June 14, 2012  |  Announcements

Cytobank Reports: Cisplatin Viability Stain for Mass Cytometry

The newest edition to our repertoire of Cytobank Reports is the work of Harris Fienberg, a Ph.D. candidate in Garry Nolan’s lab at Stanford University. Harris and colleagues developed a cisplatin-based viability stain for mass cytometry, which now allows researchers to discriminate between live and dead cells in mass cytometry experiments. You can visualize and analyze the raw data first hand on Cytobank. Click here to access the report.

You can also read more about Reports in general in our previous blog post on Cytobank Reports.

– Angela

June 11, 2012  |  Announcements

Upcoming meeting: CYTO 2012

CYTO 2012 is coming up later this month, and we thought we’d highlight some posters and talks.

Make sure to stop by the DVS Sciences booth (#412) to learn about Cytobank’s mass cytometry analysis resources, and visit the BD Biosciences booth (#101) for information on the Cytobank-powered FACSelect resource.

June 23-27, 2012
CYTO 2012
XXVII Congress of the International Society for Advancement of Cytometry (ISAC)
Congress Center Leipzig
Leipzig, Germany

Friday, June 22

Pre-Congress Course: Advanced Flow Cytometry Data Analysis

Module 2: Visualizing Data
Talk 2: Data Analysis in the Cloud: Community-based analyses, heat maps, SPADE – Jonathan M. Irish
10:45 – 11:05am

Module 4: Application-Oriented Data Analysis Issues
Talk 3: Phosphoantigens – Jonathan M. Irish
2:30 – 3:00pm
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May 5, 2012  |  Announcements

PDF Enhancements in Cytobank

On Cytobank, you can download the Illustrations you’ve built with our Print View and PDF tools. These are useful for generating figures for publications, printing for your lab notebook, and keeping a local copy of your Illustrations.

Our latest additions to this functionality include the ability for users to change the page size of PDFs such that large illustrations are no longer truncated horizontally.

Here is an overview of the changes:

Page formatting options

You can now select among a range of paper size options for PDFs, including three fixed-size options that constrain the page dimensions if you’re looking to print your plots (Letter, A4, and Poster) and two auto-fit options that scale the width and height of the PDF to exactly fit your document dimensions. The difference between the two auto-fit options has to do with limitations imposed by Adobe Acrobat Reader software, which will only open documents that do not exceed 200 inches in either dimension. So, if you plan on generating very large arrays of plots and want to use Adobe Acrobat Reader to view the PDF, you’ll need to select the “Very Large” auto-fit option, which inserts page breaks every 200 inches. If you do not want page breaks in your PDF and can use alternate software such as Adobe Illustrator to open your PDF, then choose the “Infinite” auto-fit option. With every page formatting option, if you choose a plot size and type combination that exceeds the width of the page format you have selected, an orange warning box will appear on the PDF generation page asking you to select a format with larger dimensions or to alter your plot size.


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April 30, 2012  |  Announcements

Importing Core Facility Flow Data to Cytobank

We’ve recently added functionality allowing users to import their flow cytometry data directly from their core facility to Cytobank for storage and analysis. The initial phase of this effort is a collaboration between Cytobank and the Stanford University Shared FACS Facility, where researchers can now directly import their data collected at the facility into Cytobank.

For Stanford users, there are two ways to import your data to Cytobank. One is a “Cytobank” link at the bottom of the email users receive after collecting their data.  A user can also initiate data import from the FACS facility by going to http://facs.stanford.edu and clicking on the “Data Archive” link.

Watch our short video to see this in action, or download the PDF guide.

– Angela

February 29, 2012  |  Announcements

The Benefits of a Hosted Cytobank

You are probably familiar with our main server located at http://www.cytobank.org, but did you know that we offer hosted versions of Cytobank? With a hosted model, an individual lab or company has a server reserved for their exclusive use. The primary advantages of having your own hosted Cytobank include: 1) Premium Functionality, 2) Dedicated Computing Resources, 3) Access Control and Usage Monitoring, and 4) Premium Support and Quality Assurance. An additional perk is that you choose a name for the hosted Cytobank that shows up in the address (mylabname.cytobank.org, where ‘mylabname’ is a chosen name of your lab or group).

To help you consider if a hosted solution is right for you, here are some details about these advantages:

Premium Functionality

Having a hosted Cytobank means that you will stay current with cutting edge flow cytometry analysis techniques. Our hosted servers offer premium analysis functionality, such as SPADE and Dose Response Analysis. These tools are not available on the main Cytobank server (www.cytobank.org) and include implementations unique to Cytobank.

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January 21, 2012  |  Announcements

Introducing the Newly Redesigned Cytobank Support Portal

If you’ve clicked the “Support” link at the top of the Cytobank webpage, you may have noticed that our support portal has a new look and some new features.

Search our Knowledge Base

Our new support site has a Knowledge Base filled with articles to augment your Cytobank experience. You’ll find tutorials on our functionalities using real datasets, articles guiding you in both basic and advanced Cytobank usage, and answers to frequently asked questions. You can browse through article sections or conduct a keyword search of the Knowledge Base.

What kind of support can I receive from Cytobank?

We offer a wide range of support for your flow cytometry endeavors:

  • One-on-one WebEx-based training to get you started using Cytobank
  • Biology consulting support: How to design experiments, what to measure, selecting reagents, how to build figures, how to share datasets from your peer-reviewed publications
  • Troubleshooting
  • Data security
  • Technical support for networks
  • Inquiries about getting started with premium functionalities such as SPADE and dose response

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January 21, 2012  |  Announcements

Getting Your Lab Organized on Cytobank

With a new year ahead of us, you might be thinking it’s time for a fresh start. Maybe it’s time to organize the experiments that resulted from a flurry of work at the end of last year, or maybe you manage a lab and would like to keep past and ongoing experiments organized as people join and leave the lab. In this post, we’ll share our thoughts on how Cytobank can help you achieve these goals.

Hosted models of Cytobank

You may be familiar with our main server at http://www.cytobank.org/cytobank/, but did you know that we can host an instance of Cytobank specifically for your lab group? With these hosted solutions, your lab manager or PI controls who has access to your server and can guide the group in configuring projects to keep various research branches well organized. Read our previous post on Projects to learn more about Projects. Hosted models of Cytobank also have the advantage of offering you premium functionality that isn’t available on our main server, such as SPADE and dose response.
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November 30, 2011  |  Announcements

Highlights of the Cytobank Blog

As the end of 2011 approaches, we thought we’d take this opportunity to highlight posts from earlier days.

The Cytobank Story – Read about how the need for dynamic summaries of experiment results linked to the underlying single cell data resulted in the creation of Cytobank.

 

Cytometry in the Cloud – Advances in flow cytometry now enable researchers and clinicians to simultaneously measure a large number of cellular parameters. Learn about how doing cytometry in the cloud with Cytobank can accelerate data analysis, foster collaboration, and provide data back-ups.

Mass Cytometry: Vaporizing Cells in the Name of Science – Learn about mass cytometry, where antibodies are conjugated to element isotopes instead of fluorphores, increasing the number of cellular parameters that can be assayed in one sample tube. Access the raw data from a Nolan lab dataset published in Science this year, and try your hand at analyzing mass cytometry data yourself!
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