To open an existing project select File > Open Project from the main menu. All SeqMonk project files use a .smk file extension. The file menu also contains a list of the five most recently opened projects which you can use to quickly re-open them.
A SeqMonk project stores all of the Data Set, Data Group, Probe Set and Probe List information for your project. It also remembers which annotation and data tracks were visible.
Although it stores the name of the genome you were using it doesn't contain the actual genome data. If you are using SeqMonk on a new machine it will therefore automatically download and install the required genome when you open a project file. If you want to use SeqMonk when not connected to a network you therefore need to ensure that the correct genome has been installed on your machine before disconnecting it from the internet. Once downloaded, genomes will be cached on your machine for future use.
When opening a project SeqMonk checks to see if the project file is compatible with the version of SeqMonk you are using. If you try to open a project file from a newer version of SeqMonk on an older SeqMonk version you may get an error telling you you need to upgrade to the newest version of SeqMonk. Newer versions of SeqMonk can always open project files from older versions of the program.