Sharing data via projects

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View types according to their role within BioIMAX. The View corresponding to the raw original ImageStack is represented through the type orig, whereas the two newly generated ImageStacks are described by the types web and thumb. The values of the View attributes creator_id and name are identical with the values of the attributes user_id andname of the corresponding ImageStack instance. Additionally, this step includes the definition of initial access rights for each of the three Views. The access rights are represented by the attributes all_read and all_write and their values are initially set to 0. Thus, only the owner of the ImageStacks has access rights in the first instance. Later, the owner has the option to modify these rights.

• TheViews with the typesorig,web andthumb represents the three ImageStacks and their single images, which have to be stored in the database by default. The actual raw image files of the respective ImageStacks are stored on a separate dedicated file server. In order to assign these image files to the three Views and therefore, to all other data stored in the relational database, an entry in theResult relation is created for each single image. These entries contain the path to the image files stored on the file server and are uniquely linked to the respective View instance. Each image in the Result relation is specified with the previously defined textual tag via themeta_info attribute. If the user has selected the tags from the predefined list of antibody tags, the meta_info stores the ID of the respective entry in the Antidict relation as foreign key. Otherwise the user-defined free textual tags or the file name of the image are stored.

• Finally, the list of selected antibody tags is stored with an Antidict_selection instance for potentially reusing them for further ImageStacks. Here, in addition to the unique user_id and the name for the selection list that has been defined by the user in the third step of the client upload interface, all antibody tags are combined in one XML string and stored as value of the antidict_xml attribute. The single tags are either represented by IDs being foreign keys to respective entries in the Antidict relation or by free text, which is similar to the storage of the tags in the meta_info of theResult relation.

In this way, each single image inBioIMAX is associated to one of the three ImageStacks via the respectiveView instances and thereby clearly linked to the abstractImageStack relation with its meta information and to an individual user as its owner. The role of the different multivariate ImageStack versions inBioIMAX is pointed out in the following sections of this chapter.

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a

d

b

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Figure 6.4:Administration ofBioIMAX projects. The project administration interface generally allows each project member to inspect the current status of the project, i.e., which users are participating in the project (a) and which datasets are assigned to the project (b). Furthermore, project owners especially are authorized to manipulate the current status of the project: changing write access of existing project members and deleting selected members (c), inviting new users (d) and deleting selected datasets from the project (e).

collaborating BioIMAX members. The creation, deletion and management of user-defined projects is controlled via the navigation toolbar on the main page (see Figure 6.2(e,f)). Here, users can easily create own projects only by specifying a name and short description about the purpose of the project. Once a project has been created, it is added to the list of the user’s personal projects (see Figure 6.2(e)), whereby identifying the user as the owner of the project.

Each project in the list can be managed through a separate administration window il-lustrated in Figure 6.4. The project administration window allows each project member to inspect the current status of the project, i.e., which BioIMAX users are associated to the project (see Figure 6.4(a)) and which data items are assigned to the project (see Figure 6.4(b)). In addition, project owners are authorized to manipulate the current status of the project:

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• Owners have the option to grant write access to existing project members, so that they can add new data to the project themselves. Additionally, owners can remove members from their projects (see Figure 6.4(c)).

• Owners can invite furtherBioIMAX users to their projects (see Figure 6.4(d)). Project invitations are displayed on the BioIMAX main page of the invited users (see Figure 6.2(f)) and have to be accepted before the invited users have access to the respective projects.

• Finally, owners can delete single data items from their projects (see Figure 6.4(e)).

Adding new datasets to projects is carried out with the Data Browser and is described in detail in the next Section 6.2.

Data storage

User-defined projects and information about associated members and data items are stored in the BioIMAX database as follows:

• For each newly generated project a uniqueProject instance is created that is linked to a specificUser instance via the foreign keycreator_id and is characterized by aname, a short description of its purpose through the meta_info attribute and the creation date.

• The relationProject_members linksBioIMAX users to projects by combining the user and project IDs as foreign keys of the respective User and Project instances. Ad-ditionally, the Project_members relation specifies thewrite_access status of project members.

• As mentioned before, ImageStacks and derived result data are represented inBioIMAX via a certain View instance and its respective View types. When a user adds data to a project (see Section 6.2), a new Project_views instance is created that links the view_id as foreign key of the View instance representing the respective data to a specific project. In this way, one View with its associated data can be assigned to multiple projects.

• Finally, project invitations are stored in theProject_invitations relation, until the user has accepted the invitation.

The project concept allowsBioIMAX users to easily build up small communities regarding a dedicated biological or analytical problem and to share their data and results with other users. This kind of data sharing is the first and essential step towards collaborative work in BioIMAX. Another crucial aspect covered by the project concept is data protection and security. In addition to general privilege mechanisms, i.e., access rights for each uploaded or produced dataset, data access can be limited to certain individuals and groups of researchers using BioIMAX projects, whereas project-related data remains hidden for non-members.

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