[ML-news] Announcing flowCAP - Flow Cytometry: Critical Assessment of Population Identification Methods

[Ryan Brinkman]

We are pleased to announce the opening of the first set of flowCAP
challenges. The goal of flowCAP is to assess computational approaches
for the identification of cell populations of interest in flow
cytometry data. This problem is very close to the clustering problem
in machine learning.

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 greater 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
dimensional data from a collection of millions of cells. For this
reason a reliable automated approach to flow cytometric analysis is
desirable. While there has been a growing interest among the
scientific community in developing such methods, guidance for end
users about appropriate use and application of these methods is
scarce.

In response to this need, we are conducting the Flow Cytometry:
Critical Assessment of Population Identification Methods (flowCAP)
challenge. The first set of flowCAP challenges provide the means to
objectively test approaches for the identification of cell populations
of interest in flow cytometry data by comparison to manual analysis by
experts using common datasets. Datasets and challenge guidelines are
now available at http://flowcap.flowsite.org.

Time Line

Release of materials for challenge 1 and 2: 01 MAR 2010
Submission deadline for challenge 1 and 2: 14 JUN 2010
Release of materials for challenge 3: 14 JUN 2010
Submission deadline for challenge 3: 07 JUL 2010
Release of materials for challenge 4: 07 JUL 2010
Submission deadline for challenge 4: 01 AUG 2010
Public release of the results: 01 SEP 2010
flowCAP summit: During the last weeks of September 2010

Summit

An NIH/NIAID-sponsored summit will be held at the NIH campus during
the last weeks of September 2010 for two days. flowCAP participants
(travel will be subsidized) and users will be invited to present their
work and participate in group discussion.

Cheers,
Ryan Brinkman on behalf of the the flowCAP Organizing Committee:

Ryan Brinkman, British Columbia Cancer Agency
Raphael Gottardo, Clinical Research Institute of Montreal
Richard H. Scheuermann, University of Texas Southwestern Medical
Center
Jill Schoenfeld, TreeStar Inc.

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