User Stories: Claude Chew and his experience with Cytobank 4.2 release

Welcome to Cytobank User Stories, a series featuring interviews with Cytobank users on their research, scientific vision, and use of fluorescence and mass cytometry.

This week we interview Claude Chew, a Flow Cytometry Specialist Senior at University of Virginia in
Charlottesville, VA.  We asked Claude to share with us his favorite features from our 4.2 release and to describe how this release has helped to improve his scientific workflow.

What are you excited about in science? What is your scientific vision?
Claude Chew


Claude Chew
Flow Cytometry Specialist Senior at University of Virginia

My vision is to try to bring together the technical aspects of flow/mass cytometry with biology. My experience is that there is often a disconnect between the two. Hopefully there is a way to more fully integrate these aspects to make a fully-functioning unit that will be a powerful tool for looking into how life works at the single cell level! I’m particularly excited about recent developments in the field of high-dimensional analysis with the advent of the CyTOF and the data analysis platforms that have and continue to be generated to meet the challenge of ‘big data’.
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March 20, 2015 at 10:00 am Leave a comment

User Stories: Erica Alvendia and her experience with Cytobank 4.2 release

Welcome to Cytobank User Stories, a series featuring interviews with Cytobank users on their research, scientific vision, and use of fluorescence and mass cytometry.

This time we interview Erica Alvendia, a Research Associate at Primity Bio in Fremont, California.  We asked Erica to share with us her favorite features from our 4.2 release and to describe how this release has helped to improve her scientific workflow.

What are you excited about in science? What is your scientific vision?
Erica Alvendia


Erica Alvendia
Research Associate at Primity Bio

Science has such a broad subject range that there is always something new to learn. The knowledge you can obtain seems endless and that’s what I find exciting. More specifically, I’m fascinated with reading up on the pathogenesis of various diseases (especially the rare ones) and learning about the different treatments available for them. With that said, it’s my scientific vision to find treatment options for diseases that have none. Primarily any disease that results in either a physical or mental disability.
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March 16, 2015 at 7:00 am Leave a comment

Complete your viSNE workflow and back-gate using Dot Overlays

Always listening to our user feedback, we heard your requests to complete your viSNE workflow by overlaying Populations to uniquely color the viSNE continents. Our latest release brings you a new plot type configuration we call Dot Overlays that allows you to do this, and also lends itself to traditional back-gating approaches that allow you to see child populations in the context of ancestors.

Dot Overlays

Dot Overlays

Dot Overlays allow you to overlay not just Populations, but any of the Figure Dimensions within a single Dot Plot. Now you can compare Populations, Timepoints, Conditions, Individuals, and any dimension of your choosing within Dot Overlay plots. Just drag any figure dimension into the second (overlaid) position. See how your time course stacks out, compare your stimulations/titration data, or just see how populations sit in the context of each other (traditional back-gating). Visit our knowledge base for the full scoop on how to set up Dot Overlays, including a video tutorial.
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March 12, 2015 at 8:20 pm Leave a comment

Introduction to Grant Writing: Inserting Cytobank as a line item in your submission

Data retention: key to NIH policy for successful grant funding

Data sharing and preservation are central components of successfully-funded grant submissions to the NIH. Since 2003, the National Institutes of Health has maintained the NIH Data Sharing Policy and Implementation Guidance, and even released a brochure to help guide those seeking a successfully funded grant. These policies emphasize that “Data should be made as widely and freely available as possible while safeguarding the privacy of participants, and protecting confidential and proprietary data.”

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February 12, 2015 at 12:12 pm Leave a comment

New Breakthrough Method in Mass Cytometry

Zunder and Finck et al., from the Nolan Lab at Stanford University report new cell barcoding reagents for mass cytometry that incorporate the previously unused element palladium, expanding the number of mass cytometry measurement parameters by six. Leveraging this methodology, they present a new barcoding scheme which can be used to identify and remove cell doublets, as well as provide software that deconvolves barcoded datasets via a “single-cell debarcode” algorithm [1].

The dataset for this paper is hosted and publicly available on Cytobank Community; a free resource for the analysis, workflow, and protocols represented in this paper. Cytobank is the cloud-based analytics platform for single cell analysis. In Cytobank you can easily access and analyze multi-parameter data, visualize findings, produce high-impact graphics, and securely connect and collaborate with colleagues around the world.

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February 5, 2015 at 11:06 am Leave a comment

viSNE now available on Cytobank

The Cytobank team has been working diligently to provide top tier analysis solutions for our users; viSNE in Cytobank is our most recent addition and we are very excited about what it has to offer.

What is viSNE? And how does it work?

viSNE is a tool for reducing high-parameter data down to two dimensions, making it easy for scientists to not only visually identify interesting and rare biological subsets, but also gate single cell events across different samples.

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November 13, 2014 at 10:51 pm Leave a comment

Behbehani et al. Transient Partial Permeabilization with Saponin Enables Cellular Barcoding Prior to Surface Marker Staining.

Greg BehbehaniGreg Behbehani, a physician scientist, is focused on translational research, leveraging his work treating patients in clinical trials for high-risk hematologic malignancies towards the ultimate goal of utilizing data generated in the laboratory to predict ideal chemotherapy regimens and optimal novel agents for individual patients.

Most recently Dr. Behbehani has contributed to a published paper surrounding research of new protocols for barcoding on mass and fluorescence cytometry [1]. The dataset is hosted and publicly available on Community Cytobank; a free resource for individuals interested in the analysis, workflow, and protocols represented in this paper.

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November 10, 2014 at 1:04 pm Leave a comment

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