Connection Timeout Error - STRING Network Import from PubMed Query

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Pooja Yadav R.Scholar (1643), Biotech., UIET

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Aug 21, 2025, 12:03:37 PMAug 21
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Dear Cytoscape Support Team,

I hope this email finds you well. I am experiencing a technical issue with Cytoscape and would appreciate your assistance in resolving it.

I am encountering a connection timeout error when attempting to load a STRING network from a PubMed query. The specific error message I receive is:

Unexpected error from server:
<html>Connect timed out</html>

Could you please help me troubleshoot this issue? I would like to know:

  1. Is this a known issue with the STRING database integration?
  2. Are there any network/firewall settings I should check?
  3. Is there a recommended timeout setting or alternative method to import STRING networks?
  4. Are there any recent updates or patches that might resolve this issue?

Best regards,

Pooja Yadav

Phd Scholar


Christopher Churas

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Aug 21, 2025, 12:14:02 PMAug 21
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Hi,

I just tried STRING from a pubmed query with query term set to "diabetes" and was able to get a network.  
If you are still getting the error, please send us the you are entering into the dialog as well as your framework-cytoscape.log file found under CytoscapeConfiguration/3/ directory under your home directory.

thanks,

chris


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