Samples

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Data Browser: Samples

The Sample Browser allows users to create and manage samples they are authorized to access. Access permissions are granted through lab-based, user-based, or collaborative permissions authorized by a Principal Investigator (PI).

The Sample Browser includes:

• Create New Sample button that allows creating one or multiple samples
• A Navigation Pane on the left side for switching between sample views and hierarchical organization of My & Lab data described below.
• A Sample Table for displaying rows of samples with columns representing metadata that may be sorted and filtered.
• Customization Tools in the upper-right corner to configure columns, saved views, and filters.
• Advanced Selection, Sorting, and Filtering of samples
• Ability to perform Actions quickly and easily from a context menu to one or more samples

Navigation Pane

The Navigation Pane allows users to quickly access datasets across different categories.

All Samples

Displays all samples the user can access.

My & Lab Data

Displays samples accessible via user- or lab-based permissions.

This section includes an organization mirroring a file system:

• My Collections – personal collections created by the user.
• Spawned Sample Collections - collections created by the user through multi-sample creating tool.
• Projects – high-level groupings for sample organization that mirror data organization in Dataset Browser and consists of
  • Studies – reside inside Projects
    • Collections – reside inside Studies

Sample Table

The Sample Table displays all samples for which the user has at least read access.

Table Rows

Each row highlights a sample in the NAN archive

Table Columns

Columns represent different metadata fields for the sample. There is a default list of columns that are displayed, but users can toggle different columns on and off as desired by selecting the wrench icon in the upper right hand corner of the dataset browser. Columns may be re-ordered by dragging them. The columns to be displayed, along with their order, is saved in the NAN database as a user preference and will persist across sessions, browsers, and computers. See Sample Columns for complete list of columns with a short description and the types of filters that may be applied.

Icon badges

Icon badges in the Name column represent additional information about the sample and provide navigation links as described here

• A small clock icon indicates that the dataset associated with the sample has been published. Clicking the icon will allow you to navigate to previous published versions or the datasets and associated samples
• A link icon indicates that the sample has been linked to a dataset and clicking the link icon will bring you to the Dataset Browser filtered on the linked sample.

Pagination

At the bottom of the table is a pagination control. Users can move between pages and adjust the number of rows displayed per page: 25, 50, 100, or 500 samples per page

Customization Tools

Wrench Icon

• Brings up a pull-down menu to toggle which columns are shown in the sample table.
• Allows a View to be Created, overwritten, or deleted. Note that the columns that are displayed are saved as a user preference are not tied to a View. A View defines the applied filters and sorts to the columns, and is independent on which columns are visible.

Saved Views

• Pull-down list of saved views (defined filters and sort)

Quick Filters

Quick filters apply predefined views to narrow down displayed samples. Current Quick Filters include:

• My Data – samples owned by the logged-in user.
• Hide Inactive Samples – filters the table to display only active samples, hiding those marked as inactive.

Remove Filters Icon

• When no filters are applied to any columns the icon appears faded and is not selectable
• When not faded and selectable will clear all applied filters and sorts
• if the icon has an exclamation point, it indicates hidden column filters or sorts and pressing it prompts whether to remove all or only those affecting non-visible columns.

Selection Icon

• Shown as a circle with a line through it. The Icon become visible when one or more datasets are selected and pressing it will clear all selections. Can be very handy when datasets are selected, but not visible on the screen.

Selection, Sorting, and Filtering

Selection

Samples can be selected by clicking anywhere on the corresponding row. The Sample Browser supports multi-selection, with a checkbox next to each Display Name indicating selection status.

To select multiple datasets:

• Hold the Ctrl key (or Cmd on Mac) and click on Display Names to toggle individual selections.
• Hold the Shift key to select a range from the last selected to the current dataset.

IMPORTANT NOTE: There is inconsistent behavior when using Shift and Ctrl keys with the checkboxes. It is strongly recommended to use the Display Name for selection. Treat checkboxes only as visual indicators.

By default, datasets are sorted by date, with the most recent shown first. Sorting and filtering are available for all columns.

Sorting

Each column header includes a sort button (up/down arrows). Click once to sort in ascending order; click again to sort in descending order.

Filtering

Each column header includes a filter icon that opens a filtering dialog. The available filter types depend on the column's data type. The table below summarizes available filters. See Dataset Columns for which filter type apply to each column.

Filter Types

Date	Boolean	Text	Number	Controlled List Classification	Controlled List Transfer Mode	Tags
equals	yes	equals	equals			includes
before	no	does not equal	does not equal			does not include
after	is unset	contains	greater than
	is set	does not contain	less than
		similar to
		starts with
		ends with
		is unset

For all filter types except Boolean, users can add multiple filter rules per column. If multiple rules are added, the user must specify whether to "Match All" (AND) or "Match Any" (OR). This setting is ignored if only one rule is applied.

Advanced filters can also span multiple columns. While building complex filters may take effort, users can save views for reuse. See Customization Tools for details.