Projects

A project is a grouping of samples, libraries, sequencer runs, and other related items. Each sample in MISO belongs to a specific project. By association, a sample's libraries and library aliquots belong to the same project. Some other items, such as pools and sequencer runs, may include items from multiple projects.

Projects List

The Projects list page can be accessed by clicking the "Projects" link in the Preparation list in the menu on the left side of the screen. Here you can see all of the projects that you have access to in MISO. Clicking on the project's name, alias, or short name in the table will take you to the Edit Project page, where you can see more project details, as well as all of the items associated with the project. The toolbar at the top of the table includes an "Add" button for creating new projects.

Adding Projects

To create a new project, click the "Add" button in the toolbar near the top of the Projects list page. This will take you to the Create Project page, where you can enter the project details. Choose a descriptive project alias. This is the long name for the project. The short name should be a short, alphanumeric code for the project. Depending on your site's configuration, project short name may or may not be required. Be sure to also select an accurate project status.

Reference Genome

Reference genome refers to a model genome that sequenced data should be aligned to. This should indicate the primary genome used for the project if there are multiple. The default scientific name used for samples will depend on the reference genome set on the project. For example, if the project's reference genome is "Human hg19 random," then samples created in the project will have a default scientific name of "Homo sapiens."

Default Targeted Sequencing

Default Targeted Sequencing is a project-level property. Whichever targeted sequencing is selected here will be the default value for all library aliquots created within the project. Note, however, that a library aliquot's targeted sequencing options depend on the library kit used on the library. If the default targeted sequencing value is not compatible with the library kit, it will not be selected automatically, nor will it be available for selection.

Permissions

The "Permissions" section of the Create Project page contains several options for controlling who has access to the project. These permissions will also affect the project's samples, studies, and other related items.

The project's owner is the person who should have full control over the project. They will be granted full read/write access to the project and all related items regardless of the other permissions set on the project.

If the checkbox beside "Allow all internal users access?" is checked, then all users with the Internal role will also be given full read/write access to the project and all related items.

Next, there are four lists which allow you to choose which MISO users and/or groups have read and/or write access. Checking a checkbox next to a user of group in one of these lists grants the specified permission to the user or group selected.

See User Permissions for more information about user roles and resource-level permissions.

Edit Project Page

The Edit Project page shows details about the project and all items related to it, and also provides some additional information and functionalities. To get to the Edit Project page, click the project name, alias, or short name on the Projects list page. You can edit the project's details by changing them on this page and then clicking the "Save" button to confirm.

Tracked Issues

The Tracked Issues section of the Edit Project page shows issues from an issue tracking system that are related to the project. This works by searching for any issue with a label/tag that matches the project's short name. This means that for tracked issues to show up:

your site must have issue tracker integration configured
your project must have a short name
you must add a label/tag that matches the project's short name to the issues

See the Issue Trackers section for more information on connecting issue trackers to MISO.

Project Files

Files can be attached to a project and will show up in the Project Files section of the Edit Project page. For more information about attachments, see the Attachments section.

Assigning Assays to Projects

On the Edit Project page, there is an Assays table (between Project Files and Studies). There, you may assign assays to the selected project. To add an assay, click the "Add" button on the table, and select the assay you would like to add. To remove assays, click the checkboxes that correspond to the assays you want to remove, and then click the "Remove" button. For more information about assays, see the Assays Section.

Subprojects

Note: This item only applies if your site uses detailed sample mode.

In some cases, it may be useful to divide a project's samples into several smaller groups. For this purpose, MISO has subprojects. Subprojects may be designated as high priority, which will cause "PRIORITY SUBPROJECT" messages to appear in several places. They may also specify a different reference genome than the project they are a part of.

The subprojects within a project are listed near the bottom of the "Project Information" section of the Edit Project page. Clicking on a subproject name will take you to the project's samples list and filter it to show only the selected subproject. You can reset the table to show all of the project's samples by clearing the search box at the top right of the table and pressing the Enter key.

To view a list of all subprojects in all projects, click to expand the Configuration menu within the main navigation menu, then click the "Subprojects" link. This will take you to the Subprojects list page. Controls at the top of the table allow you to create, edit, and delete subprojects.

Adding Subprojects

There are two paths to the bulk Create Subproject page. The first is to click the "Add new subproject" link near the bottom of the "Project Information" section of the Edit Project page. The second is to click the "Add" button in the toolbar at the top of the table on the Subprojects list page. This second option will allow you to create multiple subprojects at once - enter the quantity that you would like to create in the dialog, then click the "Create" button.

Once on the Create Subproject page, fill out the subproject information, including the project that it falls within, an alias, the reference genome to use, and optionally a desription. If this is a high priority subproject, select "True" in the priority column. When you are done, click the "Save" button at the top right to create the subproject(s).

Editing Subprojects

Subprojects can only be modified by a MISO administrator. If you are an administrator, you can get to the bulk Edit Subproject page by first going to the Subprojects list page, checking the checkbox beside each subproject that you would like to modify, then clicking the "Edit" button in the toolbar at the top of the table. This will take you to the bulk Edit Subproject page, which is identical to the Create Subproject page. Make any changes you would like, and then click the "Save" button at the top right of the screen to confirm. Keep in mind that these changes will affect any samples already included in the subproject.

Deleting Subprojects

A subproject can only be deleted by a MISO administrator, and only if there are no samples belonging to the subproject. To do so, go to the Subprojects list page, check the checkbox beside each subproject that you would like to delete, then click the "Delete" button in the toolbar at the top of the table.

Deleting Projects

To delete projects, go to the Projects list page, select the projects that you wish to delete, and click the "Delete" button in the toolbar at the top of the table. A project can only be deleted by its creator or a MISO administrator, and only if it does not contain any samples.