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September 29, 2016  |  Announcements, Cytobank, User Stories

Customer Story: Reema Baskar, Stanford Medicine

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 Reema Baskar, a graduate student in the Cancer Biology Department at Stanford University, co-mentored by Sean Bendall and Sylvia Plevritis. We asked Reema about how she uses Cytobank’s high-dimensional tools to help elucidate mechanisms of drug resistance in cancer, and her early experience beta-testing our new CITRUS implementation.

What is an important problem in human health and/or fundamental biology that you’d like to address? What is your scientific vision?
ReemaBaskar_userstoryphoto400px
Reema Baskar
Cancer Biology Dept.
Stanford University

My vision is to develop high-dimensional techniques and computational tools to address the challenge of ‘big data.’ My hope is that these tools may be broadly applied to aid our understanding of the human condition. Technology, such as mass cytometry (CyTOF), has made it possible to capture different facets of biology such as cell function, epigenetic traits, and transcriptional readouts with infinitesimal single-cell granularity. More »

August 31, 2016  |  Announcements, API, Cytobank

Streamline and Automate Analysis with Our New API

CytobankAPIAchieve better results, faster. Automate your end-to-end pipelines with the Cytobank Platform via The Cytobank APIThe Cytobank API extends the power of the Cytobank Cloud to any software application. Now bench scientists can more seamlessly interact with computational biologists and reviewers to assess results of internal algorithms and pipelines. 

Now available in the Enterprise versionour RESTful API endpoints offer powerful advantages More »

August 12, 2015  |  Announcements, Publications

A Framework for Modeling the Immune System

Spitzer and Gherardini et al., from the Nolan Lab at Stanford University, report a novel bioinformatics approach to mapping the immune system called Scaffold (Single-Cell Analysis by Fixed Force- and Landmark-Directed).

Scaffold allows clustering of samples independently, thus allowing addition of new sample data over time. This approach requires users to develop or use a pre-defined reference map.

In their recent publication in Science, the authors reveal maps comparing immune organization among several tissue compartments, among mouse strains, between circadian states, and between species (mouse and human).
More »

June 19, 2015  |  Announcements, Cytobank, Flow Cytometry

Visit us at CYTO and FOCiS!

Come visit the Cytobank team at FOCiS and CYTO next week to learn more about what we’ve been up to, for some hands-on help, to share your wish list or just to chit-chat. We look forward to seeing you there!

Check out the various talks and posters at CYTO featuring Cytobank:

Saturday June 27, 2015

11:00 (Room: Alsh) – The First Multi-center Comparative Study Using a Novel Technology Mass Cytometry Time-of-Flight Mass Spectrometer (CyTOF2) for High-Speed Acquisition of Highly Multi-parametric Single Cell Data: A Status Report A. Nasaar, B. Carter, J. Lannigan, R. Montgomery, N. Paul, M. Poulin, K. Raddassi, A. Rahman and N. Rashidi. Yale Univ. Sch. of Med., Stanford Shared FACS Facilities, Univ. of Virginia Sch. of Med., Dana-Farber Cancer Inst., Fluidigm, Cambridge, MA, Icahn Sch. of Med. at Mount Sinai and Ragon Inst. of MGH, MIT and Harvard.

11:40 (Room: Alsh) – High Content Dissection of Human Melanoma Tumor Heterogeneity during Treatment Using Mass Cytometry J. Irish, D. Doxie, A. Greenplate, K. Diggins, H. Polikowsky, K. Dahlman, J. Sosman and M. Kelley. Vanderbilt Univ. Sch. of Med.

More »

June 12, 2015  |  Cytobank

Cytobank 5.0: Sweeping ease-of-use improvements

Cytobank 5.0 is on its way to customer sites, and includes sweeping ease-of-use updates driven by customer feedback, enabling you to reach your goal faster. We’ve implemented a three-level system, centralizing site-wide, experiment-wide, and page-specific actions and reducing time-to-goal.

We encourage you to watch our 90 second overview of the new navigation (below), or attend an upcoming webinar. You can also view the full contents of this release.

March 20, 2015  |  User Stories

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’.
More »

March 16, 2015  |  Cytobank, User Stories

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.
More »