Answers.Body: <p>Cytoscape 3.10 only works with Java 17 and if not found on the system a version from <a href="https://adoptium.net/" rel="nofollow noreferrer">Adoptium</a> is automatically downloaded for mac and windows users.</p>
  <p><a href="https://apps.cytoscape.org/apps/keggscape" rel="nofollow noreferrer">KEGGscape</a> does <strong>not</strong> add an entry to the &quot;<strong>Apps</strong>&quot; menu.</p>
  <p>Details on how do do this can be found at this link: <a href="https://github.com/idekerlab/KEGGscape/#quick-start" rel="nofollow noreferrer">https://github.com/idekerlab/KEGGscape/#quick-start</a></p>
  <p>To learn more about Cytoscape you can visit:
  <a href="https://tutorials.cytoscape.org/" rel="nofollow noreferrer">https://tutorials.cytoscape.org/</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-10-14T18:02:11.787Z
Answers.Text: yes i understand now but when i import the xml file it all shows gibberish how do i fix that all the nodes say eco:234 etc similar to that my network is not matching with the network image shown and expected in the tutorial despite downloading the same file? what do i do?
Answers.UserDisplayName: user21741
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-10-17T17:29:38.293Z
Answers.Text: I just did the import using the quick start and noticed all the nodes are stacked on top of themselves. It appears the style was not loaded properly. I have sent a message to the app author to see if they have a resolution.
Answers.UserDisplayName: Christopher Churas
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-10-10T17:47:55.673Z
Answers.LastActivityDate: 2024-10-10T17:52:36.977Z
Answers.LastEditDate: 2024-10-10T17:52:36.977Z
Answers.UserDisplayName: Christopher Churas
Body: <p>I am having trouble using KEGGscape in Cytoscape on Windows 11. I've tried installing and reinstalling KEGGscape multiple times, and even uninstalled and reinstalled Cytoscape itself, but the issue persists. I downloaded Java 23; idk if it is the right one but given that all other apps work I don't think it's Java and Cytoscape is updated to the latest version.</p>
  <p>Although Cytoscape shows that KEGGscape is installed, it never appears in the &quot;Apps&quot; section. Other apps I installed from the Cytoscape App Store work perfectly and show up without any issues.</p>
  <p>To install KEGGscape, I searched for it in the Cytoscape App Store, which redirected me to Google for the download. I'm unsure if I did something wrong during the process. I'm not familiar with using the terminal, but I haven't seen any error messages when starting the software.</p>
  <p>Can someone please help me with this issue? It’s urgent.</p>
  <p>Additionally, I would appreciate any advice on learning Cytoscape concepts for free. I'm an undergraduate student trying to become proficient in Cytoscape and apply these concepts to real-life situations. I am very new to this and eager to learn something new.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-10-04T16:23:53.033Z
Comments.Text: I fear you will probably need to ask the developers of this tool, but they do say Java11 and Cytoscape 3.8 so it is possible that it just doesn't work on the much newer versions you are using.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-10-05T01:16:38.960Z
Comments.Text: [Java 17](https://manual.cytoscape.org/en/stable/Launching_Cytoscape.html#install-java). "With v3.10, we droppped support for Java 11, for the same reason [Oracle and other JVM suppliers have dropped Java support for that version]"
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-10-05T01:18:55.843Z
Comments.Text: How do you know what KEGGscape isn't working? What are you having trouble with; where would you expect it to appear?
Comments.UserDisplayName: gringer
Tags: <cytoscape>
Title: Keggscape Install bug
ThreadText: # Keggscape Install bug
  
  (Asked by: username_0 on 2024-10-04)
  
  I am having trouble using KEGGscape in Cytoscape on Windows 11. I've tried installing and reinstalling KEGGscape multiple times, and even uninstalled and reinstalled Cytoscape itself, but the issue persists. I downloaded Java 23; idk if it is the right one but given that all other apps work I don't think it's Java and Cytoscape is updated to the latest version.
  
  Although Cytoscape shows that KEGGscape is installed, it never appears in the "Apps" section. Other apps I installed from the Cytoscape App Store work perfectly and show up without any issues.
  
  To install KEGGscape, I searched for it in the Cytoscape App Store, which redirected me to Google for the download. I'm unsure if I did something wrong during the process. I'm not familiar with using the terminal, but I haven't seen any error messages when starting the software.
  
  Can someone please help me with this issue? It’s urgent.
  
  Additionally, I would appreciate any advice on learning Cytoscape concepts for free. I'm an undergraduate student trying to become proficient in Cytoscape and apply these concepts to real-life situations. I am very new to this and eager to learn something new.
  
  **Tags:** cytoscape
  
  > **Comments:**
  > **username_1**: I fear you will probably need to ask the developers of this tool, but they do say Java11 and Cytoscape 3.8 so it is possible that it just doesn't work on the much newer versions you are using.  
  > **username_2**: [Java 17](https://manual.cytoscape.org/en/stable/Launching_Cytoscape.html#install-java). "With v3.10, we droppped support for Java 11, for the same reason [Oracle and other JVM suppliers have dropped Java support for that version]"  
  > **username_2**: How do you know what KEGGscape isn't working? What are you having trouble with; where would you expect it to appear?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2024-10-10. Score: 0
  
  Cytoscape 3.10 only works with Java 17 and if not found on the system a version from [Adoptium](https://adoptium.net/) is automatically downloaded for mac and windows users.
  
  [KEGGscape](https://apps.cytoscape.org/apps/keggscape) does **not** add an entry to the "**Apps**" menu.
  
  Details on how do do this can be found at this link: <https://github.com/idekerlab/KEGGscape/#quick-start>
  
  To learn more about Cytoscape you can visit:
  <https://tutorials.cytoscape.org/>
  
  > **Comments:**
  > **username_0**: yes i understand now but when i import the xml file it all shows gibberish how do i fix that all the nodes say eco:234 etc similar to that my network is not matching with the network image shown and expected in the tutorial despite downloading the same file? what do i do?  
  > **username_3**: I just did the import using the quick start and noticed all the nodes are stacked on top of themselves. It appears the style was not loaded properly. I have sent a message to the app author to see if they have a resolution.  
  
  ---
  
  