In the beginning, we wanted software that would give us a “big picture” view of our flow cytometry experiments. We initially created a software tool to make heatmaps using flow cytometry files. However, as we shared analyses with each other, we realized that this big picture view wasn’t enough. We also needed to explore the single cell data to derive deeper meaning from our flow cytometry experiments. In short, we wanted to have it both ways: we needed dynamic summaries of experiment results linked to the underlying single cell data, so that rare cell subsets and heterogeneous populations were not overlooked.
As we developed this software project, we realized that a web-based tool would solve a number of frustrating issues. We needed to share analyses with collaborators in other buildings, other cities, and other countries, and our datasets were too big to send by e-mail. We needed a system to annotate the data, so that we could remember what was in each flow file – the type of cells used, how the cells were stimulated, and which individual patient they represented. These annotations were in our written notebooks, but we wanted to be able to search this information electronically and group experiments into projects. We also wanted the analyses to be clear and organized for new lab members who might follow up on our research. Finally, we wanted the data to be securely stored and backed up, while also accessible, with the proper permissions, from any computer we were using.
By the time we had finished creating a web-based tool that met these needs, which we named Cytobank (see our paper in Current Protocols in Cytometry), hundreds of researchers around the world had uploaded several thousand experiments. The clear need for Cytobank led us to found Cytobank, Inc. in order to professionally develop, hone, and support web-based flow cytometry data analysis. We hired an outstanding development team and now provide multiple Cytobank solutions, including the free limited edition that is available at www.cytobank.org, as well as hosted solutions from Cytobank Inc.
– The Cytobank Team
Kotecha N, Krutzik PO, Irish JM. Web-based analysis and publication of flow cytometry experiments. Current Protocols in Cytometry. 2010. 53:10.17.1–10.17.24. PMID: 20578106