Cytobank – As the cell flows

Cytometry in the Cloud

April 9, 2011 at 12:15 pm Stephanie Huang 3 comments

At Cytobank, we do cytometry in the “cloud”. What does that mean and how can that help you?

• Surviving the Data deluge
• Clarity, Access, and Collaboration
• Security and Back-up

Surviving the Data Deluge

Advances in flow cytometry now enable researchers and clinicians to simultaneously measure a large number of cellular parameters. Along with that informational power comes a tremendous increase in the scale of data and a concomitant increase in demand for computational solutions.

Uploading your raw data to the cloud and analyzing this data in the cloud enables you to take advantage of computing power that may not be accessible in your own lab or department. Even smaller datasets can benefit from analysis in the cloud, which makes your results searchable and available from anywhere.

When you upload and analyze your files on Cytobank, you can avoid tying up local computational resources (i.e. computers in your lab or flow facility). We’ve made a number of recent updates to boost performance on Cytobank. Additionally, any new functionality we add to Cytobank (e.g. new plot types or statistics) is instantly available to all users.

The big data problem has been discussed by prominent journals. Nature Reviews Genetics last year published a review article titled “Computational solutions to large-scale data management and analysis”. (Our advisor Garry Nolan is an author on the article.) Also look for Cytobank’s cameo in the accompanying online slideshow! Science recently featured a recent multi-journal feature on the issues and solutions surrounding big data.

Clarity, Access, and Collaboration

Analysis of flow cytometry data is a complex, multi-step process often performed in multiple programs. This composite approach to data analysis, as well as the complexity of analysis (e.g. compensations, gates, etc.), presents a significant hurdle to researchers when sharing details of flow cytometry experiments with colleagues. With data and analyses in the cloud, there is no longer a time or space limitation to what you can share with colleagues. All they need to do is access the cloud and look for the details they need, whether it is the raw data, the final images, or something in between.

Cytobank was built with data management and sharing in mind. Sharing an experiment with another user on Cytobank (who can be located anywhere in the world) makes visible any of the important details you need to share, such as gates or scale settings. Depending on the level of access that you set (see below), your colleague can adjust your gates or compensation settings, make their own copy of your data, or construct their own plots – in other words, every step of the analysis can be shared, permitting maximum openness.

This is a key need in today’s multi-site and multi-disciplinary collaborations where different groups of users require different levels of access to the data.

Security and Back-up

With data in the cloud, there are understandable concerns about the security of data.

At Cytobank, you control who can see your data and how much access they have. In addition, we provide different versions of Cytobank – Cytobank HQ, Hosted Cytobank, or Deployed Cytobank – to meet the different needs of our users.

Another advantage to storing copies of your data on Cytobank is that our database is regularly backed up. If your computer (containing your FCS files and analyses) suddenly fails, those files and analyses are easily accessible on Cytobank and can be recovered.

Uploading data to the cloud also provides a convenient way to manage files in research groups – PIs or group managers can avoid having to chase down FCS files and analyses on members’ laptops, especially when those members transition to new positions. FCS files and experiments can be uploaded to Cytobank and categorized into projects, ensuring that files and analyses aren’t lost when researchers leave.

More questions about cytometry in the cloud? Send us an email or leave a comment below.

- Stephanie and Nikesh

Entry filed under: Cytobank, Flow Cytometry. Tags: access, back-up, big data, clarity, cloud, cloud computing, collaboration, cytometry in the cloud, data analysis, data deluge, data safety, flow cytometry, performance, sharing, web-based.