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Installing Sci2

Q: I am having trouble installing and running Sci2. 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 or newer. If you are having trouble installing Sci2, you may want to install the latest version of Java. 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 version of Java You will want to target the javaw.exe file – which is likely located in the C:\Program Files\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:

 

-vm
C:\Program Files\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.

Loading Data

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

 A: Web of Science recently changed the format for their data. Try updating your version of Sci2 to the newest, v1.0 alpha. Also, see the page about the ISI format, which includes a work-around for loading ISI data in older versions of the tool.

Network Extraction

Q: How are networks extracted from my data?

A: First a data set is loaded into Sci2. This tool can handle a variety of different data formats, to see all the data formats supported by Sci2 check the data formats section of our documentation.  Now, once a data set has been loaded, it can be viewed as a comma separated value (CSV) file. Simply right click on the table icon in the data manager of Sci2 and view the table in the spreadsheet program of your choice.

Once loaded into Sci2, all data assume the table format. In the CSV file pictured above, each column head represents a different attribute of the network and each row represents a node in the network. For example, if a directed network were to be extracted from the table above with a target column of Award Number and a source column of NSF Organization

Then the resulting network visualization will look like this:

Note, the above network was generated in Sci2 and then opened in Gephi, where the color and labels were added.  Sci2 v1.0 alpha supports a bridge to Gephi

 

In the network above, the green nodes represent the NSF organizations in this data set and the blue nodes represent the awards (labeled by award number) associated with those NSF organizations. You will notice that since the NSF organization was selected as the source node, each organization is represented in the network only once, while it may appear multiple times in the original data set. This is because each row in the data set is associated with a specific award, the target in this extraction. In some cases this is a one-to-multiple relationship and in others a one-to-one, depending on how many awards are associated with a particular organization. This is an example of just one type of network that can be extracted from data loaded into Sci2. You can create your own data set in Excel or any other spreadsheet program, save the data as a CSV (*.csv) file, load it into Sci2, and perform a variety of analyses and visualizations.

You can also practice with the variety of sample data sets located here.  It is highly recommended that you follow the sample workflows provided on this documentation wiki.

 

Q: I am trying to extract a network by using more than two attributes of the data set as input parameters in a network extraction algorithm. Is this possible?

A: Yes, often times you will want to have multiple attributes available in your network extraction. For example, you may want to extract a directed network from NSF principle investigators (PIs) to their awards and size the award nodes by amount awarded. However, you will notice the Extract Directed Network algorithm only allows for two input parameters: source column and target column. More attributes can be added to the network by using property files (aggregate function files). These are simple text files that can be added to many network extractions to aggregate data, allowing you to have more than two attributes in a network with one extraction. More information, including how to create your own property files, can be found here.

 

Q: While trying to extract a network from a CSV file and using a comma “,” in the text delimiter field I got an error.

A: The parameter field will not accept a comma. This is due, in part, to the Prefuse library that was created back in 2006 and the CSV parser is still not able to handle a comma in the same column. You can simply use a “;” or a “|” instead. If your data set contains many commas consider opening the file in Excel and using a macro to replace the commas with another acceptable symbol.

Database Functionality

Q: Is there database functionality for Sci2 v1.0 alpha?

A: Currently, there are ISI, Medline, and Scopus databases for Sci2 v1.0. However, the database plugin not ready for release yet. We need another sprint to get them ready. However, the plugin that allows files to be loaded as databases is available for Sci2 v0.5.2 alpha or older. Be sure to check the Sci2 news page for updated information on current and upcoming releases of the tool. https://sci2.cns.iu.edu/user/news.php

Global Level Studies - Macro

 Q: I am interested in visualizing some of my geospatial data, but I only see a world map and a U.S. map. Are there country-specific maps on which I can overlay a country-specific geospatial network? 

A: Unfortunately the U.S. map and the world map are currently the only maps we have available.  However, if you would like to submit a feature request it can be done by visiting the Sci2 development page. https://sci2.cns.iu.edu/user/developer.php

Saving and Visualizing Networks

Q: GUESS is taking a very long time to visualize my network. Is there any way to speed up this process? 

 A: Unfortunately GUESS only uses one core in the CPU instead of multiple and this means visualizing large networks can take some time. Since GUESS is a third party visualization tool supported by Sci2 we don’t have control over how many cores are used in processing. However, the latest release, Sci2 v1.0 alpha, supports Gephi (http://gephi.org/) a visualization tool that handles large networks well. For more information see our documentation on Gephi.

 

Q: I saved my visualization as a Postscript file, but I am having trouble converting the Postscript file to a PDF so it can be viewed. 

A: Converting Postscript files can be tricky. If you have a version of the Adobe suite (or the Pro version of Adobe Acrobat) installed on your machine, the converter will come pre-installed. However, there are also some free options available for postscript conversion: Ghostscript and GSviewer. Ghostscript is a PostScript interpreter, and GSview is a graphical interface for Ghostscript; you can download both from Ghostscript, Ghostview and GSview. Both are freeware. The GSview/Ghostscript combination is capable of  opening PostScript level two files, which are the type generated by Sci2. See the following web page for a useful tutorial on how to install Ghostscript: http://pages.cs.wisc.edu/~ghost/doc/gnu/7.05/Install.htm


Q: I am having trouble entering commands in the Interpreter.

 A: Typing commands into the Interpreter can be tricky, but once you learn it can be an extremely powerful way to manipulate a network visualization. Here a few common mistakes to avoid:

  1. After typing a ":" you will need to hit "enter" and "tab" to start the new line, followed by another "enter" to execute the command. This is most common in the following scenario:
     

    >for n in g.nodes:
         n.strokecolor = n.color
  2. When you type an command in the interpreter you do not need to type ">" to begin, simply begin with the text of your command. To learn more about how to manipulate network visualizations see our documentation on GUESS.

Q: I load the network into GUESS but no node is showed 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.

*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

 

Don't see what you are looking for in Sci2?

Development services can be performed by our team. You can submit a feature request at the Sci2 by visiting the Sci2 web site: https://sci2.cns.iu.edu/user/developer.php. Also, development services can be performed for a fee, prices vary according to the scope of work. Previous paid development/services performed by our center have included evaluation and monitoring, data compilation, visual interfaces for community data, VIVO researcher networking, and consulting/training services. To get an estimate for your project contact our center:  http://cns.slis.indiana.edu/


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