP IP address IPv4 of the computer where the session was in use User Windows user name 4 10 Usage statistics 55 Option Description out The location and name of the output file Example out c NetkeyReports usage Q1_2011 txt inp The location of the NetKey _LOG txt file optional Def
61. ft Visual C 2010 Redistributable Package x86 Installing Microsoft NET Framework 3 5 SP1 Windows Feature Figure 3 1 The Prerequisites dialog Click on the Install button to start the installation of the missing prerequisites not able to download and install the Microsoft NET Framework 3 5 SPI u It is recommend to install the Setup prerequisites as described in 2 prior to launching the Setup in Silent installation mode see 3 6 For example the silent installation will fail if the Setup is 12 3 Installation procedure 3 1 2 Existing instances detected The BioNumerics 6 5 or later Setup package supports installing multiple instances of the same application side by side Each BioNumerics instance will have a dedicated application installation path and will have a set of start menu and desktop shortcuts If an instance of BioNumerics 6 5 or later is already installed then the Existing Installed Instances Detected dialog will appear when launching the Setup executable see Figure 3 2 BioNumerics InstallShield Wizard Installed Instances Detected Ry Zz appropriate application instance to maintain or update d Setup has detected one or more instances of this application already installed on your system You can maintain or update an existing instance or install a completely new instance nstall a new instance of this application Maintain or update the instance of this application selected
62. h temp NetKeyConfigLog txt e License Activation backup v2c file temp NetKeyConfig_autoActivate_backup_0 v2c A complete system or full backup scheme must be in place to protect the NetKey license server where a soft lock key has been activated Changing the hardware configuration e g MAC address CPU hard drive will cause the protection key to render invalid hence the protection key must be transferred to another intermediate computer before modifying the hardware and transferred back to the source computer after the hardware component s have been replaced This also applies to virtual environments for example moving a virtual NetKey server guest image to another host server may invalidate the protection key Hence the key must be transferred to another intermediate computer before moving the guest image to another host server and transferred back after the virtual guest image has been moved In case of doubt please contact the support team before changing the hardware configuration of a NetKey server that contains a SentinelHasp soft lock protection key 3 4 3 3 Manual Activation If no internet connection is available on the NetKey server computer or on any of the computers where the NetKey configuration tool is installed then the Manual Activation option can be selected in the Acti vate Hasp license dialog see Figure 3 24 It is recommended to activate the software lock SL key using automatic activation This requires an
63. he NetKey server program must have a free USB port for attaching the hardware security key Internet licenses do not require a hardware security key hence an USB port is not needed A 64 bit processor and Windows version are required for systems with more than 4 GB of RAM installed The actual hardware requirements will largely depend on the features that will be used in BioN Y umerics the database platform used to store the BioNumerics data and the size of the data For example the Power Assembler feature of the Sequence data module requires a 64 bit processor and a minimum of 8 GB installed memory 2 1 2 Recommended hardware configuration The recommended hardware configuration for a computer running the latest Windows and Office versions and the BioNumerics application are 6 2 System requirements e Processor 1 8 gigahertz GHz processor or higher Processor Type Intel Core 2 Duo Processor or higher compatible processor e Memory 2 GB or higher e Hard disk 2 GB of free disk space application files only fast hard drive for storing database files e g 7200 RPM SATA drive e Display WXGA 1440 x 900 or higher resolution monitor True Color 32 bit graphics card with dedicated video memory When purchasing a new computer that will run BioNumerics make sure that you choose a 64 bit Windows version to allow for future memory expansion At least 4 GB of RAM should be installed when purchasing a new system A recent g
64. his session can be launched by the software is displayed in the Wait number column Detailed session information is shown in the right panel when selecting a session in the left panel _f NetKey Configuration administrator mode Local Sessions Server localhost Sessions Licenses i E AMCM 4JFP BVC7 ANGV UVHP QV4N Id ClientId IP address Status AccessRules No filter Id 0 Sessions Figure 4 13 List of connected sessions and sessions that are present in the waiting queue In Administrator mode messages can be sent to any or all connected clients for example in case the server computer will be shut down or if a session will be disconnected see Table 4 1 To send a message to a client select a session of the client in the Sessions panel see Figure 4 13 and press the Notify button see Figure 4 13 Alternatively select the session under the Sessions option in the left panel and select the lt Notify gt button Enter a message string and press lt OK gt see Figure 4 14 The message is sent to the corresponding client A message can be sent to all users with Notify All All active users will receive the message in a dialog box All connected sessions on the clients and sessions present in the waiting queue can be closed by the Ad ministrator see Table 4 1 To close a session select the session in the Sessions panel see Figure 4 13 and disconnect the session with Release Alternative
65. ication Select filter mode Filter by IP Ip address Access specification Deny Q Allow Limit number of allowed sessions to sessions Limit number of allowed sessions per client to sessions Figure 4 11 The Access rule properties dialog box A range of IPv4 addresses can be specified if the Range option is checked in the upper Client identification panel Optionally a limit on the number of allowed concurrent sessions can be specified in the lower Access specification panel when the Allow option is checked see Figure 4 11 Note that NetKey does not support the Filter by IP filter mode for IPv6 addresses Pressing the lt Add gt button adds the rule to the Access rules list see Figure 4 10 Each access rule is identified by an unique identifier 1d The filter mode is displayed in the Client filter column and the Sessions column displays the number of allowed concurrent sessions to all clients If no limit has been set this column will display Limit by license The Sessions per client column displays the number of allowed concurrent sessions for each client If no limit has been set this column will also display Limit by license Both these sessions columns will display Deny if this has been specified as the Access specification The Connected sessions column shows the number of currently connected sessions The number of sessions that are queued on a waiting list are shown in the last Waiting sessions column The access
66. igure 4 16 to delete the current NetKey configuration All NetKey settings will be deleted after clicking Yes Select the Administrator option in the upper Application mode panel Verify and update the Port and Admin port TCP port numbers if needed Make sure that the TCP port numbers are not in use on the NetKey server computer Click lt Continue gt and select Connection in the left panel to display the Service settings Click Start in the lower Service panel This brings up the Change server password dialog Enter a secure NetKey Administrator password in the New password and Confirm password text boxes This password will be required to be able to start the NetKey Configuration tool in Adminis trator application mode Restart the NetKey Configuration tool Select the Administrator option in the upper Application mode panel and enter the Administrator Password created in the previous step Click lt Continue gt to connect to the NetKey service Now you are ready to start configuring the access rules for your BioNumerics license 4 8 Repairing the NetKey service The following steps allow you to repair the NetKey service without deleting the current configuration 1 Select the Administrator option in the upper Application mode panel 2 Enter the NetKey Administrator Password and click the lt Continue gt button 4 9 Overview of configuration rights 53 Important IMPORTANT WARNING
67. inel Run time Environment for the HASP SL or HL protection keys can be downloaded from the following web site http www applied maths com haspdriver The above URLs will redirect you to the appropriate download page on the SafeNet Sentinel customer web site After installing the drivers and connecting the USB dongle the protection key should appear under Univer sal Serial Bus controllers in the Windows device manager see Figure 3 23 The Windows device manager can be accessed via Control Panel gt System and Security gt Administrative Tools gt Computer Management 4 Universal Serial Bus controllers Intel R ICH9 Family USB Universal Host Controller 2934 Intel R ICH9 Family USB Universal Host Controller 2935 Intel R ICH9 Family USB Universal Host Controller 2936 Intel R ICH9 Family USB Universal Host Controller 2937 Intel R ICH9 Family USB Universal Host Controller 2938 Intel R ICH9 Family USB Universal Host Controller 2939 Intel R ICH9 Family USB2 Enhanced Host Controller 293A Intel R ICH9 Family USB2 Enhanced Host Controller 293C SafeNet USB SuperPro UltraPro Figure 3 23 Universal Serial Bus controllers If the USB dongle is not listed in Windows device manager then download and install the latest version of the driver from the SafeNet web site and reboot the computer Please contact the Applied Maths support team supportO applied maths com if Windows still is unable to detect the protection key aft
68. istrators Windows group thus granting full access to the BioNumerics instance of Microsoft SQL Server 2008 R2 Express and the BioNumerics databases 18 3 Installation procedure 3 1 10 NetKey connection settings After pressing the lt Next gt button the NetKey connection settings dialog box will appear see Figure 3 10 if a network license string was entered in the Customer Information dialog box see Figure 3 4 and if the BioNumerics application feature was selected for installation see Figure 3 7 The NetKey Server name Server port and Admin port numbers can be entered in the NetKey connection settings dialog box see Figure 3 10 These parameters will allow the BioNumerics application to connect to the NetKey server and request a session for the client computer e NetKey Server name Name of the computer where the NetKey license service is running e Server port number TCP listening port number of the NetKey service running on the NetKey server e Server admin port number TCP listening port number for configuring the NetKey server This can be the same number as for the Server port but to increase security a different TCP port number can be configured for administrating the NetKey license server This way the Windows firewall on the NetKey server can be configured to only allow remote NetKey administration from specific computers Please make sure that you enter available TCP port numbers for the NetKey Server
69. ity File Action View Help es Af i9 BI m Windows Firewall with Advanced Security on Local Computer E Inbound Rules ES Outbound Rules da Connection Security Rules Microsoft SQL Server BioNumerics E Monitoring Microsoft SQL Server Browser BioNumerics 4 m Figure 7 4 Windows firewall rules By default the BioNumerics database engine is configured to use dynamic TCP listening ports Hence the SQL Server Browser service should be running and the Startup Type should be set to Automatic to allow client applications to request SQL Server TCP connection information Figure 7 5 File Action View Help eiml sisilissi sunun v Name Description Status Startup Type Log On As amp SQL Server BIONUMERICS Provides sto Started Automatic Local Service SA SQL Server MSSQLSERVER Provides sto Manual NT Service MSSQLSERVER CE SQL Server Agent BIONUMERICS Executes jo Disabled Network Service Ga SQL Server Agent MSSQLSERVER Executes jo Manual NT Service SQLSERVERAGENT T SQL Server Browser Provides SQ Started Automatic Local Service Ga SQL Server Integration Services 11 0 Provides m Manual NT Service MsDtsServer110 S5 SQL Server VSS Writer Provides th Automatic Local System Extended A Standard Figure 7 5 Windows Services If you are unable or not allowed to use SQL Server Browser service then the TCP port number must be specified in the SQL Server instance name when crea
70. lation of the service allowing you to enter and confirm a new NetKey server password see Figure 4 4 A user will be required to enter the NetKey server password each time the configuration tool is started in Administrator application mode After the user clicks Continue in the Login window the configuration tool will connect to NetKey server via the specified Server config Port or Admin port to verify the credentials After clicking lt OK gt in the Change server password dialog box the password is encrypted and stored in the NetKey Config txt XML file The Service status will change to Started if no error has occurred In case of error the NetKey _LOG txt log file can be checked to verify the error message see 4 6 The log file is stored in the same ProgramData or Application Data folder as the NetKey ini file depending on the Windows version Once the service has been installed and started the service can be stopped by pressing the lt Stop gt button and can be removed by clicking the Remove button in the lower Service panel 2 The Service panel will be disabled grayed out if the configuration tool is launched without Windows elevated privileges AM uos Old password New password Confirm password Figure 4 4 Specify server password The NetKey server program is a Windows service Once the service is installed it can be managed from the Services control panel On Windows Vista or later the Servic
71. le to communicate with the NetKey service through the specified port numbers then check your security settings to make sure that the TCP ports are accessible For example if a software firewall has been enabled on the NetKey server or on the BioNumerics client computer then the firewall may need to be configured to allow traffic for the Applied Maths executables and or the applicable TCP port numbers Continue with 4 3 if you want to set up the BioNumerics license string s to allow access for the client computers Click the x sign in the top right corner or press ALT F4 to close the NetKey Configuration tool Closing the NetKey Configuration tool will not affect the current status of the NetKey service If the service 1s running then clients will be able to connect to the NetKey server if the configuration was successful 4 3 Configuring licenses Adding and configuring licenses can only be done by running the NetKey Configuration tool in Adminis trator application mode with or without Windows elevated privileges Run as administrator see Table 4 1 After selecting the Administrator mode in the Login window the correct NetKey server password can be entered in the Password field see Figure 4 2 The settings in the lower Connect to panel correspond with the settings stored in the NetKey ini file These settings can be changed if the tool was started with Windows elevated privileges Click the lt Continue gt button to conne
72. leted In addition the uninstall information for the selected instance will be removed from the computer A confirmation dialog will appear asking you to confirm the removal of the selected BioNumerics instance see Figure 3 22 Click Yes to start the deletion of the BioNumerics application Select lt No gt to return to the previous Welcome dialog box BioNumerics InstallShield Wizard Do you want to completely remove the selected application and all of its features Figure 3 22 Confirm removal of selected features Completely uninstalling an instance of BioNumerics which includes the NetKey server pro gram may affect other BioNumerics users that use the corresponding NetKey service to re quest license sessions Make sure that no other users are using the NetKey service prior to uninstalling the NetKey server program feature or completely uninstalling the BioNumerics instance The Uninstall Complete dialog box will be displayed after the selected BioNumerics instance has been removed Click the lt Finish gt button to exit the Setup program The Setup will not delete BioNumerics program folder because it contains the SetupLogs sub folder holding the log files for each Setup that has been run Also any file that has been added to the program folder and which was not originally installed by the Setup program will not be deleted from the hard drive 3 4 Installing Protection Keys 3 4 1 Protection Key Types
73. lt setup configuration will install all BioNumerics features with default settings These settings include the destination paths for the application and data and the database engine configuration Note that the Default setup configuration does not include the NetKey server program The Custom setup configuration allows you to select the features you want to install choose the target paths for the application and data and the database engine configuration The Custom setup configuration also allows you to install the NetKey server program IET via M z E eee A T Se ur Type y gt Select the setup type that best suits pour needs Click the type of setup you prefer All features will be installed with the default settings Requires the most disk space Installation directory C Program Files 485 Applied Maths BioNumerics 19 Database home directory C AUsers Public Documents BioNumerics Data 70 SOL data files directory c Program Files Microsoft SQL Server MSSQL10 50 BIONUMERICS MSSQL Select which features you want installed configure the installation directories and database engine settings Recommended for advanced users Figure 3 5 Choose setup type 3 1 7 Choose destination location The installation directory for the BioNumerics application and the database home directory can be entered in the Choose Destination Location dialog box see Figure 3 6 The top lt Browse gt button allows you to navigate to a custo
74. ly select the session under the Sessions option in the left panel and select the lt Release gt button A list of all sessions that are running on the ocal computer and that are put on hold can be consulted in 4 6 Logging data SI Send notification Message Server computer will shut down at 11 a m Please make sure all data is saved in your session s Figure 4 14 Notification message the NetKey Configuration window when logged in as Administrator or as User with Full or Limited view mode Selecting the Local Sessions option in the left panel shows all connected local sessions and local sessions that are present in the waiting queue below the Loca Sessions option in the left panel see Figure 4 13 The Status Connected or Waiting and Time in use are shown next to each local session Detailed session information is shown in the right panel when selecting a local session in the left panel 4 6 Logging data When the NetKey Configuration program is launched in Administrator mode or in User mode with Full view the Logging option is displayed in the left panel see Table 4 1 and Figure 4 15 Pressing the Logging option in the left panel shows all logged information in the right panel This logged information is stored in a text file called NetKey _Log txt This file is located in the folder containing application data for all users CommonAppDataFolder The path of this folder depends on the operating System ve
75. m installation path for the BioNumerics ap plication A BioNumerics shortcut will be created on the desktop when the option Create a BioNumerics shortcut on the desktop is checked Two default locations can be selected for the database home directory In Common Documents and In My Documents The In Common Documents option will store the BioNumerics databases in the public documents folder As a result the databases will be available to all users on the local computer The In My Documents option will store the BioNumerics databases in the personal documents folder and by default the databases will only be available to the current user The third Custom option allows you to enter a path on the local computer or even on a remote file server via a permanent network drive The lower lt Browse gt button will be enabled if the Custom radio button has been selected for the database home directory Note that all BioNumerics users that will access data in the database home directory must have MODIFY NTFS permissions In addition the FULL CONTROL permissions must be granted at the file share level when the directory is located on a remote file server 3 1 Installing a new BioNumerics instance 15 C Program Files x86 Applied Maths BioNumericd w Create a BioNumerics shortcut on the desktop Database home director C In Common Documents C Users Public D ocuments BioNumerics D ata Databases installed here will be Stile to all local users D f C
76. ment can be printed to the default printer by clicking the lt Print gt button The lt Save gt button allows you to browse to a folder where you want to save the Applied Maths EULA PDF Acrobat document 3 1 Installing a new BioNumerics instance 13 ving license agreement carefully IMPORTANT PLEASE READ THIS END USER LICENSE AGREEMENT CAREFULLY DOWNLOADING INSTALLING OR USING APPLIED MATHS SOFTWARE CONSTITUTES ACCEPTANCE OF THIS AGREEMENT Software End User License Agreement APPLIED MATHS IS WILLING TO LICENSE THE SOFTWARE TO YOU ONLY UPON THE CONDITION THAT YOU ACCEPT ALL OF THE TERMS CONTAINED IN THIS LICENSE AGREEMENT BY DOWNLOADING OR INSTALLING THE SOFTWARE YOU ARE BINDING YOURSELF AND THE BUSINESS ENTITY THAT YOU REPRESENT COLLECTIVELY CUSTOMER TO THIS AGREEMENT IF YOU DO NOT AGREE TO ALL OF THE TERMS OF THIS AGREEMENT THEN APPLIED MATHS IS UNWILLING TO LICENSE THE SOFTWARE TO YOU AND YOU SHOULD NOT DOWNLOAD INSTALL OR USE THE SOFTWARE The Software As used in this Agreement the term Software means collectively i the software product identified above ii all the contents of the disk s CD ROM s electronic mail and its file attachments or other media with which this Agreement is provided including the object code form of the software delivered via a CD ROM electronic mail or Web page iii digital images stock photographs clip art or other artistic works iv related explanatory written materials
77. n the client computer stating how many sessions have to close before the session can be launched by the software see Figure 4 12 As soon as one of the connected sessions of the corresponding license is closed on one of the clients the first session in the waiting list automatically opens on the client computer and all waiting numbers of the remaining sessions in the waiting queue are updated Press the lt Close Application gt button 1f you wish to remove the session from the waiting list 4 5 Monitoring sessions A list of all sessions that are running on the client computers and that are put on hold can be consulted in the NetKey Configuration window when logged in as Administrator or as User with Full view mode see 50 4 NetKey configuration License Problem m ya You are number 1 in the waiting queue Figure 4 12 Waiting queue Table 4 1 Selecting the Sessions option in the left panel shows the sessions in the right panel see Figure 4 13 Each connected session and session present in the waiting queue is identified by a unique session identifier ID column The access rule ID that grants access to the license is displayed in the Linked rule column Information of the associated client computer is shown in the Client Id Name and IP address columns The Status of each connected session is set to Connected When a session is put on the waiting list Waiting status the number of sessions that have to close before t
78. n to create a new rule for the selected license The Access rule properties dialog box pops up see Figure 4 11 The following filter 4 3 Configuring licenses 47 License string AMCM 4JFP BVC7 ANGV UVHP QV4N ir AMCM 4JFP BVC7 ANGV UVHP License status Active i No filter Id 0 e RA License key code 779 975 411 Product BioNumerics 7 0 Licensed modules Fingerprint types Character types Cluster Analysis Identification Quantification Unlicensed modules cr ee so Po Genome analysis tools Whole genome maps Usage time 2 hours Idle time 1 hours Timeout 5 min Allowed sessions 5 Connected sessions 2 Waiting sessions 0 4 Local Sessions E Server localhost i i AMCM 4JFP BVC7 ANGV UVHP QV4 Id Client filter Sessions Sessions per di AccessRules 0 Nofiter Limitbylicense Limitbylicense i No filter Id 0 add Remove change ue om Figure 4 10 Access rules for a license modes can be used for granting Allow or refusing Deny access to the license e No filter Anyone can access the license e Filter by ClientId Physical Address MAC of the client network adapter e Filter by Computer Name TCP IP Host name of the client computer with or without domain name 48 4 NetKey configuration e Filter by User Name Windows login name without domain name e Filter by IP Single or a range of IPv4 addresses of client computers Access rule properties Client identif
79. ning NetKey service is installed in a different folder then the program folder of the current BioNumerics instance then the service will not be removed 5 3 Setup processes 63 The Database Installed handler function is called by the Setup just after the sample database feature has been installed This function will set the Current Database value in the HKEY_CURRENT_USER hive of the registry if the string value does not already exist The DeleteOldFiles function will delete legacy files from the BioNumerics program folder which are no longer included in the current Setup package Only legacy files with the following file extensions will be deleted from the program folder BXT DLL EXE AVI PYC and XML The sSentinelInstalled function will check the Windows Installer database to verify if the minimum required version of the Sentinel System Driver Installer is already installed If the USB Driver feature is not installed then the function assumes that the Sentinel System Driver package 1s incomplete and will instruct the Setup to re install the package The HasDongles function will launch the setlic exe executable to verify if hardware security keys or dongles are connected to the target system The function will check the exit code of the setlic exe program to verify if dongles were detected In silent mode the CheckLicense function will first attempt to read the license string from the Setup INI XML file Next the function will read th
80. nization for which you work and the BioNumerics license string User Name lt My Name gt Organization Name My Organization Name gt License String Please enter the License String E Please contact your software vendor to obtain your license string Figure 3 15 The Customer Information dialog box 3 2 4 Choose destination location The Choose Destination Location dialog box see Figure 3 16 will only appear when upgrading a BioNu merics version older than 6 5 see 3 2 1 1 If you enter the installation directory of the currently installed version then this version will be replaced by the newer version n The Choose Destination Location dialog box will not appear when upgrading a BioNumerics 2 6 5 or newer instance see 3 2 1 2 3 2 5 Select features After clicking Next the Select Features dialog box see Figure 3 17 will be displayed allowing you to choose which features to update or to uninstall Typically you should accept the default feature selection or select additional features to install Install application software e In case of a standalone license the Application software needs to be installed on each computer that you want to use to run the software Please note that only on the computer where the dongle is attached to you will be able to work with the software e In case of an internet license the Application software needs to be installed on the computer that you want to
81. o ensure the use of manual settings disable automatic configuration Automatically detect settings Use automatic configuration script Proxy server Use a proxy server for your LAN These settings will not apply to connections dial up or VPN Address proxy dom com Port 8080 Advanced V Bypass proxy server for local addresses Le cae Figure 2 1 The LAN Settings dialog box Network licenses of BioNumerics require that a NetKey server has been configured to manage the license sessions All computers running BioNumerics must be configured to allow access to the listening TCP port on the NetKey server computer Also the server computer must allow incoming access for the TCP ports used by the NetKey server program For details please check 4 10 2 System requirements Chapter 3 Installation procedure 3 1 Installing a new BioNumerics instance 3 1 1 Prerequisites The Prerequisites dialog shows the items that are required to be installed on the local computer before any of the BioNumerics features can be installed see Figure 3 1 BioNumerics InstallShield Wizard n pr BioNumerics requires the following items to be installed on your computer Click Install to begin installing these requirements Status Requirement Succeeded Microsoft Visual C 2010 Redistributable Package x64 Installing Microsoft NET Framework 3 5 SP 1 Windows Feature Pending Microso
82. ogram will optionally install the Database Engine and install or upgrade the Sentinel and HASP drivers The BioNumerics Setup package is regularly updated and can be delivered on CD ROM or can be down loaded from the Applied Maths website http www applied maths com download software 1 Introduction Chapter 2 System requirements 2 1 Hardware requirements 2 1 1 Minimum hardware requirements The minimum hardware requirements for running the BioNumerics application are the cumulative require ments needed to run the Operating System the BioNumerics application the optional Database Engine and any third party software that will run concurrently e g Microsoft Office The typical minimum hardware requirements for a computer running Windows Vista Microsoft Office 2003 and the BioNumerics application are e Processor 1 6 gigahertz GHz processor or higher e Processor Type Intel Pentium Dual Core or higher compatible processor e Memory 2 GB or higher 1 GB if the Database Engine feature will not be installed e Hard disk 2 GB of free disk space application files only e Display WXGA 1280 x 800 or higher resolution monitor True Color 32 bit e USB port Depending on the license type a free USB port may be required For standalone licenses each computer that will run BioNumerics must have an available USB port for connecting the Sentinel hardware security key For network licenses the computer that will be running t
83. onfirm that you want to enable the active content in the Setup log XML file If the Setup is running in normal non silent installation mode and a warning or error event has occurred the Setup will automatically display the Setup log XML file in Internet Explorer Additional messages will continue to be written to the log file and the file will automatically be updated in Internet Explorer If you have scrolled down on the Setup log web page your current position will be lost after the web page has been 3 5 Setup log T 2 C Program Files x86 Applied Maths BioNumerics 7 01 SetupLogs Setup 1 log xml O X Setup Started on 12 12 2012 16 16 16 End 12 12 2012 16 25 00 Show Messages S E Feature Microsoft SQL Server 2008 R2 Native Client Feature installation start 12 12 2012 16 23 37 Feature installation End 12 12 2012 16 23 37 PSSade Feature Install application software Feature installation start 12 12 2012 16 23 37 Feature installation End 12 12 2012 16 24 08 Show Messages Feature HPC Pack 2008 MS MPI Redistributable Package Feature installation start 12 12 2012 16 24 06 Feature installation End 12 12 2012 16 24 07 iit 2 Feature Install sample database Feature installation start 12 12 2012 16 24 08 Feature installation End 12 12 2012 16 24 09 w M Feature Install sample and tutorial data Feature installation start 12 12 2012 16 24 09 Feature installation End 12 12 2012 16 24
84. only be visible and available for installation if a network li cense string has been entered in the Customer Information dialog box see Figure 3 15 The NetKey server program feature must only be installed on the computer in the network where the hardware security key will be connected to De selecting already installed features in the Select Features dialog box see Figure 3 17 will Y cause these features to be uninstalled during the update A message box will appear if you de select the main BioNumerics application feature see Figure 3 18 Select lt No gt if you do not want to uninstall the BioNumerics feature Figure 3 18 Warning message 3 2 6 NetKey connection settings After pressing the lt Next gt button the NetKey connection settings dialog box will appear if a network license string was entered in the Customer Information dialog box see Figure 3 4 and if the BioNumerics application feature was selected for installation see Figure 3 7 Typically during an update you can accept the NetKey Server name and Port numbers from the previous installation These parameters will allow the BioNumerics application to connect to the NetKey server and request a session for the client computer 3 3 Maintenance Installation 25 e NetKey Server name Name of the computer where the NetKey license service is running e Server port number TCP listening port number of the NetKey service running on the NetKey serv
85. orm of the software delivered via a CD ROM electronic mail or Web page iii digital images stock photographs clip art or other artistic works iv related explanatory written materials and any other possible documentation related thereto Documentation and v upgrades modified versions updates additions and copies of the Software if any licensed to Customer by Applied Maths under this Agreement License Conditioned upon compliance with the terms and conditions of this Agreement Applied NV its subsidiary lie ancina the Caftausren inertas af Annlind Mathe NIV Pl Aanlied Mathe arante ta M C n accept the terms of the license agreement i Figure 3 14 The License Agreement dialog box 3 2 3 Customer information If you are installing a new major or minor version of BioNumerics the Customer Information dialog box will be displayed after clicking the lt Next gt button see Figure 3 15 This dialog allows you to update the 22 3 Installation procedure license string for the new version of BioNumerics By default a new license string is required for each new minor or major version of BioNumerics For example updating version 6 6 4 to 7 0 0 will require a new license string while updating 6 5 0 to version 6 5 1 will not You must enter a valid license string to be able to continue with the installation In addition the user and organization names cannot be empty Please enter your name the name of the orga
86. ow by default lt PATH gt 1s the full path to the script file e openmain 0 1 Whether or not the Main window should be opened This option is only valid in combination with the script option As always the case with the Windows command prompt file paths that contain spaces should be enclosed with double quotes The command line syntax is quite flexible 99 gt Options can be provided as is or they can start with a hyphen or 7 slash Examples bn exe database DemoBase bn exe database DemoBase bn exe database DemoBase Options are not case sensitive Examples bn exe database DemoBase bn exe DataBase DemoBase bn exe DATABASE DemoBase Options and their values can optionally be quoted Examples bn exe database DemoBase bn exe database DemoBase bn exe database DemoBase Option names and their values can be separated with or Examples bn exe database DemoBase bn exe database DemoBase 6 2 Running the startup program from the command line The BioNumerics software startup program BnStart exe can be started from the command line Following options are available e homedir lt HOMEDIR gt the BioNumerics home directory lt HOMEDIR gt is the full path to the home directory e licensestring lt LIC gt the license string see 4 3 needed to activate the software license These options will be passed on to bn exe see 6 1 Chapter 7 Granting access
87. per quarter Each lab should be billed the respective portion of each license e LABI users Peter S Jake Tim e LAB2 users Jane Peter V Sophie Anna e LAB3 users Tom Catherine Luke An example NetKey log file named Netkey LOG demo TXT can be downloaded from the Applied Maths website http www applied maths com download sample data click on Example NetKey log file As the NetKey server program logs all opened sessions we will use the ParseUsage exe tool to create a usage report for the first quarter of 2011 10 1 On the command line specify ParseUsage out c Users Public Documents usage_Q1_2011 txt inp c Users Public Documents Netkey _LOG_demo txt begin 2011 01 01 end 2011 03 31 and press Enter Obviously if the example Netkey _LOG_demo TXT file is located in a different directory the command line should be adapted accordingly 56 2 0 3 anu Ah WN NIN RRA ke eR RR ke PS amp Gaewtans BEES 3 J 4 NetKey configuration The instructions given below are for Microsoft Excel 2010 For other versions of Excel we refer to the corresponding user manual 10 2 Open the usage Q1 2011 TXT file with MS Excel and add a column for the Lab according to the list of lab members shown above see Figure 4 18 for an example 1 2 3 4 5 6 Ei 8 9 A Start 1 01 2011 9 34 1 01 2011 9 34 1 01 2011 9 34 1 01 2011 9 34 1 01 2011 9 34 2 01 2011 9 34 2 01 2011 9 34 3 01 2011 9 34
88. properties for a selected rule can be modified by clicking the Change button If multiple access rules have been specified for a license the order of the rules can be changed with the lt Up gt and Down buttons When a client tries to open a session a session request 1s sent to the server containing computer information of the client computer name Windows user name IP address and MAC address and the license string The server checks the access rules of the license string that 1s sent with the session request and based on the access rules the server grants or denies the client access to the license Each session that is granted access to a license 1s identified by a unique identifier the session ID The session identifier 1s sent to the client and the session is launched on the client computer or the session is put on a waiting list in case the number of allowed sessions on the client is reached The client stores the session ID of the session and closes the connection with the server computer On regular time intervals a renew session request of each connected session and session that is put on hold is sent to the server Based on these renew session requests the server keeps track of the status of the sessions on the client computers The server might disconnect a session if the Usage time Idle time or Timeout value for a session is reached e Usage time The Usage time or time in use of each session that is granted access to a li
89. raphics card with dedicated video memory is recommended Choosing a basic Windows theme instead of a Windows 7 or Vista Aero theme may be required if the computer is not equipped with sufficient dedicated video memory Some features of BioNumerics may require hardware specifications that exceed the above rec ommendations For example the Power Assembler feature of the Sequence data module requires a 64 bit processor a minimum of 8 GB installed memory and a fast storage system SSD 2 2 Operating system Generally Applied Maths will support installing BioNumerics on Windows operating system versions for which the Microsoft Extended Support Phase see http support microsoft com gp lifeselect has not been retired This will allow you to obtain support and security updates from Microsoft for the target operating system e Windows XP with Service Pack 3 Note that the Microsoft Extended support for Service Pack 3 will end on the th of April 2014 e Windows Vista with Service Pack 2 e Windows 7 e Window 8 e Windows 2003 Server with Service Pack 2 e Windows 2008 Server RTM with Service Pack 2 or R2 Applied Maths recommends installing BioNumerics on a workstation or server with the latest Microsoft ser vice packs installed BioNumerics can be installed on 64 bit versions of Windows if the WoW64 Windows 32 bit On Windows 64 bit subsystem is installed and enabled The NetKey licensing server program should preferably be install
90. rics executables bn start exe and bn exe the DLL and BXT sub folders and specific file extensions dll mdb bpl in the application and database folders In addition the anti virus software must be properly configured to be compatible with the database plat form used to host the BioNumerics databases Most database software vendors require that the directories containing data and log files are excluded from anti virus scanning If the Database Engine feature has been selected for installation the following exclusions should be config ured in the anti virus software e Do not scan files with the mdf 1df ndf and bak file name extensions e Exclude the Microsoft SQL Server 2008 R2 Express process from virus scanning Program Files Microsoft SQL Server MSSQL10_50 BioNumerics MSSQL Binn sqlservr exe For Microsoft SQL Server please check the following article for more details Guidelines for choosing anti virus software to run on the computers that are running SQL Server http support microsoft com kb 309422 2 9 2 Firewall and proxy servers For BioNumerics internet and evaluation licenses network filtering software and firewall devices may need to be configured to allow access to TCP port 80 on the Applied Maths license servers Currently the following license servers are active to verify internet licenses 2 9 Security software 9 licensel applied maths com 81 246 4 66 license2 applied maths com 8
91. rsion e Windows Vista or later C ProgramData Applied maths NetKey e Windows XP C Documents and Settings All Users Mpplication Data Mpplied maths NetKey When verbose logging is enabled additional information messages are logged in the text file see Figure 4 15 Selecting the lt Change gt button changes the verbose logging status To clear the log file press the lt Clear log gt button Enabling disabling verbose logging lt Change gt and clearing the log file lt Clear log gt is only possible in Administrator mode see Table 4 1 4 7 Resetting the NetKey settings When the NetKey Configuration tool is run with Windows elevated privileges Run as administrator the lt Reset service gt button is displayed in the Login window see Figure 4 2 This button allows you to delete all current NetKey settings including the Administrator password Furthermore this operation will delete all licensing information and access rules you may have configured previously Hence the reset service function should be used with caution Use the following steps to stop the NetKey service and delete the NetKey settings 52 4 NetKey configuration Z NetKey Configuration administrator mode Log file size 70 KB Local Sessions Id 8 Connected In use 3 min 3 sec a Server localhost E Licenses AMCM 4JFP BVC7 ANGV UVHP QV4N ge AccessRules No filter Id 0 S Sessions Verbose Off
92. s group will also be a member of the sysadmin fixed SQL server role on the local BioNumerics instance of the Microsoft SQL Server 2008 R2 SPI Express database engine Hence members of this group will be able to perform any activity on the BioNumerics database engine If BioNumerics database sharing has been enabled in the Database Engine Properties dialog see 3 1 9 then the Microsoft SQL Server BioNumerics inbound Windows firewall rule will be enabled and TCP IP and Named Pipes connections to the database engine will be allowed To manually enable remote access to the BioNumerics database engine the appropriate network proto cols TCP IP must be enabled in the SOL Server Configuration Manager tool Figure 7 3 In addition the Microsoft SQL Server BioNumerics and the Microsoft SQL Server Browser BioNumerics inbound Windows firewall rules will need to be enabled to allow incoming access to the database engine Figure 45 File Action View Help e E as8 fa SQL Server Configuration Manager Local Protocol Name Status g a ss Y Shared Memory X Enabled a QL Server Network Configuration 32bit Named Pipes Enabled Y TCP IP Enabled Y VIA Disabled a SQL Native Client 10 0 Configuration 32bit 4 a SQL Server Network Configuration E Protocols for BIONUMERICS e SQL Native Client 10 0 Configuration Figure 7 3 The SQL Server Configuration Manager tool 71 Windows Firewall with Advanced Secur
93. server localhost gt lt property netkey_server_port 1080 gt lt property netkey config port 1080 gt lt property netkey_refresh_rate 30 gt lt property desktop shortcut 1 gt lt feature gt lt feature display_name Install Database Engine gt lt property enable remote access 1 lt property restart sql server_service 0 gt lt property user database directory C Program Files Microsoft SQL Server MSSQL10_ 50 BNSOFTWARENAME MSSQL gt lt property sysadmin_group CN Domain Users CN Users DC domain DC local gt lt feature gt lt property log dir C Program Files x86 Applied Maths BnSoftwareName 7 SetupLogs gt lt property install dir C Program Files x86 Applied Maths BnSoftwareName 7 0 gt lt property database home _dir C Users Public Documents BnSoftwareName Data gt lt property registered user user name gt lt property registered organization organization name gt lt property license string license string gt lt feature display name Microsoft SQL Server 2008 R2 Native Client gt feature display name Microsoft System CLR Types for SQL Server 2008 R2 gt feature display name Microsoft SQL Server 2008 R2 Shared Management Objects feature display name HPC Pack 2008 MS MPI Redistributable Package feature display name Install sample database feature display name Install sample and tutorial data gt feature display name Install Sentinel drivers
94. st after the NetKey server program feature has been installed If the NetKey sub folder in the Applied Maths common application data folder already contains a NetKey _CONFIG txt file then the Setup will call the WMI_ServiceStart function to start the NetKey service The NetKey_UnInstalling event handler function is called by the Setup just before the NetKey server pro gram feature is removed from the target system This process will first call the WMI ServiceExists function to verify if the NetKey service exists If the service exists then the Setup will check if the path of the service executable matches the program folder configured for the current instance If both paths are equal then the function will call WMI_ServiceStop to stop the NetKey service If the running NetKey service is installed in a different folder then the program folder of the current BioNumerics instance then the service will not be stopped The NetKey_UnInstalled event handler function 1s called by the Setup just after the NetKey server pro gram feature has been removed This process will first call the WMI_ServiceExists function to verify if the NetKey service exists If the service exists then the Setup will check if the path of the service executable matches the program folder configured for the current instance If both paths are equal then the function will call the built in ServiceRemoveService InstallShield function to remove the NetKey service If the run
95. stem32 cmd exe CiN gt ed C Program Files x86 gt Applied Maths BioNumerics C Program Files x86 gt Applied Mathsx BioNumerics gt bn exe_ Figure 6 1 Running BioNumerics from the command line When the executable is called without any options the program will open the last opened database as read from the Windows registry However the flexibility associated with running BioNumerics from the command line comes with the additional options that can be specified Following is a list of available options with their values e database lt DBNAME gt The BioNumerics database that will be opened lt DBNAME gt is the name of the database folder without the path e homedir lt HOMEDIR gt The BioNumerics home directory lt HOMEDIR gt is the full path to the home directory e bnuser lt USERNAME gt The BioNumerics database user e bnpwd lt PWD gt The password for the specified database user e licensestring lt LIC gt The license string see 4 3 needed to activate the software license e runbnstart 0 1 Whether or not the startup program should be ran after the main program is closed e logfile Allows to specify a custom log file different from the default BNLOG TXT The custom log file needs to reside in the BioNumerics home directory 68 6 Command line options e id ID The ID which should be written in the protection dongle e script lt PATH gt Runs a script and does not open the Main wind
96. talling Protection Keys 8 Click lt Finish gt to save the protection key request file Choose whether you want to activate a license or transfer an activation Automatic activation requires active internet connection Manual activation Figure 3 27 Transfer activation Transfer activation Select the appropriate transfer step NetKey is running on the source computer Step Step 1 Create request file Destination computer Step 2 Create transfer file Source computer Step 3 Apply transfer file Destination computer Figure 3 28 Transfer activation The second step 1s creating the protection key transfer file on the source computer 1 Copy the protection key request file from the target to the source computer 2 Start the NetKey configuration tool on the source computer 3 Select Licenses in the left pane select the license string 4 Click the lt Activate gt button 33 5 Select Transfer activation in the Activate Hasp license dialog see Figure 3 27 and click lt Next gt 6 In the top Computer section select NetKey is running on the source computer 34 3 Installation procedure se ep ce T Create request file Create a transfer request file on the destination computer Request file Browse Note the created request file should be transferred to the source computer where it can be used to create a transfer file Step 2 Figure 3 29 Create request
97. the InstallShield installation script It is not intended to provide a detailed description of all functions implemented in the installation script The BioNumerics installation process can be divided into three main blocks the initial dialog sequence the feature installation or removal processes and a final sequence running a cleanup process and showing the finish dialog A subset of dialogs D1 to D9 is displayed during the initial dialog sequence when the Setup is running in normal non silent mode Next the OnMoveData process will install the selected features and uninstall the de selected features The Setup will call the appropriate functions for each feature that is being installed or removed feature Installing and lt feature gt _Installed during installation and lt feature gt _UnInstalling and lt feature gt _UnInstalled dur ing removal Each lt feature gt _ feature function will either call the FeatureStart or the FeatureEnd function to create the feature node in the Setup log XML file with the proper time stamp elements The feature nodes contain the information warning and error messages for a specific feature In normal non silent mode the final sequence will display the finish dialog The CleanUp function will display the Setup log file in Internet Explorer if warning or error messages were written to the Setup log file 5 2 Setup dialog list The following table lists the dialogs that are displayed during a normal Setup
98. ting a new BioNumerics database Figure 7 6 In this case the full SQL Server instance name for the BioNumerics database engine will be formatted like lt Computer Name gt lt SQL Instance Name gt lt TCP port number gt For example e LOCALHOST BioNumerics 49191 e SQLSERVERI domain local BIONUMERICS 1445 72 7 Granting access to BioNumerics databases This wizard will help you create an ODBC data source that you can use to connect to SQL Server What name do you want to use to referto the data source Name Database How do you want to describe the data source Description BioNumerics SQL Database Which SQL Server do you want to connect to Server LOCALHOST BIONUMERICS 49191 Figure 7 6 Creating a new data source
99. tion Manual activation D Transfer activation NetKey Config must be run locally Figure 3 24 Activate Hasp license 3 4 3 2 Automatic Activation It 1s recommended to activate the software lock SL key using automatic activation This requires an active internet connection on the computer running the NetKey configuration tool Note that the SL key can only be activated once however it is possible to transfer the lock to a different computer afterwards see 3 4 3 4 Click lt Next gt to display the Customer details dialog and enter the contact person s name email address and organization name you want to use the register the software activation If possible please use the contact details of the person who ordered the software at Applied Maths NV Activate Hasp license Customer details Please enter the required customer details First name Last name Email Company Note fields with an asterisk are mandatory Figure 3 25 The Customer details dialog Click lt Finish gt to start the activation process The NetKey configuration tool will connect to a secured license server to check if there is a SentinelHasp soft lock protection key available for the entered license string If a protection key is available the NetKey configuration tool will connect to a secured activation server to upload a fingerprint of the NetKey computer and subsequently download and install the cor r
100. to a Setup INI XML file This file will be saved to the SetupLogs sub folder of the BioNumerics installation directory The file name format is Setup_x_ini XML where x is a counter to make sure that the file name is unique in the SetupLogs folder Each time the Setup program has been launched and features were installed or removed a Setup INI XML file will be created The file will not be created if the Setup was canceled during the initial dialog sequence Please attach the Setup log and INI XML files to your e mail message when reporting Setup issues to the Applied Maths help desk After a manual installation of BioNumerics the Setup INI XML file can subsequently be used to perform silent installations see 3 6 20 3 Installation procedure 3 2 Updating a BioNumerics instance 3 2 1 Welcome dialog 3 2 1 1 Updating a 6 1 or older instance of BioNumerics If no existing BioNumerics 6 5 or later instances were detected and an older version of BioNumerics was already installed then the update Welcome dialog box will be displayed when launching the Setup exe cutable see Figure 3 12 The Welcome dialog box will show the version number of the installed instance of BioNumerics and the version that is included in the Setup package Click lt Next gt if you want to update the existing version If you enter the installation directory of the currently installed version in the Choose Destination Location dialog box then the older version will be
101. to be installed on the computer that you want to use to run the software Please note that a permanent and stable internet connection is required to run the internet license e In case of a network license the Application software needs to be installed on the computers in the network that you want to use to run the software Install Database Engine e Checking this option will install the BioNumerics instance of Microsoft SQL Server 2008 R2 Express SP1 Database Engine The location of the data files can be specified in the next step Install sample database and Install sample and tutorial data e The Sample database and Sample and tutorial data that are contained in the Setup package are used in the manual to illustrate the features of the software Selecting these features will install the Sample database and Sample and tutorial data in the BioNumerics home directory that is specified in the Choose Destination Location dialog box see Figure 3 6 Install Sentinel drivers The Install Sentinel drivers feature will install version 7 5 7 of the Sentinel System Driver In addition this feature will also install the Sentinel Run time Environment previously known as HASP version 6 51 if the NetKey server program feature has been selected for installation The Sentinel Run time Environment will not be installed if a standalone license string was entered in the Customer Information dialog box e In case of a standalone license the Sentinel dri
102. try or InstallShield log file e Read the Setup INI XML file and check if the file contains a valid license string The Setup will run in silent mode if the license string is valid The Setup will abort if a Setup INI XML file has been specified using the ini command line parameter and the file does not contain a valid license string e Read the paths of the Setup log installation and home directories from the Setup INI XML file e Read the requested features listed from the Setup INI XML file The NetKey feature will only be available for installation if a valid network license has been specified in the Setup INI XML file 5 3 3 Write global variables The WriteGlobalVariables function will save the paths of the Setup log installation and home directories to the Setup INI XML object if the Setup is running in normal non silent mode This function will also save the registered user and organization names and the license string to the Setup INI XML object 5 3 4 Save Setup INI XML file If the Setup is running in normal non silent mode the XML_Savelni function will save the contents of the INI XML object from memory to the Setup INI XML file 5 3 5 Read requested features In silent mode the ReadGlobalVariables function will read the requested features listed in the Setup INI XML file The NetKey server program feature will only be available for installation if a valid network license has been specified in the Setup INI XML file
103. tten permission of the authors Copyright 1998 2014 Applied Maths NV All rights reserved BioNumerics is a registered trademark of Applied Maths NV All other product names or trademarks are the property of their respective owners BioNumerics includes the Python 2 6 release from the Python Software Foundation http www python org and a library for XML input and output from Apache Software Foundation http www apache org The BLAST sequence search tool is based on the NCBI toolkit version 2 2 10 http www ncbi nlm nih gov BLAST Chapter 1 Introduction 1 1 Purpose The purpose of this document is to provide understandable and detailed information on how to install the various features of BioNumerics These features include the application software sample and tutorial data the NetKey server program and the Sentinel drivers 1 2 Target audience The target audience for this document is anyone who is responsible for installing and configuring BioNu merics or the NetKey licensing server program This document assumes that the person who will install BioNumerics or the NetKey service has a basic knowledge on how to administer a Windows client com puter 1 3 Overview The BioNumerics Setup program is an InstallShield installation wizard that allows a person with Adminis trator privileges to install the BioNumerics application or the NetKey licensing server program on a target computer In addition the Setup pr
104. uration s 700000 500000 300000 200000 100000 Total 4 A E LAB1 LAB2 LABS LABI LAB2 LABS ABCD 82FP 234N 2N8V VVHP UR99 XYZQ 82XP 134N 2N9V WWHP UP99 Lic v Lab v B Total Currently usage times are expressed in absolute values seconds but we can change the display setting for the Sum of Duration s to relative values 10 6 Right click on the Sum of Duration s cell and choose Show values as gt of Parent Total with the base field Lic 10 7 You can then easily add a Cost column to this PivotTable and see the respective value per lab per license see Figure 4 20 4 10 Usage statistics A B C 1 Row Labels v Sum of Duration s Cost 2 ABCD 82FP 234N 2N8V VVHP UR99 100 00 350 00 3 LAB1 33 79 118 26 4 LAB2 38 63 135 22 D LAB3 27 58 96 53 6 XYZQ 82XP 134N 2N9V WWHP UP99 100 00 500 00 7 LAB1 34 28 171 40 8 LAB2 38 36 191 80 9 LAB3 27 36 136 79 10 Grand Total Figure 4 20 Calculated license costs per lab and per license 57 58 4 NetKey configuration Chapter 5 Installation process 5 1 Overview The purpose of this chapter is to provide a general technical explanation on the Setup behavior and a basic Setup flow diagram of the installation processes This chapter contains a partial list of the main functions that are applied in
105. use to run the software Please note that a permanent and stable internet connection is required to run the internet license 3 2 Updating a BioNumerics instance 23 Installation director C Program Files x86 Applied Maths BioNumericd w Create a BioNumerics shortcut on the desktop C n Common Documents C Users Public D ocuments BioNumerics D ata Databases installed here will be Milo to all local users D f C In My Documents i CAUsers Jil APPLIED MAT entsiBioNumericsiD ata Jill or cessible to the current user CAUsersiPublic DocumentsBioNumericsD ata I Figure 3 16 The Choose Destination Location dialog box Select the features you want to install and deselect the features you do not want to install Y Install application software IM Install Database Engine Select this feature to install the ViInstall sample database BioNumerics application Vi Install sample and tutorial data software Install Sentinel drivers Y Install NetKey server program 4 Pd p 724 53 MB of space required on the C drive 14061 05 MB of space available on the C drive Figure 3 17 The Select Features dialog box e In case of a network license the Application software needs to be installed on the computers in the network that you want to use to run the software Install Database Engine e Checking this option will install the BioNumerics instance of Microsoft SQL Server 2008 R2 Express SP1 Database Engine
106. vers need to be installed on each computer that you want to use to run the software e In case of an internet license you only need an internet connection to run the software The Install Sentinel drivers option does not need to be checked e In case of a network license the Sentinel drivers only need to be installed on the NetKey server computer in the network Install NetKey server program e The NetKey server program feature will only be visible and available for installation if a network license string has been entered in the Customer Information dialog box see Figure 3 4 The NetKey server program feature must only be installed on the computer in the network where the hardware security key will be connected to A message will appear when selecting the Sentinel drivers feature and the minimum required version is already installed see Figure 3 8 3 1 Installing a new BioNumerics instance 17 A This feature can not be selected SL The Sentinel drivers are already installed Figure 3 8 Sentinel drivers are already installed Properties Data Files location and Remote Access SOL Data Files Location n Program Files C Program Files Microsoft SQL Server MSSQL10_50 BIONUMERICS MSSGL C n Database Home Directory C Users Public D ocuments BioNumerics D ata MSSQL10_50 BIONUMERICS C Custom c Program Files Microsoft SUL Server MSSQL1 0_50 BIONUMERICS AMSSOL Available disk space 174917 54 MB ic

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