The application layer is not the applications a user runs on their system. Rather, this layer is made up of protocols that support these applications. When a user is performing some action with an application and then wants to send this data as a message, application layer protocols are called on to package the data (using headers and footers) and pass the data on to the next layer (in this case, the presentation layer). The message will continue to move down the OSI model as each layer performs its duties on the message, until it eventually reaches the target system and moves in reverse through the model. When the target system's application layer receives the message, it looks at the headers and footers that were placed there by the user's application layer and processes the data in the correct manner.
As another example, say you want to mail a letter to your friend. You write the letter and hand it to me, the application layer. I take the message and put it in an envelope and pass it on to the other layers which will eventually add the address and name of the recipient. When the recipient receives the letter, she removes the envelope (strips off the headers and footers) and is presented with your message. This is similar to how the application layer functions.
Some protocols that function at this layer include Simple Mail Transfer Protocol (SMTP), Hypertext Transfer Protocol (HTTP), Line Printer Daemon (LPD), File Transfer Protocol (FTP), Telnet, and Trivial File Transfer Protocol (TFTP). Each of these has an application programming interface (API) that defines how they can be called by an application. When an application, such as a mail client, wants to send a message it will call on a protocol; in this case, SMTP. The API of SMTP says how the information must be presented to the protocol for it to do its job. After the mail client makes a call to the SMTP API, SMTP adds its information to the user's message and passes it on to the presentation layer.
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