- Inbox and Recent tasks
- Overview of the Experiment Manager
- The Numbers before the experiment name
- Finding Experiments: Filtering, Searching, and Grouping linked experiments
- Customizing your Experiment Manager
Welcome to Cytobank! The Experiment Manager is the first page you are directed to upon signing in to Cytobank. It contains the Experiments you own or have permission to view. Experiments in your Experiment Manager can be searched, filtered, and organized with Labels. Clicking on an Experiment from the Manager will open the Expanded Detail View, a preview pane summarizing the experiment.
Inbox and Recent tasks
If you have experiments that were recently shared directly with you by another user, or background tasks in progress or recently completed (e.g. algorithm runs or large exports), you will see Inbox and Recent Tasks sections at the top of the experiment manager (link to Inbox article) when viewing the “All” filter.
The Inbox is a subsection of the Experiment Manager that appears at the top of the Experiment Manager when the ‘All’ filter, is selected and unviewed experiments to which the user was granted full, direct-share access (non-project). These experiments will be labeled “New” in front of the experiment name. If you want to remove an experiment from your Inbox, you can click the checkbox to the left of the experiment name, then click the button Mark as viewed at the top of the Experiment Manager.
The Recent tasks subsection will also show up in the Experiment Manager if you have background tasks (e.g advanced analyses like viSNE, FlowSOM runs or large statistics export tasks) that are ongoing or recently completed unviewed tasks.
If you don’t have any ongoing background tasks or unviewed items, then the inbox or the Recent tasks will not show in your experiment manager.
Overview of the Experiment Manager
(click to expand)
1) Click the Cytobank logo to return to the Experiment Manager at any time.
2) Click the "New Experiment" button to create a new Experiment and upload files. A new Experiment can also be created at any time from the “Experiments” menu.
3) Filter the Experiments in the Manager by ownership (All, Mine, Shared with me, Public, Cytobank Curated, or experiments in the Trash).
4) Search experiments by words found in your experiment name or keywords.
5) Metadata data columns indicate information about the experiment such as the number of FCS files, illustrations, and advanced analysis runs.
6) Choose Settings to select additional column metadata to display in (5).
7) Identify Cytobank curated public experiments by the Cytobank thumbnail.
8) Circled numbers indicate the number of linked clones and manually linked experiments (blue) and advanced analyses (purple) associated with that experiment.
9) Click on an experiment name to open the Expanded Detail View with an overview of the experiment details (see below).
The Numbers before the experiment name
Top-most ancestors display blue and/or purple-circled numbers, representing the number of linked experiments that they contain:
- The purple number represents linked advanced analyses, such as viSNE, SPADE, FlowSOM, and CITRUS.
- The blue number represents all other types of linked descendants (such as clones or manually linked experiments)
Finding Experiments: Filtering, Searching, and Grouping linked experiments
You can easily find the experiment you need by using the pre-set ownership filters in the left panel of the Experiment Manager (All, Mine, Shared with me, Public, Cytobank curated, or Trash).
All: all experiments you have permission to access
Mine: Experiments that you are PR or PI
Shared with me: Projects shared with you directly or through Project access
Public: Experiments designated as Public. (You will have to clone Public experiments to do any analysis on them.)
Cytobank curated: Experiments uploaded by the Cytobank team that contain demo datasets featuring fluorescence and mass cytometry, including up-and-coming technologies.
Additional filters will be shown if applicable to your experiments:
Archived: Experiments that have been tagged as archived. Note that data are not actually removed from the system.
Trash: Experiments that have been deleted within the past 30 days.
PR: If experiments are shared with you, you will see a PR filter with a list of PRs for experiments shared with you.
Advanced analyses: Filters will be shown for SPADE, viSNE, CITRUS, and FlowSOM experiments if you own or have access to any.
Labels: Filters for custom labels applied to experiments
Hidden filters: Filters that are toggled to Hidden
The number to the right of each of these headings is the number of experiments with that characteristic, regardless of whether Group linked is checked. E.g. you may have linked experiments hidden from Experiment Manager with Group linked checked, but they will still be accounted for in the left filter panel.
For a more customized search, use the search bar at the top of the Experiment manager. You can search by terms including Experiment ID, name, label, project, PR, SPADE, viSNE, CITRUS, FlowSOM. Structure your search in the syntax operator:searchterm, for example, “is:mine” (without the quotes). The search bar accepts multiple strings simultaneously (e.g. “is:mine has:visne”), giving you power beyond the defined filters. Tips: 1) Don’t leave any spaces around the colon. 2) For examples of how to structure your search, see the text that appears in the search box when you select filter on the left.
3) Group linked experiments
There is a toggle on the Experiment Manager header bar that lets the user "Group linked," experiments together. The toggle is checked by default.
When Group linked is checked:
- Only parent experiments are shown in the Experiment Manager. Linked descendants of the parent experiments are hidden.
- When you search or filter experiments, if the query matches descendants but not the top-most ancestor, then the matching descendants are shown and the top-most ancestor is not. If the query matches descendants as well as the top-most ancestor, only the top-most ancestor is shown, not the descendants.
When Group linked is not checked, all experiments are displayed, including any nested linked experiments.
Customizing your Experiment Manager
To help organize your Experiment Manager, you can customize the appearance in several ways:
- Sort order
Adjust the order in which experiments are listed by clicking on any of the column headings to sort by increasing or decreasing value, numerically or alphabetically.
- Experiment Manager Settings
Adjust which metadata columns are displayed by clicking the blue “Settings,” link. If you have an Inbox available, the Settings options can be customized separately for the Inbox. Options are available to adjust the number of rows displayed per page, and toggle on and off columns for Experiment ID, Experiment Name, number of FCS files, illustrations, SPADE, viSNE, CITRUS, or FlowSOM analyses, Primary Researcher, Primary Investigator, Project, Experiment Size, dates Created, Last updated, or Last viewed. Your preferred view will persist when you navigate away and later revisit the Experiment Manager.
- Create labels
Create custom labels for a single or multiple experiments by clicking on the checkbox to the left of the experiment name. Click the button that appears above called “Apply label.” This will create a colored label that appears next to the Experiment Name, as well as generate a filter for that label that appears in the left pane.
You can type in a new label name or choose an existing label to apply to the selected experiment.
To display only experiments with a specific label, click that label that now appears in the left pane. From this view, you can also customize the color of your label.
If you want experiments with a specific label to always appear with your primary filters on the left, click the circled number to the right of your label and options will appear to Star or Hide the filter. Choose “Star this filter,” to include it with the primary filters (as shown for the “Important,” label below), or “Hide this filter,” to hide the filter from the list of filters while keeping the experiment label.