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Are questions about application level network protocols, not connected with network infrastructure (e.g. HTTP, FTP, email protocols) ok here?

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There is no single answer to this question as this would depend on the protocol and the actual nature of the question.

If you are talking about routing protocols or the use of tools commonly used by network engineers (for example, SNMP), then this is likely on topic.

If you are talking about historic protocols that are irrelevant to modern networking these may be off topic.

If you are talking about protocols such as HTTP or FTP, then they are likely off topic.

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From the What topics can I ask about here? in the Help Center, under Off-Topic:

protocols above L4 in the OSI model (e.g. HTTP, FTP, etc)

This is something that may possibly be discussed in chat (for questions which are off-topic on Network Engineering), but you are probably better off asking on ServerFault.

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