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NetCrafter Tutorial

1. Launching NetCrafter	1.1 Install NetCrafter on Windows
2. Main Functions of NetCrafter	2.1 Running NetCrafter
	2.2 Loading Data
	2.3 Visualization of Network
	2.4 Saving Data
3. Customizing Network - Control Panel	3.1 Scoring Method
	3.2 Node Labeling
	3.3 Edge
	3.4 Tanimoto Cutoff
4. Customizing Network - Cluster
5. Notice for NetCrafter use

• 1. Launching NetCrafter
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• 1.1 Install NetCrafter on Windows
• To launch NetCrafter:
•    1)  Go to the the main NetCrafter page.
•    2)  Click the button to download the NetCrafter Desktop Application.
•    3)  Open ‘NetCrafter.zip’ file and uncompress the file.
•    4)  Click the right button on the mouse to install NetCrafter1.21.exe and select Run as administrator.
•    Guide to all process for installation are started from the following window.
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• *캡쳐 화면 필요함



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• 2. Main Functions of NetCrafter
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• This program is mainly draw network automatically based on Tanimoto coefficients using Gene and GO inputs.
  The results can be saved as a file of PDF, JPG, and PNG format.



• 2.1 Running NetCrafter
• When NetCrafter starts, the main windows will appear that looks like this (captured on Window):
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• 2.2 Loading Data
• To obtain the sample loading data, you can download the file from the main page of NetCrafter.
•    1)  Select the data type; Gene or Function.
•    2)  Click the [Open] button.
•    3)  Select your input file as csv format.
•    4)  When the data file is opened successfully, the matrix data will be visualized in the main panel.
•    5)  You can deselect each Gene or GO term that will not be displayed in the network.
           Deselecting data will immediately update the count of selected items at the bottom.
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• 2.3 Visualization of Network
• Now that you have loaded your data file, you are ready to visualize the network.
•    1)  By clicking the [Network] button, a new window will pop up, displaying the network.
          You can view names of each node by hovering your mouse over it.
•    2)  The number of nodes displayed in the network is shown in the upper right corner.
•    3)  You can customize network by manipulating control panel, under the number of nodes.
          We will cover network control in Chapters 3 and 4.
•    4)  At the bottom, the functions representing the groups will be displayed.


• The following new window will be displayed:
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• 2.4 Saving Data
•    1)  Click the [Save Plot] button at the bottom of the control panel on the right.
•         You can save your data file as PDF, JPG, and PNG format.
      

  Format	Description
  PDF	Portable Document Format, ideal for sharing and printing
  JPG	Image file of high-quality resolution
  PNG	Image file with lossless compression



•    2)  Enter a name to saved file and click Save button.



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• 3. Customizing Network - Control Panel
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• This program provides five options to edit the visualization. You can easily optimize network by controling the options in the panel on the right, without needing any graphic-editing skills.
  After modifying the options, press [UPDATE] button to regenerate the network. Clicking the button will randomly distribute the network based on the input values.
  
  In this Chapter, we will cover the four options in order, from top to bottom, with the remaining option discussed in Chapter 4.
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• 3.1 Scoring Method
• For gene networks, the application offers three scoring methods:
  one standard and two weighting options, including linear and curved methods.



• 3.2 Node Labeling
• You can enable node labeling in the network by checks the checkbox.



• 3.3 Edge
• There are two options for controlling edges: thickness and length.
  Increasing the number will make the edges thicker and longer.



• 3.4 Tanimoto Cutoff
• You can adjust the Tanimoto cutoff using the scaling slider.
  Only nodes connected by edges with a Tanimoto score above the cutoff will be displayed in the network.



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• 4. Customizing Network - Cluster
• 
• NetCrafter software automatically calculates similarity based on Tanimoto coefficients using Gene and GO (function) inputs, and visualizes the network accordingly.
  
  The fifth option of customizing network is Selecting Clusters. The representative functions of the groups, distinguished by their connected nodes, will be displayed in the bottom section of the interface.


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   1)  Deselect clusters prefer not to display on the network.
   2)  Click the [Select Cluster] button.
         The changes will then be applied to the network.


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• 5. Notice for using NetCrafter
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• There are several notice points to use the NetCrafter.


• 5.1  Input File
•      NetCrafter only recognize the input file with extension type of 'csv'.
•      And the input file does not need to include column names in the first row or column.



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• Last update: August. 23, 2024 by