A Server Project is a project that is created on the server, rather than on the user’s client machine.  This project is cached locally, in case of loss of connection to the server, but is automatically updated each time the user logs in or clicks the save button. The cache is stored in the user’s home folder, typically “My Documents\Omicsoft\ServerProjects”. 

A Server Project, when stored locally in the cache folder, is a different suffix than a regular project (.ossprj) and can only be opened when the user is connected to the server.

Notice that the Server Project will have “(Server Project)” written after the name as it appears in the solution explorer:

For Server Projects, all data extraction or data addition is done on the server side, by Array Server, instead of the individual client’s computer.  This provides a number of benefits.  First, it ensures the rule that all raw data be on the server before being imported into an Omicsoft project file.  Second, it allows the user to use the power of the server, instead of their individual client, for the importing of data.  This is extremely important for some memory/cpu intensive importing operations, for instance, alignment of a fastq file to the genome for NextGen sequencing data.

However, after data extraction, almost all analysis is still done on the client side.  So, the data is extracted on the server, then downloaded to the client side, where the user can add views, run analysis, etc.  Anytime the user saves the project, it is synced with the version on the server.  The exception to this is NGS analysis, and this is covered in its own section below.