Version 2.2, January 16, 2013
Contents 1. Introduction... 3 1.1 Requirements of Client PC... 3 1.2 Flow Chart of Client PC Setup... 4 2. Setting of Windows OS... 5 2.1 Setting to Display File Type Extension (Mandatory)... 5 3. Setting of Web browser... 6 3.1 Change Pop-up Blocker Settings (Mandatory)... 6 3.2 Enable Java script (Mandatory)... 6 3.3 Permit Cookies (Mandatory)... 6 4. Setup of Java... 7 4.1 Verify Java Version... 7 4.2 Download of Java... 7 4.3 Installation of Java... 8 5. Setup of Mass++... 9 5.1 Confirmation of Data Management Software... 9 5.3 Installation of Mass++... 11 5.4 Initial Setting of Mass++... 18 5.4.1 Setting of Proxy... 18 5.4.2 Setting of MassBank... 19 6. Setup of Record Editor... 20 6.1 Download of Record Editor... 20 6.2 Decompression of Record Editor Archive File... 21 6.3 Security Setting of Microsoft Excel... 22 Part3-2
1. Introduction This manual illustratively shows the procedure to set client PCs up. MassBank records and manages user s MassBank data on data server. This PC generates and edits user s Client PC is not a specific but an ordinary PC. Ordinary PCs become client ones by installing necessary software and by setting a specific environment up. 1.1 Requirements of Client PC Client PCs should be operated on Microsoft Windows OS. The following hardware is recommended and software is required. Category Subcategory Requirements Hardware CPU Main memory HDD Dual or more core processor and 2 GHz or higher. 1 GB or more 1 GB or more and 5,400rpm or higher. OS (*1) Windows XP Vista 7 Web browser (*1) Internet Explorer 6 or later, or Firefox 2 or later. Excel (*1) Microsoft Excel 2007 2010 Software Data management tools (*1),(*3) Xcalibur MassLynx Analyst etc. Java (*2) JRE(Java Runtime Environment)5.0 or later Mass++ (*2),(*4) Record Editor (*2) 2.1.0 or later 2.1.0 or later Others User accounts Administrator privilege *1 They should have been installed on PC. *2 They would be installed in this manual. *3 Mass++ requires these tools to input raw data. *4 Mass++ is software that inputs raw data and outputs MassBank records. Part3-3
1.2 Flow Chart of Client PC Setup Chap 2. Setting of Windows OS - Display of file type extension Chap 3. Setting of Web Browser - Setup of pop-up blocker, Java script, and Cookie Chap 4. Setup of Java - Installation of Java Chap 5. Setup of Mass++ - Data management tools - Setup of Mass++ Chap 6. Setup of Record Editor - Setup of Record Editor - Security setting for Excel macro Part3-4
2. Setting of Windows OS Default settings of Windows OS should be modified. 2.1 Setting to Display File Type Extension (Mandatory) File name extension should be displayed. << On Windows 7 >> (1) Click Control panel on the start menu. (2) Select category in View by, then Small icon. (3) Click Folder Options from the list. (4) Select Display tab in the Folder Options window. (5) Remove the check of Hide extensions for known file type, then click OK. << On Windows XP >> (1) Click Control panel on the start menu. (2) Click Change Windows to Classic View. (3) Click Folder Options from the list. (4) Select Display tab in the Folder Options window. (5) Remove the check of Hide extensions for known file type, then click OK. Part3-5
3. Setting of Web browser Web browsers should be set up so that users could access to MassBank data servers. 3.1 Change Pop-up Blocker Settings (Mandatory) Pop-up from the following URLs should be permitted. [1] Open Internet browser. [2] On the Tools menu, point to Pop-up Blocker, and then click Pop-up Blocker Settings. [3] Type the address (or FrontServer URL) of the following sites in the Address of Web site to allow box, and then click Add. - http://www.massbank.jp/ - http:// Host name of the front server /MassBank/ (See 3.2 Initial Setting of MassBank in Setup of Data Server or 3.1.3 Change of Home Page URL in Setup of In-House Data Server ). More about pop-up blocker, visit the Microsoft page (http://windows.microsoft.com/en-us/windows7/intern et-explorer-pop-up-blocker-frequently-asked-questions). 3.2 Enable Java script (Mandatory) Java script on the internet browsers should be enabled. << Example: Internet Explorer >> [1] Click Tools in the menu bar, then click Internet Options. [2] Select the Security tab. [3] Select Internet in the Web content zone, and click the Custom Level,,,, button. [4] On the Security Setting window, enable Scripting of Java applets, Active scripting, and Allow paste operations via script. [5] Click OK on the Security Setting window. If warning is displayed, click OK. [6] Click OK on the Internet Option window. [7] Close the internet browser, then restart PC. 3.3 Permit Cookies (Mandatory) Cookies on the internet browser should be permitted. << Example: Internet Explorer>> [1] Click Tools in the menu bar, then click Internet Options,,,,. [2] Select the Privacy tab in the Internet Options window, then click the Advanced,,, button. [3] Check Override automatic cookie handling on the Advanced Privacy Setting window. [4] Accept First-party Cookies and Third-party Cookies. [5] Check Always allow session cookies. [6] Click OK on the Advanced Privacy Settings window. [7] Click OK on the Internet Options window. [8] Close the browser and restart PC. Part3-6
4. Setup of Java Java Runtime Environment (JRE) is required when client PCs access to data server to view the data and when Record Editor acquires values from KEGG. The following is an example of downloading, installing and setting of the Java version 6 update 31. The latest version of JRE is recommended. 4.1 Verify Java Version Check to ensure that you have the latest version of Java installed on your PC on the Web site (http://www.java.com/en/download/installed.jsp). When it is the latest, skip Sections 4.2 and 4.3 4.2 Download of Java Download the JRE from the Web site (http://www.java.com/en/download/ ) and install it on an internet browser. The following example shows the procedure of Java installation and setup on Internet Explore 9, though the procedure is dependent on the version of the internet browser. Click Free Java Download. Click Agree and Start Free Download. Click Save to store the download on the desktop or other folder. Part3-7
4.3 Installation of Java Double-click the Java install file to start the installation. Because the installation is dependent on the version of Java to be installed, see more details on the site (http://www.java.com/en/download/help/download_options.xml). Click Install. Wait until the installation is completed. Click Close. When Restart browser or Restart PC message appears, restart that. * You are highly recommended uninstall all older versions of Java from your system. Keeping old and unsupported versions of Java on your system presents a serious security risk and impedes the PC performance. To remove the older versions, see the page http://www.java.com/en/download/uninstall.jsp. Part3-8
5. Setup of Mass++ Mass++ imports raw data, and generates and outputs MassBank records that are ready for the import by Record Editor. In this section, setting procedure of Mass++ V.2.1.0 (32 bit version) is shown as an example. Mass++ is software for proteomics and metabolomics analysis to solve or compensate for the problems of conventional software supplied with mass spectroscopes. It is a free software that Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Co. and Eisai Co. Ltd. have been developing. For the details of the software, see the Web page (http://www.first-ms3d.jp/english/achievement/software/1130.html). 5.1 Confirmation of Data Management Software Mass++ is able to import various types of raw data that are analyzed and stored on data management tools attached to mass spectrometers. For the functionality, Mass++ should be installed with data management tools on the same client PC. On the client PC in advance, users should install data management tools under the license from the vender. Data management tools are dependent on vendors of mass spectrometers. They should be installed on the client PCs before Mass++ installation. XCalibur with MSFileReader from Thermo Fisher Scientific For more details, see http://sjsupport.thermofinnigan.com/public/detail.asp?id=703. Analyst QS from Applied Biosystems MassLynx from Waters LCMS Solution with DataExport module from Shimadzu Part3-9
Part 3: Setup of Client PC 5.2 Download of Mass++ Download Mass++ from the web page (http://www.first-ms3d.jp/achievement/software/). [1] Mass++ Web page [2] Click the download link. [3] Input your mail address. [4] Click Accept when you agree with the software license agreement. *** Mass++(Ver.2) download information *** Thank you for requesting to use Mass++(Ver.2). Click on the following URL to download the software. http://www.first-ms3d.jp/download?em=massbank@iab.keio.ac.jp Your support is much appreciated. [5] Download URL is notified by email. --------------------------------------------------------- * Funding Program for World-Leading Innovative R&D on Science and Technology * "Development of the next generation mass spectrometry system and contribution toward drug discovery and diagnostics" project Mass++(Ver.2) development team Please send your questions or requests to us from the following webpage. http://www.first-ms3d.jp/english/mass2-contact --------------------------------------------------------- [6] Click the link to start the download. Part3-10
5.3 Installation of Mass++ Install Mass++ on the client PC. Mass++ requires the following software; Microsoft Visual C++ 2008 and 2010 Redistributable Packages, and Microsoft.NET Framework 4. When they are not installed on the client PC, they are automatically installed. [1] Extract the zip file you just downloaded (Masspp2_1_0-x86.zip). Folder Masspp2_1_0-x86 is created. [2] To launch the installer, open the folder Masspp2_1_0-x86. Run the installer Masspp2_1_0-x86.exe. When User Account Control warning dialog or the following dialog box appears during the installation, click OK or Run to continue. Click Next to continue. [3] Read the License Agreement. [3] Click Next as you accept the license agreement. Part3-11
[4] Specify the destination location. [4] Click Next to continue. [5] Select the components. [5] Select Full Installation. Click Next. When the following dialog window appears, click OK to continue. [6] Select the start menu folder. [6] Click Next to continue. Part3-12
[7] Create the desktop icon. [7] Check Create. Click Next to continue. [8] Confirm the settings for the installation. Click Install to start the installation. [9] Installing page. Indicator shows the installation progress. Wait until the installation is complete. Part3-13
The following procedure [10] to [12] is not shown when Microsoft Visual C++ 2010 x86 Redistributable Package was installed on the client PC. [10] Installation of Microsoft Visual C++ 2010 x86 Redistributable Package Check I have read and accept the license terms. to the license agreement. Click Install to start the installation. [11] Installing page Indicator shows the installation progress. Wait until the installation is complete. [12] Installation is completed. Click Complete. Part3-14
The following procedure [13] to [16] is not shown when Microsoft Visual C++ 2008 Redistributable Package was installed on the client PC. [13] Installation page of Microsoft Visual C++ 2008 Redistributable Package Click Next. [14] License terms and installation of Microsoft Visual C++ 2008 Redistributable Package Check I have read and accept the license terms., then click Install to start the installation. [15] Installing page Indicator shows the installation progress. Wait until the installation is complete. [16] Installation is completed. Part3-15
Click Finish. The following procedure [17] to [19] is not shown when Microsoft.NET Framework 4 was installed on the client PC. [17] Installation page of Microsoft.NET Framework 4 Check I have read and accept the license terms., then click Install to start the installation. [18] Installing Indicator shows the installation progress. Wait until the installation is complete. Part3-16
[19] Installation is completed. Click Finish. [20] Installation of Mass++ is completed. Click Finish. Part3-17
5.4 Initial Setting of Mass++ Initial setting is necessary to use the Mass++ functions. Mass++ is configured once, the setting is saved for the later uses. 5.4.1 Setting of Proxy On generating the MassBank record, Mass++ accesses MassBank on the internet by using API. It is often the case in institutions that users connect to the internet through proxy servers. Such users have to set up their proxy configuration. Network administrators show the users the URL, IP address, port, user ID and password of proxy servers. When no proxy server is used, skip the proxy setting. [1] Select Tools from the menu, then click Options. [1] Options Dialog Window appears. [2] Select Setting, Network, then Proxy. [2] [3] [4] [5] [6] [7] [3] Input URL or IP address of the proxy server. [4] Input the port number of the proxy server. [5] Input the user name who uses the proxy server. [6] Input the password. [7] Click OK to finish. The values shown in the figure are examples. [8] Restart Mass++. Restart Mass++ when you modified the proxy settings. Part3-18
5.4.2 Setting of MassBank This section shows the setting for generating MassBank records on Mass++. [1] [1] Select Tools from the menu bar, then Options. [2] Select Settings, Search Engine, then MassBank, [3] Input MassBank URL http://www.massbank.jp/ [4] Check Use Proxy when proxy server is used (see the section 5.4.1 Setting of Proxy ). [2] [4] [3] [5] [6] [7] [5] Input the author names to Authors. They are the value of the AUTHORS: field in the MassBank record (see the section 2.1 MassBank Record in Part 4 Data Preparation ). [6] Input the copyright of the MassBank record (see the section 2.1 MassBank Record in Part 4 Data Preparation ). [7] Click OK to finish. The values shown in the figure are examples. Restart Mass++ when you modified the proxy settings. Part3-19
6. Setup of Record Editor Record Editor is a Excel-based tool for the users who manually generate and edit MassBank records. Each MassBank record is a text-format file that describes the data of one mass spectrum. By adding the chemical information of chemical compounds on Record Editor, users complete their MassBank records (recdata.zip and moldata.zip) that are ready for the upload to the MassBank data servers (see the sections 2.1 MassBank Record and 2.2 Chemical Structure Data in Part 4 Data Preparation ). Microsoft Excel 2007 or 2010 and Java should be installed with Record Editor on the PC (see the chapter 4. Java setting ). 6.1 Download of Record Editor An archive of Record Editor is downloadable from the MassBank Web site (http://www.massbank.jp/en/download.html). [1] [2] [1] Click massbank-record-xxx.zip to download. [2] Save the archive temporally on the desktop. Part3-20
6.2 Decompression of Record Editor Archive File Unzip the Record Editor archive file massbank-record-xxx.zip on the desktop. The archive file of Record Editor does not function as Record Editor because Record Editor uses macros. [1] [1] Right-click massbank-record-xxx.zip, then click Extract All. [2] [2] Change the destination to desktop. [3] Uncheck Show extracted files when complete. [3] [4] Click Extract to start the decompression. [4] [5] [5] Double-click the folder massbank-record-xxx to confirm Record Editor. RecordEditor.xlsm is Record Editor. It is a book file using macros that functions on Microsoft Excel 2007 and 2010. RecordEditor2003.xls is for the use on Microsoft Excel 2003. Although it has the same functions as RecordEditor.xlsm, their availability is less by the functional restrictions of Microsoft Excel 2003. Thus this manual does not describe about the setting of RecordEditor2003.xls. Part3-21
6.3 Security Setting of Microsoft Excel Record Editor contains macros. Excel2007 or Excel2010. To use them, users have to set the security of Microsoft <<Excel 2007 >> [1] Launch Excel2007 from the Start menu. [2] Click Microsoft Office button, then Excel Options. [1] [2] [3] Click Trust center, then Trust Center Settings. [3] Part3-22
[4] Click ActiveX Settings, then select Prompt me before enabling all controls with minimal restrictions. [5] Click Macro Settings, then select Disable all macros with notification. [6] Close all the windows by clicking OK and terminate Excel. - Macros setting are enabled after Excel is restarted. Part3-23
<<Excel 2010 >> [1] Launch Excel2010 from Start menu. [2] Click File tab, then Options. [2] [3] Click Trust Center, then Trust Center Settings. [3] Part3-24
[4] Click ActiveX Settings, then select Prompt me before enabling all controls with minimal restrictions. [5] Click Macros Settings, then select Disable all macros with notification. [6] Close all the windows by clicking OK and terminate Excel. - Macros setting are enabled after Excel is restarted. Part3-25
Contact Please contact the MassBank Group if you have any problems, questions, and suggestions. massbank@iab.keio.ac.jp +81-235-29-0800 http://www.massbank.jp/