In order to continue with your analysis session later on, you have to save it by selecting File->Save session. All the datasets and their relationships are saved as a session, which is packed into a single compressed file. Session files have an extension .cs (for Chipster Session). You can continue the session also on another computer by copying the session file there, or you can share it with your colleague.
Session can be loaded by selecting File->Open session. By default the current data is cleared before another session is loaded, but you can select "Add to current session" from the session file dialog to combine the existing session with the one from the session file.
Note! Sessions are an extended version of the previous workspace system. If you have saved a workspace with an earlier Chipster version, you can open it by selecting File->Open workspace (session) saved with Chipster 1.1. Unlike the old workspace system, the new session system also allows you to create workflows from datasets that were loaded from a session and you can view all the details for them (including the source code) in the analysis history.