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Table of Contents

Installing Sci2

Windows

Q: I am having trouble installing and running Sci2 on a Windows PC. What should I do?

A: One common problem when initially installing Sci2 is not having a current version of Java. Sci2 runs on Java 1.6 (32 bit) or newer. If you are having trouble installing Sci2, you may want to install the latest 32 bit version of Java. Make sure you install the 32 bit version, as Sci2 will only run with a 32 bit version. You can run 32 bit and 64 bit versions of Java simultaneously. If you have the latest version of Java installed, but is not being detected by Sci2, you can tell tool specifically where to look for the newer must specify the correct path to be used by the tool to locate the correct version of Java. You will want to target the javaw.exe file – which is likely located in the C:\Program Files (x86)\Java\jre7\bin directory, assuming you have installed Java in the default place.

 Now, you will have to tell Sci2 to look in this directory. In your Sci2 installation, open sci2.ini (with Notepad or any other plain text editor), delete the contents, and replace them with this:

 

Code Block
-vm
C:\Program Files (x86)\Java\jre7\bin\javaw.exe
-vmargs
-Xms15m
-Xmx350m

If you're installation of Java is located in another directory on your system, you'll need to replace the path to javaw.exe with the one you find on your system. Save the file in the Sci2 installation and you should be able to start the tool.

Q: I am having trouble running Sci2 on a Windows, I received an error message that starts with, "Java was started by returned exit code=13". What should I do?

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A: The error message that you have received is caused by trying to run Sci2 with the incorrect version of Java required by the tool. For example, if you download the 64-bit version of Sci2, but only have a copy of 32-bit Java installed on your computer, Sci2 will try to run but it will produce this error. To solve this problem, you will need to verify the version of Java installed on your computer.

If Sci2 fails to run, and you find that Java is installed in the Program Files (86x) directory, then you have 32-bit Java installed and need to install 64-bit Java. Likewise, if Java is installed in the Program Files directory, hen you have 64-bit Java installed and need to install 32-bit Java.You will need to either try downloading the appropriate 32-bit or 64-bit version of Sci2, or install the appropriate version of Java and make sure that Sci2's instillation file is updated with the correct path to the new version of Java,

Macs

Q: I am having trouble installing and running Sci2 on a Mac OS X Mavericks or later. What should I do?

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A: Recent updates to Apple's Mac OS X Mavericks have included security that prevent Sci2 from running on a machine if the program is not available from the Mac App store or an identified developer. To get Sci2 to run on your machine, you will have to change the system preferences. Instructions about how to update the Mac OS X's Gatekeeper are available at the Apple website (https://support.apple.com/en-us/HT202491).

Q: I am having trouble installing and running Sci2 on a Mac OS X Sierra. What should I do?

A: Sci2 users trying to install the tool on Mac OS X Sierra will first want to install the legacy edition of Java 6 for OS X 2015-001 (https://support.apple.com/kb/dl1572?locale=en_US).

After installation of the appropriate version of Java, You will need to update the Sci2.ini file

Code Block
-startup
plugins/org.eclipse.equinox.launcher_1.2.0.v20110502.jar
--launcher.library
plugins/org.eclipse.equinox.launcher.carbon.macosx_1.1.100.v20110502
-vmargs
-Xms256m
-Xmx1024m

After making the modification to the Sci2.ini file, to run the tool, you will need to use the unix-executable file to launch Sci2. The Sci2 Unix Executable file is found by selecting Control on the keyboard and then click Sci2 icon, which will show a drop down menu. In the menu select "Show Package Contents". Next, in the new directory, navigate to Contents>MacOS and select the file labeled "Sci2." Selecting this file will launch a terminal window and a separate tool window.

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Sci2 Locale Issues

Q: I am having trouble loading data into Sci2 and having trouble converting PostScript files to PDF files.

...

If you are working on a Mac, open System Preferences and choose Language and Text. Then go to the Formats tab and set the Region to the United States.

Loading Data

General Data Loading

Q: Does it matter that my data file has the same file format extension used in Sci2 documentation or may I just use the .txt and .csv extensions?

Sci2 documentation often references data formats through the use of file extensions (.isi, .nwb, .mat, .enw), which indicate the type of data being loaded into Sci2 for parsing. Yet often data are exported by other tools and and databases as files with the file extension .txt, which can indicate one of two possibilities: that the data are formatted as a tab separated columns; or that the data is for written in a machine readable format. For data saved as a Tab Separated format, you will need to convert these tables into CSV formats before you load these files into Sci2.

However, if the data is written in a Machine readable format, such as Web of Science (.isi) files and Endnote Export format file (.enw), Sci2 will parse data loaded with the .txt extension, provided that you know the correct data formatting used in the file. For example, when you export data from EndNote Web or Endnote desktop as the Endnote Export format, files are given the .txt extension. You may maintain this extension or change it to .enw. Changing the extension allows Sci2 to automatically read in the data without selecting the data format parameter. Whereas, by keeping the .txt file extension, you will have to select the parameter “Refer Scholarly format” when loading the data into Sci2.

ISI Format Loading questions

Q: I am having trouble loading an ISI file that I downloaded from Web of Science. What should I do?

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A: It depends on the data format, but there are some options for tidying up your data under the Preprocessing menu in Sci2. If you are working with a large dataset in CSV format, you may need to do a lot of the data cleaning prior to loading the file into Sci2. You can do a lot of this data cleaning in Excel or with Google Refine, an extremely useful program for cleaning data.

Q: The ISI data I downloaded was not formatted in the same way as those used in your workflows?

Web of Science provides researchers with two ways to gather citation data: Citation Lists are detailed article records that may be generated through the search interface or the marked list tool in; Citation Reports simplified citation information and a citation statistics for the articles selected by a user that can be exported into tabular formats. Citation List text files are the format used in our network analysis workflows; in particular, this format can be acquired with cited reference lists that are important creating citation networks and document co-occurrence networks. These types of records can be loaded into a Sci2 directly and they are reformatted by the Sci2 program into CSV files for further analysis. Instructions on how to download Web of Science Citation List records in this format can be found in the Data Acquisition portion of the manual.

Network Extraction

Q: How are networks extracted from my data?

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Q: I load the network into GUESS but no node is shown or the network is loaded without Graph Modifier panel.

 A: There are some attribute names are reserved in GUESS. The same attribute name in the data could cause conflict in GUESS. Rename the following attribute names in your data if exist. Then save the data and reload into Sci2. 

  • count
  • size
  • type

The following show sample data issues in NWB file format. Simply rename the attribute to size_d, type_d, count_d would solve the problem. See our documentation on GUESS to learn more about GUESS.

Code Block
*Nodes
id*int label*string size*float type*string count*int
1	"Amber" 4.0 "ellipse" 4
2	"Azizha" 4.0 "ellipse" 5
3	"Brend" 4.0 "ellipse" 6

 

Third-Party Plugins and Licenses

Q: What are the third-party plugins used by Sci2 and what are their terms of use?

A: Sci2 has been released under the Apache 2.0 license. Licenses for the various components used by Sci2 can be found under the "licenses" folder in your Sci2 installation directory.

The Sci2 v1.0 build released as of September 2013 will include additional third-party plugins :

  • Google Scholar Citation Reader
  • Bing Geocoder
  • Flickr Reader
  • Facebook
  • Twitter Reader

Each plugin as it's own data usage policy as dictated by it's license and terms of use:

  • Facebook plugin only allows users download their own data. For more information, see http://www.givememydata.com/.
  • Twitter Reader plugin allows users to download the tweets of any twitter user, however the user and the application have to first be registered and authenticated by the API before performing any queries. For more information please see: https://dev.twitter.com/terms/api-terms
  • Google Scholar Citation Reader will fetch data indexed by the Google Scholar search engine. For data usage policies please review the Google license.
  • Bing Geocoder plugin will require an authentication key (Basic Key or Enterprise Key). The usage policy depends on the type of key. For more information, see http://www.microsoft.com/maps/
  • Flickr Reader plugin downloads image URLs through REST service with API key without authentication. For more information, see see http://www.flickr.com/services/api/

Please note that if required all plugins can be uninstalled separately.


Q: Does Sci2 perform any encryption or utilize any encryption processes?

A : Sci2 by itself does not perform or use encryption, however plugins such as the Facebook plugin and the Twitter Reader plugin use encryption for user authentication and data downloads.

 

Q: Does Sci2 have ECCN?

 A : No, Sci2 does not have a ECCN

 

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