What is Cytobank?

 

 

Cytobank is a way to manage, analyze, and share your flow and mass cytometry data on the web. Using a web browser, users can log in to the Cytobank website, create a new experiment, and upload a set of flow cytometry standard (FCS) files associated with that experiment. Each experiment can also contain attachments (such as Adobe PDF and PowerPoint documents and Excel spreadsheets). Users have an email-like interface (the Experiment Inbox) to organize and search their experiments. Users can also share their experiments with other users on Cytobank. The ability to do this from any computer with a web browser and Internet connection has many benefits that includes centralized and backed-up storage for your flow cytometry data and eliminating the need to clog up your Email inbox with FCS files. Furthermore, the experiments are searchable and sortable, and sharing can be managed per experiment or via collections of experiments (projects).

A common hurdle during flow analysis is keeping track of experiment details such as doses, compounds, timepoints, and other experimental variables. Cytobank's analysis system is designed to allow users to pivot, filter and organize their figures using Sample Tags, which is how scientific and experimental variables are stored in Cytobank. The more details that are provided, the more flexibility the user has in figure organization and pivoting. Users can now focus on questions such as which populations respond to an increase in dose or which patients have a low T cell count instead of trying to remember which FCS file the 1 ng/ml dose corresponds to.

Users can also choose to share their results with colleagues via a web link or URL. Clicking on this URL allows one to start with experiment results, drill down to the underlying raw data and facilitate sharing and discussion with labmates, colleagues, and others in the scientific community. Users can analyze their flow cytometry data and visualize results using standard flow cytometry plots (e.g. histograms and contour plots), via aggregate visualizations such as heatmaps and histogram overlays, and also via advanced visualization and dimensionality reduction algorithms such as SPADE, viSNE, and CITRUS.

In addition, communicating results is not useful if appropriate experiment details are not provided along with an experiment. In Cytobank, users are already providing these details during the course of analysis and are a few clicks away from sharing these details with collaborators around the globe.

Cytobank fills a key NIH mandate for making published data and results available to the scientific community, and has a Reports system for hosting an interactive analysis to accompany a journal publication.



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