October 30, 2011  |  Cytobank, Flow Cytometry  |  By  |  1 Comment

Cloning Experiments in Cytobank

Something we’ve found useful in analyzing our own data here at Cytobank is the ability to clone an experiment instead of having to download and re-upload files. If a colleague has shared an experiment with you and you don’t want to erase their hard work as you begin your analysis, make a clone! If you simply want to save time performing iterations of your own experiment analysis, make a clone! Experiment clones link back to the original experiments from which they were created on the Experiment Details page, so you’ll always have easy access to the original context. We’ve given you a variety of options for cloning, and you can find them under the “Cloning/Copying” section of the Actions box on the Experiment Details page.

 

CLONE EXPERIMENT

Choosing to clone an experiment makes a full copy of the experiment, complete with all FCS files, gates, annotations, reagent labels, compensation matrices, protocols, and attachments. Let’s suppose a collaborator has shared an experiment with you. You want to tweak the existing gates without having to redraw them entirely, but don’t want to overwrite the collaborator’s own gates. You can clone a full copy of the experiment and then make the changes in your clone, saving yourself the time that would have been spent redrawing gates and the headache of realizing you erased someone else’s hard work. From an organizational standpoint, you may also want to clone a copy of an experiment shared with you if you want a copy that contains only your own saved illustrations, notes, and attachments, including presentations.

With your own experiments, you might also want to make full clones if you want to subtly tweak existing gates or annotations to perform slightly varying analyses of your own data. “Clone Experiment” can help you do just that.

When you clone an experiment, the clone name contains “(Clone)” at the end, by default.

SELECTIVE CLONE

Selective Cloning allows you to choose subsets of FCS files to copy into a new experiment while specifying whether to bring over the gates, compensation matrices, annotations, reagent labels, protocols, and attachments – you can choose to copy over some or all of these components, helping you make copies of experiments that can be analyzed in different ways. Perhaps you want to preserve how files are categorized into Conditions and Timepoints, but draw gates from scratch for an alternative analysis – use Selective Clone to clone all files with all annotation, but no gates. Maybe you want to alter how files are categorized into Conditions and Sample Types, but want to preserve gated populations – use Selective Clone to copy all files and gates, but none of the annotations. Selective Clone can help you perform iterations of experiment analysis without having to start from scratch, whether on your own experiments or experiments shared with you.

You can also use Selective Clone to split off smaller pieces of a large experiment for separate analysis, or to separate files that require different annotation, gating, or compensation.

CLONE FCS FILES

There may be times when you want a completely fresh start, for example if you are using a dataset to teach flow cytometry analysis, or if you are a computational biologist trying to automate analysis. Clone FCS files is also useful if you want to share only the raw data with a colleague without sharing your analyses and other related information. By cloning FCS files only, you are copying the raw data into a new experiment without bringing over any gates, annotations, reagent labels, compensation matrices, protocols, and attachments that are associated with the original experiment.

Let us know if you have any questions about this functionality or any others!

– Angela