Libraries

Naming Scheme

MISO can be configured with a naming scheme appropriate for your organization. For more details about this configuration, see Naming Scheme in the Site Configuration section.

For libraries, the naming scheme specifies whether or not duplicate aliases are allowed, and may also specify a pattern that all library aliases must follow. If such a pattern is specified, then the aliases will be compared to this pattern whenever saving a library. If the alias does not follow the pattern specified by the naming scheme, or if there is a duplicate alias when not allowed, the save will fail and a validation message will state the cause.

The naming scheme may also specify a library alias generator. This means that users will not have to choose library aliases because they will be generated automatically when saving libraries. The user is still free to choose a library alias by typing it in manually if they would like.

Libraries List

To get to the main Libraries list page, click "Libraries" in the Preparation list in the menu on the left side of the screen. This list includes all libraries from all projects in MISO. The toolbar at the top of the table includes many controls for working with libraries.

You can find a similar list in the Libraries section of the Edit Project page. The list on the Edit Project page only includes the libraries belonging to the project being viewed/edited. This list has the same controls as on the main Libraries list page.

Propagating Libraries from Samples

To make libraries from samples, go to the Samples list and check the checkbox(es) next to the sample(s) you wish to propagate from. If your site uses detailed sample mode, only aliquot samples can be propagated to libraries. After you have made your selections, click the "Propagate" button in the toolbar at the top of the table. In the dialog that appears, choose the number of replicates you would like to propagate from each of the selected samples. If you would like to specify a different number of replicates per selected sample, check the "Specify replicates per sample" checkbox. This will cause another dialog to open after the current one and ask you for the number of replicates for each sample. There is also an option to create a new box for the new libraries. See Creating Boxes in the box section more more information on this feature. Click the "Propagate" button when you are done in the dialog.

This will take you to the bulk Create Libraries from Samples page. Enter all of the library information and then click the "Save" button at the top right of the screen when you are done. For additional information regarding some of the fields in the table, check the Quick Help section near the top of the screen. If any of the libraries fail to save, a message will be displayed at the top of the screen explaining the problem(s). You can then make the appropriate adjustments and click the "Save" button to try again.

Receiving Libraries

When libraries are received from an external collaborator rather than being created in-house, we can create these libraries directly without creating the samples first. MISO does require a sample, so one will be created automatically. The bulk Create Libraries page will ask for some sample information, so that you can enter any sample-level data that you have, which may be useful for analysis purposes. If your site uses detailed sample mode, the entire sample hierarchy will be created when receiving a library, so the form will include many details.

To get to the bulk Create Libraries page, click the "Receive" button in the toolbar at the top of the Libraries list. In the dialog that appears, choose the quantity of libraries you would like to create. If your site uses detailed sample mode, you will have to choose the aliquot class to use when creating the ghost samples that these libraries are parented to. There is also an option to create a new box for the new libraries. See Creating Boxes in the box section more more information on this feature. Click the "Receive" button when you are done in the dialog.

The bulk Create Libraries page works similarly to the bulk Create Libraries from Samples page, except that more data will be required. This additional data is used in creating the sample(s) that the libraries are parented to so that we can store sample-level data, primarily for use in analysis. If a date of receipt and other receipt information is entered, a receipt transfer will be created. See the Transfers section for more information.

Library Templates

A library template is a set of attribute values that can be applied to a library. Its purpose is to reduce repetitive input. If you find that you are creating many similar libraries, you can create a library template so that you only have to select the template, and several other attributes will be selected automatically. A library template must be associated with a project in order for it to appear as an option for libraries created within that project. It is possible to associate a library template with multiple projects.

Library Templates List

The Edit Project page includes a list of Library Templates associated with the project being viewed/edited.

The main Library Templates list can be accessed by clicking the "Library Templates" link in the Misc menu on the left side of the screen. This list includes all the library templates that have been created in MISO, and includes some extra capabilities not included on the project-specific list.

Creating Library Templates

Click the "Add" button in the toolbar at the top of the Library Templates list to create new library templates. This will take you to the Create Library Template page. Enter an alias for the template. This is the name that will appear in the template dropdown when creating new libraries. All other fields are optional. Any values you select for a template will be automatically applied to any library that this template is applied to. Any fields left blank or "Unspecified" will not be affected when applying this template to a library. If you started by clicking the "Add" button on the project-specific Library Templates list, the template will automatically be associated with the project whose page you were on. If you clicked the "Add" button on the main Library Templates list page, the template will not be associated with any projects automatically. You can also edit the project associations before saving. See Adding/Removing Library Templates from a Project below for more information on adding and removing projects. After you have made your selections, click the "Save" button at the top right of the page to create the template.

Editing Library Templates

Library templates can be edited individually or in bulk. Bulk editing is convenient when you have several templates to modify at once. Editing individual templates is sometimes preferable because it provides a few additional options, and allows you to see a more detailed view of the template. Note that when editing library templates, the changes will have no effect on libraries that the templates were previously applied to.

To edit a single library template, click on its alias in the Library Templates list. This will take you to the Edit Library Template page, which works the same as the Create Library Template page. Make any changes you would like and then click the "Save" button at the top right to confirm the changes. The Edit Library Template page also allows you to specify indices. See Specifying Library Template Indices below for more information.

To bulk edit library templates, go to the Library Templates list, select to the template(s) you would like to modify, and click the "Edit" button in the toolbar at the top of the table. This will bring you to the bulk Edit Library Templates page. Make any changes you would like, then click the "Save" button at the top right of the page to confirm.

Adding/Removing Library Templates from a Project

Changing which projects a library template is associated with can be done on the Edit Library Template page, or from the main Library Templates list page.

To add a project association to a single library template, go to the Edit Library Template page and click the "Add" button in the toolbar at the top of the Projects list section. In the dialog that appears, type in the name, alias, or short name of the project and click the "Search" button. Click the project alias in the results dialog to complete the association. Be sure to click the "Save" button at the top right of the page to confirm your changes.

To remove a project association from a single library template, go to the Edit Library Template page, select the projects you would like to remove in the Projects list section, and click the "Remove" button in the toolbar at the top of the list. Be sure to click the "Save" button at the top right of the page to confirm your changes.

To add a project association to multiple templates at once, go to the Library Templates list page, check the checkboxes beside the templates you would like to associate with a new project and click the "Add Project" button in the toolbar at the top of the table. In the dialog that appears, type in the name, alias, or short name of the project and click the "Search" button. Click the project alias in the results dialog to complete the association.

To remove a project association from multiple projects at once, go to the Library Templates list page, check the checkboxes next to the appropriate templates and click the "Remove Project" button in the toolbar at the top of the table. In the dialog that appears, click the alias of the project that you would like to remove the template(s) from.

Specifying Library Template Indices

A library template may specify indices to add to libraries based on the library's box position. When applying a template to a library that is in a box, the indices specified for the box position that the library occupies will be selected. If the library is not in a box, no indices will be selected automatically.

Library template indices can be edited from the Edit Library Template page using the controls in the Indices list section at the bottom of the page.

To add indices, click the "Add" button in the toolbar at the top of the list. In the dialog that appears, enter the quantity of box positions you would like to add indices for and click "Create." This will take you to the bulk Create Library Template Indices page. Enter the box positions and select the indices for each, and then click the "Save" button at the top right of the page to confirm.

To edit indices, select the positions you would like to modify and click the "Edit" button in the toolbar at the top of the list. Change any indices you would like, and then click the "Save" button at the top right of the page to confirm.

To remove indices, select the positions you would like to remove index specifications from, and click the "Remove" button in the toolbar at the top of the list. Be sure to click the "Save" button at the top right of the page to confirm.

Deleting Library Templates

To delete library templates, go to the Library Templates list, check the checkboxes next to the templates you wish to delete, and click the "Delete" button in the toolbar at the top of the table. The templates will be removed from all projects they were associated with, and deleted. This will not affect any libraries that the templates were previously applied to.

Editing Libraries

Libraries can be edited individually or in bulk. Bulk editing is convenient when you have several libraries to modify at once. Editing individual libraries is sometimes preferable because it provides a few additional options, and allows you to see a more detailed view of the library.

Editing a Single Library

To get to the single Edit Library page, click on the library's name or alias in the Libraries list. Links to the Edit Library page appear on several pages for related items as well, including:

  • Library Name and Library Alias columns of the Library Aliquots tables on the Edit Pool page
  • Library Name and Library Alias columns of the Library Aliquots list page

The Library Information section of the Edit Library page contains a list of fields, most of which may be modified. You can make any changes you would like and then click the "Save" button at the top right to confirm the changes.

Below, there are sections for Notes and QC's, which are discussed in other parts of this section of the user manual. Other sections list the library aliquots that have been created from the library, the pools that those library aliquots have been added to, the runs that those pools have been loaded into, and the library's change log.

Editing Libraries in Bulk

To get to the bulk Edit Libraries page, go to the Libraries list, check the checkboxes beside the libraries you wish to modify, then click the "Edit" button in the toolbar at the top of the table.

The bulk Edit Libraries page works similarly to the bulk Create Libraries from Samples page. You can make the changes you would like, then click the "Save" button at the top right to confirm. If there are any problems with the data you've entered, the error messages will be displayed at the top of the screen and you can adjust as necessary before clicking "Save" again.

Batches

A library batch is a set of libraries that were created together. Batches are created automatically and group libraries based on creation date, creator, SOP, kit, and kit lot. If any of these things were not specified on the library, it will not be included in a batch. If additional libraries are later created with all of these attributes matching an existing batch, the new libraries will be included in the existing batch as well. Changing any of these attributes will also change the batch that a library is included in.

Batch IDs are created using identifiers from all of the grouping attributes, and will look similar to "2020-08-25_u1_s5_k123-00004567." The Edit Library page shows the library's batch ID if applicable. Clicking on the batch ID will take you to the Library Batch page, which includes summary information and a list of all libraries in the batch.

Notes

The single Edit Library page includes a Notes section. Notes can be used to record additional library information that is otherwise not recorded in MISO. More information on working with notes can be found in the Notes section.

Attaching Files

You can attach any type and number of files to a library in MISO. This feature might be used to attach QC output or a spreadsheet of library data provided by a collaborator. For more information, see the Attachments section.

Propagating Libraries to Library Aliquots

To make library aliquots from libraries, go to the Libraries list, check the checkboxes next to the libraries you wish to propagate from, then click the "Make aliquots" button in the toolbar at the top of the table. Further details of propagating libraries to library aliquots will be discussed in the Library Aliquots section - Propagating Library Aliquots from Libraries.

Printing Barcodes

Barcode labels can be printed for a series of libraries from the Libraries list. See the Barcode Label Printers section - Printing Barcodes for details on how to do this.

Downloading Library Information

It is sometimes useful to have library information in spreadsheet form for use outside of MISO. To download library data, go to the Libraries list, check the checkboxes next to the libraries that you would like to export, and click the "Download" button in the toolbar at the top of the table. A dialog will appear in which you can choose the type and format of the spreadsheet before downloading. Different spreadsheet types include different columns. Feel free to try out the different types to see which ones will be useful to you. MISO supports exporting spreadsheets in Microsoft Excel (xlsx), Open Document (odt), and comma-delimited (csv) formats.

If you have a list of library names, aliases, or barcodes, you can use this list to select and act upon the libraries instead of having to search for and select them manually. For more information on this feature, see the General Navigation section - Selecting by Search.

You can find items related to selected libraries using the "Parents" and "Children" buttons in the toolbar at the top of the Libraries list. For more information on this feature, see the General Navigation section - Finding Related Items.

Library QCs

Any number of quality control measures may be recorded for a library. For more information on this feature, see the QCs section.

Adding Libraries to a Workset

It can sometimes be difficult to find and select a group of libraries that you want to work with. To make this easier, you can create a workset that includes all of the libraries that you want grouped together. For more information on this feature, see the Worksets section.

Deleting Libraries

To delete libraries, go to the Libraries list, check the checkboxes next to the libraries that you wish to delete, and click the "Delete" button in the toolbar at the top of the table. A library can only be deleted if it has no library aliquots. Any library aliquots must be deleted before the library can be deleted. A library can only be deleted by its creator or a MISO administrator.