2. Project Files:

Making FAKtory Support Multiple Users

A project file is FAKtory's record of all work that has been performed on a particular sequencing data set. The project file contains all the sequencing data that has been entered, all configuration settings, and all assemblies and other work performed to date. An invocation of the FAKtory works on one active project at a time. From a list of project files on the FAKtory System panel one may open a project making it the currently active project. All panel displays come to the screen exactly as they were when the project was last closed. One may close the currently active project at any time, either saving all work or discarding all work performed in the session. A new project may also be started at any time. The initial configuration for such a project is established as described in Section 1.

We designed FAKtory with the idea in mind that more than one user may be involved in determining a particular target sequence. First, all configuration information is classified as either project-based or user-based according to whether its setting affects the results obtained, or only the nature of the processing and presentation of data. For example, the stages in the pipeline, the fields in a fragment data entry, and the configuration of a prescreening stage of the pipeline are project-based, whereas the modes in which pipeline stages operate or the colors used by the system are user-based. Project-based configuration information is shared by all users working on a project, so if one user sets an option, all subsequent users see the changed option. On the other hand, a user-based configuration is specific to each user, i.e., the FAKtory remembers each user's user-based settings separately. Thus if one user changes, say a color preference, other users on the same project do not see the change.

One may also open a FAKtory project in one of two modes: read-only or edit-lock. Only one user can have the project opened with an edit-lock at any given time. This user is free to enter, edit, and manipulate the data in the project. Any user can at any time open a project within read-only mode, but they are restricted to simply examining the state of the project. This mechanism prevents two users from simultaneously modifying a project at the same time. Finally, it is expected that users will use the file protections of the underlying operating system to ensure the security of a project file and to restrict sharing to certain groups or individuals.