Welcome to the Cytobank platform! The Experiment Manager is the first page you are directed to upon signing into the Cytobank platform. 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.
Use the links below to jump to a specific section in this article:
- Overview of the Experiment Manager
- Customizing your Experiment Manager
- Inbox and Recent tasks
- The numbers before the experiment name
-
Finding experiments:
- Filter
- Search
- Group linked experiments
- 21 CFR Part 11 supporting tools
Overview of the Experiment Manager
(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.
(3) Use the Experiments and Projects menus to create new experiments and projects or to access an existing one.
(4) Filter the experiments in the Experiment Manager by ownership: All, Mine, Shared with me, Public, Cytobank Curated, or experiments in the Trash.
(5) Search experiments by words found in your experiment name or keywords.
(6) Displayed linked experiments and analyses grouped under the top-most ancestor experiment name.
(7) Metadata data columns indicate information about the experiment such as the number of FCS files, illustrations, or creation date and time.
(8) Choose Settings to select additional column metadata to display.
(9) Circled numbers indicate the number of linked clones and manually linked experiments (blue) and advanced analyses (purple) associated with that experiment.
(10) Identify Cytobank curated experiments by the Cytobank thumbnail.
(11) Click on an experiment name to open the Expanded Detail View with an overview of the experiment details.
(12) Access your profile settings.
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.
(Sort experiments by decreasing number of FCS files by clicking the column icon.)
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
- Automatic gating, Dimensionality reduction, clustering or CITRUS analyses
- Primary Researcher (PR)
- Primary Investigator (PI)
- 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 Apply label button. 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.
(Click Apply label to create and apply a new label or apply an existing one.)
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 Rename the label, customize the color or delete it. Deleting a label will not delete the labeled experiments.
If you want experiments with a specific label to always appear with your primary filters on the top left, click the circled number to the right of your label name 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.
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 unfiltered Experiment Manager.
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 or access the shared experiment.
The Recent tasks subsection will also show up in the Experiment Manager if you have background tasks (e.g. advanced analyses like tSNE-CUDA, FlowSOM runs or large export tasks) that are ongoing or recently completed unviewed tasks.
The Numbers before the experiment name
Top-most ancestor experiments 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 Automatic gating, dimensionality reduction, clustering 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
Filtering
You can easily find the experiment you need by using the pre-set ownership filters in the left panel of the Experiment Manager:
All: all experiments you have permission to access.
Mine: Experiments for which you are Primary Researcher (PR) or Primary Investigator (PI).
Shared with me: Experiments shared with you directly or through Project access.
Public: Experiments designated as Public.
Cytobank curated: Experiments uploaded by the Cytobank team that contain demo datasets featuring fluorescence and mass cytometry.
Trash: Experiments that have been deleted within the past 30 days.
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.
PRs: If experiments are shared with you, you will see a PR filter with a list of Primary Researchers for experiments shared with you.
Advanced analyses: Filters will be shown for each advanced analysis type in the Cytobank platform 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.
Searching
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, primary researcher, advanced analyses name. Structure your search in the syntax operator:searchterm, for example, is:mine. 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.
Group linked experiments
There is a toggle on the Experiment Manager header bar that lets you 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.
21 CFR Part 11 supporting tools
If your server has 21 CFR Part 11 supporting tools enabled, the Experiment Manager will include access to a Records page and Signatures status information. If you are interested in getting access to these tools, please contact us for more information.
Click on the Records menu on top of the Cytobank platform to access the Records page.
The Records page includes Experiment Records and Project Records that can be filtered and exported by typing on the Search box or clicking on the Export button.
The Signatures status is displayed as a metadata column and as a filter on the left side of the Experiment Manager.
If you have an Approve signature role assigned in a Project, the Inbox subsection of the Experiment Manager will appear when a new experiment is ready for you to sign and approve.
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