Cytobank – As the cell flows

A New Way to Publish Data: Cytobank Reports

May 6, 2011 at 5:15 pm cytobank 4 comments

We’re excited to announce Cytobank Reports, a new feature on Cytobank that will soon enable users to “publish” their data and findings. We’re also excited to announce that the first Cytobank Report (available here) features the mass cytometry study published today in Science, reporting on the simultaneous measurement of 34 parameters in single hematopoietic cells.

Also, more details to come, but stay tuned for a new resource from BD Biosciences powered by Cytobank Reports. (If you’re attending IMMUNOLOGY 2011 or CYTO 2011 this month, stop by our booth to preview this resource!)

In developing Cytobank Reports, we are moving towards realizing one of our key goals: effective communication of flow cytometry results. Figures in a journal article represent only one end of the information spectrum. Though easy to read, static figures fail to capture details of analysis and lack the depth of information necessary for true transparency and openness, particularly in a field like flow cytometry.

The new functionality on Cytobank enables us to create a customizable Report that not only includes plots and descriptions but also links to Saved Illustrations in Cytobank, gating hierarchy for the experiments shown, and sections for abstracts, protocols, and other pertinent details. From the Report, readers can log into Cytobank to view and interact with the data.

Why We Need Reports

With its sharing features, Cytobank helped to fill a key NIH mandate for making published data and results available to the scientific community. Cytobank Reports builds on this by providing a public interface from which to view analyzed data and to access the raw data. Cytobank Reports will work together with existing flow cytometry data standards, including MIFlowCyt (Minimum Information about a Flow Cytometry Experiment) and ACS (Analytical Cytometry Standard). (Learn more about these data standards here.)

Quick dissemination of data and findings is one important reason for Cytobank Reports. The rapid pace of research compared with the relatively slow turn-around time on peer-review and publication sometimes results in a disconnect between the most recent findings from the lab and published articles. Cytobank Reports can provide flow cytometry researchers with a medium in which they can quickly pull together plots and other information from experiments stored on Cytobank and assemble a Report to share exciting new findings with their colleagues.

The mass cytometry study (read our take on it here) demonstrates other reasons why a resource like Cytobank Reports is necessary. Both the size of the dataset (3.3GB) and the complexity of analysis preclude the utility of simple file-sharing to adequately make available all of the information necessary for understanding the details of the analyses and for deeper mining of the rich data set. With Cytobank Reports, plots and information can be organized neatly (much as they are in a journal article) and include links to directly access the analysis and the online data stored in Cytobank.

View the first Cytobank Report by going to the Nolan Lab’s Public Cytometry Collection and clicking on the “View Data” link. Anyone can view the Report, but, in order to access the data and analysis in Cytobank, an account on Cytobank is required (register for free).

Report functionality will be made available to users in the near future. In the meantime, we’d love to hear your questions, comments, and suggestions.

- The Cytobank Team

References:

Bendall SC, Simonds EF, Qiu P, Amir ED, Krutzik PO, Finck R, Bruggner RV, Melamed R, Trejo A, Ornatsky OI, Balderas RS, Plevritis SK, Sachs K, Pe’er D, Tanner SD, Nolan GP. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science. 2011 May 6; 332(6030):687-96. Abstract.

Spidlen J, Shooshtari P, Kollmann TR, Brinkman RR. Flow cytometry data standards. BMC Res Notes. 2011 Mar 7;4:50. PMID: 21385382 Open Access Article

Entry filed under: Announcements, Cytobank. Tags: Cytobank Reports, CyTOF, mass cytometry.