FlowCAP-3: Evaluation of automated flow cytometry data analysis methods now open

[Ryan Brinkman]

We are pleased to announce the opening of the FlowCAP-III competition, evaluating automated flow cytometry data analysis methods. To register and obtain download information for the FlowCAP-III datasets please send an email to flo...@flowsite.org<mailto:flo...@flowsite.org>.

Flow cytometry has been widely used by immunologists and cancer biologists for more than 30 years as a biomedical research tool to distinguish different cell types in mixed populations based on the expression of cellular markers. It has also become a widely used diagnostic tool for clinicians to identify abnormal cell populations associated with disease. In the last decade, advances in instrumentation and reagent technologies have enabled simultaneous single-cell measurement of tens of surface and intracellular markers, as well as tens of signaling molecules, positioning flow cytometry to play an even bigger role in medicine and systems biology. However, the rapid expansion of flow cytometry applications has outpaced the functionality of traditional analysis tools used to interpret flow cytometry data such that scientists are faced with the daunting prospect of manually identifying interesting cell populations in 20 (and now 40-100) dimensional data from a collection of millions of cells. For these reasons a reliable automated approach to flow cytometric analysis is desirable. While there has been a growing interest among the scientific community in developing these methods, guidance for end users about appropriate use and application of these methods is scarce.

In response to this need, we are pleased to announce the Flow Cytometry: Critical Assessment of Population Identification Methods (FlowCAP-III) challenges (http://flowcap.flowsite.org/). The goal of FlowCAP is to advance the development of computational methods for the identification of cell populations of interest in flow cytometry data. FlowCAP is providing the means to objectively test these methods using common datasets. A manuscript detailing the results of the first two FlowCAP challenges is currently under revision for peer-reviewed publication. FlowCAP-III consists of challenges for prediction of a clinical/biological outcome as well as comparison with manual gates in cross-institute studies. A full description of the challenges is attached, and available from the FlowCAP website.

An NIH/NIAID-sponsored summit will be held for participants at the NIH campus from 29 to 30 Nov 2012. Several travel awards are available to our best participants. To register for the meeting (free!) please see registration website: http://palladianpartners.cvent.com/d/jcqwb4.


Ryan Brinkman, on behalf of the FlowCAP Organizing Committee:

Nima Aghaeepour, British Columbia Cancer Agency
Ryan R. Brinkman, British Columbia Cancer Agency
Greg Finak, Fred Hutchison Cancer Research Center
Raphael Gottardo, Fred Hutchison Cancer Research Center
Tim R. Mosmann, University of Rochester Medical Center
Richard H. Scheuermann, J. Craig Venter Institute

[Niko]

Hi Ryan, sorry maybe I have missed something but are the dates right?  Is the summit really going to be held in two months?

On Thursday, 27 September 2012 01:45:41 UTC+1, Ryan wrote:

[Ryan Brinkman]

Yes, the timeline (at the bottom of the summary document) is:

Timeline
· Call for participants: 26.Sept.2012
· Primary deadline for submitting results to challenge 1: 23.Oct.2012
· Deadline for submitting results to challenge 4: 01.Nov.2012
· Deadline for submitting results to challenges 2, 3, and the second part of challenge 1: 08.Nov.2012
· The third FlowCAP summit will be held on NIH's Campus, Bethesda, MD, 29-30.Nov.2012 (http://palladianpartners.cvent.com/d/jcqwb4). A limited number of travel awards will be available to our best participants.

What is the cause of your concern?

Cheers,
Ryan

On 2012-09-27, at 5:44 AM, Niko wrote:

Hi Ryan, sorry maybe I have missed something but are the dates right? Is the summit really going to be held in two months?

On Thursday, 27 September 2012 01:45:41 UTC+1, Ryan wrote:

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[Ryan Brinkman]

Sure thing Chris, very happy to have proprietary solutions involved in FlowCAP and use it for comparison purposes. Post peer-reviewed publication all datasets, results, our code for processing the results to get scores, etc. (basically everything you need to reproduce FlowCAP) is freely released to the community for any use. We'd even be happy to walk you through F-measure statistics code (everything was done in R) should you get stuck when comparing your results to the ensemble of the current methods (which gives the best performance). We are resubmitting FlowCAP 1&2 manuscript next week and so we hope you can start with those pretty soon. We learned a great deal putting the first two FlowCAPs together and we expect that publication and release of FlowCAP-3 shouldn't take anywhere near as long. In the meantime the data from the first 2 FlowCAPs should keep you busy enough I expect.

I'll send out another announcement about FlowCAP 1& 2 datasets being available as soon as we hit the newsstands.

Cheers,
Ryan


On 2012-09-27, at 1:04 PM, Chris Bray wrote:

> Hi Ryan,
>
> Thank you for informing me of the next round of Flow CAP challenges. We at
> Verity agree that it is important to have well evaluated and tested methods
> for analyzing flow data. The flow community in general is becoming more
> aware of the need for these methods to be automated. We appreciate your
> efforts to advance the interest and development in this area.
>
> We understand your desire to have the participating methods open and
> completely reproducible. However, given the importance of this type of
> analysis, is there a way that a proprietary analysis technology could be
> tested and compared in Flow CAP?
>
> Regards,
> Chris
>
> Chris Bray
> Software Engineer
> Verity Software House
> Phone: 207-729-6767 x106
> Email: c...@vsh.com

[Nikolas Pontikos]

Hi Ryan, probably I've misunderstood something but I was under the
impression that once the datasets were released then we would have
more time to develop a solution to one of the challenges.

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