Cytobank User Stories: Harris Fienberg
Welcome to Cytobank User Stories, a series featuring interviews with Cytobank users on their research, scientific vision, and use of flow cytometry.
This time we interview Harris Fienberg, a Ph.D. candidate in the Nolan Lab at Stanford University. Harris’s most recent publication features his work developing a cell viability detection protocol for mass cytometry using a platinum-based reagent. You can view and analyze the data firsthand via his Cytobank Report.
Send us feedback and let us know who you’d like to hear from (including yourself)!
| What are you excited about in science? What is your scientific vision? |
 Over the last 30 years we’ve gained an extraordinary understanding of the molecular components that make up cellular signaling cascades. However, we’re just beginning to understand how the various components of the cell work together to integrate signals and relay these signals to form phenotypic outcomes. I’m interested in gaining a more holistic understanding of cellular communication. In the future I believe that specific proteins will be seen less in the context of certain signaling pathways and more as words that the cell uses to make a message. I think that reaching this more comprehensive understanding of cellular signaling will be more about about integrating data with smart data analytics than gaining more and more “-omics” style data sets.(more…) |
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.
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
Cytobank User Stories: Joshua Brody, M.D.
Welcome to Cytobank User Stories, a series featuring interviews with Cytobank users on their research, scientific vision, and use of flow cytometry.
This time we interview Joshua Brody, M.D., Director of the Lymphoma Immunotherapy Program at Mount Sinai School of Medicine. Joshua’s recent publications include his studies showing that in situ vaccination with a TLR9 agonist induces systemic anti-lymphoma clinical responses, as well as his studies using immunotransplant to preferrentially expand T-effector cells to cure large lymphoma tumors.
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| What are you excited about in science? What is your scientific vision? |
 Joshua Brody, M.D. (more…) |
Making Beautiful Plots: Data Display Basics
You’ve labored at the bench and generated data that you’re about to meticulously analyze before preparing the results of your hypothesis-testing for presentation. In this post, we’ll discuss elements that factor into making beautiful (and consistent) displays of data. View our recent post on Analysis Consistency in Flow Cytometry for a discussion of broader themes relating to analysis consistency.
To summarize what will follow in short: make sure all of your data are on scale, accurately compensated, and make sure all your plots are well-labeled.
Choosing plot types, appropriate statistics, and telling the full story
There are a number of plot types that can help you tell your story in different, visually pleasing ways when used appropriately. Among the flashier ways to display data are heatmaps, histograms, and histogram overlays. These one-dimensional representations owe their appeal largely to their ability to convey an easy-to-understand message: “This population changed in X amount in Y condition.” Where this gets tricky is if you’re trying to describe a heterogeneous population. When deciding on a plot type to use to convey your story, you’ll want to make sure you’re telling the whole story, and not omitting important information about the behavior of subsets in the course of eliminating a dimension of data display. In Cytobank, you can mouse over a heatmap square to display the underlying dot plot, which will reveal another dimension of information of your data.
Figure 1. Example of a well-labeled figure using one- and two-dimensional representations.
Excerpted from Irish JM et al (2010) PNAS, 107(29):12747-54, Figure 1B.
(Click on the image for higher resolution)
(more…)
Cytobank User Stories: Ernesto Diaz-Flores, Ph.D.
Welcome to Cytobank User Stories, a series featuring interviews with Cytobank users on their research, scientific vision, and use of flow cytometry.
This time we interview Ernesto Diaz-Flores, Ph.D., a postdoctoral fellow in Mignon Loh’s lab and previously in Kevin Shannon’s lab, both located at UCSF. Ernesto’s recent publications include his contributions to studies of p53 loss in acute myeloid leukemia, STAT5 activation in myeloid malignancies, and K-Ras(G12D) expression in primary hematopoietic stem/progenitor cells.
Send us feedback and let us know who you’d like to hear from (including yourself)!
| What are you excited about in science? What is your scientific vision? |
 Ernesto Diaz-Flores, Ph.D. Science is a very exciting field because every new question represents a new challenge. As a scientist, my biggest contribution would be to tease out the biochemical mechanisms leading to leukemia and use that information to predict therapeutic responses prior to subjecting the patient to the treatment. (more…) |
