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Challenge NIH Single Cell Analysis Challenge: Follow That Cell
NIH Single Cell Analysis Challenge: Follow That Cell
STATUS: Awarded
Active Solvers: 696
Posted: Aug 15 2014
Challenge ID: 9933618
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Many biological experiments are performed under the assumption that all cells of a particular “type” are identical. However, recent data suggest that individual cells within a single population may differ quite significantly and these differences can drive the health and function of the entire cell population. Single cell analysis comprises a broad field that covers advanced optical, electrochemical, mass spectrometry instrumentation, and sensor technology, as well as separation and sequencing techniques. Although the approaches currently in use can offer snapshots of single cells, the methods are often not amenable to longitudinal studies that monitor changes in individual cells in situ.

The NIH Single Cell Analysis Program (SCAP) is searching for novel methods for analyzing dynamic states of individual cells that can serve as the basis for predicting alterations in cell behavior and function over time. The ultimate goal is to develop new tools and methods that allow time-dependent measurements at the single cell level in a complex tissue environment to assess functional changes, provide information on the health status of a given cell, and help guide diagnosis and therapeutic treatments related to human disease states. Technological breakthroughs in this arena could allow researchers and physicians to identify rare cells in a mixed population such as individual cells that can transform and become cancerous; cells that are latently infected with a pathogenic virus; or cells that develop resistance to drugs over time. This challenge is structured in 2 phases: Phase 1 is a Theoretical Challenge and Phase 2, a Reduction to Practice Challenge. Phase 1 may award up to 6 prizes from a total prize award pool of $100,000 for the theoretical portion of the competition.

In addition to the direct monetary awards, the prize winners and selected runners-up will be recognized by the NIH Common Fund Single Cell Analysis Program and invited to attend The 3rd Annual Single Cell Analysis Investigators Meeting in Rockville, Maryland, USA on April 20, 2015. In addition to the public announcement, this opportunity may include paid travel and accommodations to the event and potential participation as an invited speaker at the discretion of the NIH.

Prize winners and selected runners-up with a qualifying score in Phase 1 will be invited to participate in Phase 2, which is a Reduction to Practice challenge to provide proof of concept data related to their Phase 1 entries. Phase 2 may award up to 2 winning solutions from a total pool of $400,000.

Phase 1 (Theoretical) Challenge requires only a written proposal.

Phase 2 (Reduction to Practice) Challenge will require documentation of Phase 1 implementation including the submission of data.


Single cell analysis is a rapidly evolving field that encompasses many disciplines. For example, recent advances in single cell RNA and DNA sequencing technologies have showed great promise, but researchers must still be able to differentiate between biological variation and technical noise in the context of dynamic cellular states. The NIH Single Cell Analysis Program (SCAP) seeks novel robust methods for analysis of individual cells that can serve as the basis for assessment  of changing cell behavior and function over time either as a result of natural state changes or when perturbed (e.g. by a drug, biological stimulus, infectious agent, pathological lesion, or mechanical forces). The Solver must rationalize how the application of the proposed method will successfully allow for monitoring of meaningful state changes in a single cell across time to answer at least one impactful, biological or clinical question.

Submissions to the Phase 1 Challenge must be received by 11:59 PM (US Eastern Time) on December 15, 2014. Late submissions will not be considered.

Phase 1 is a Theoretical Challenge that requires only a written proposal to be submitted. The Challenge award will be contingent upon evaluation of the written proposal by a technical evaluation panel serving the Seeker. Individuals and teams invited to participate in Phase 2, Reduction to Practice, may add members, who meet the eligibility requirements, to help support or sponsor efforts in Phase 2.

To receive an award, Solvers will not be required to transfer their exclusive IP rights to the Seeker. Instead, Solvers will grant to the Seeker a non-exclusive license to practice their solutions.


This Challenge is being held under the America COMPETES Authority where awards may only be awarded to individuals (participating singly or in a team) who are citizens or permanent residents of the United States.  Only U.S. citizens and permanent residents are eligible to win a prize for this Challenge. Foreign citizens can participate as a member of team but will not be eligible to win a prize; however, acknowledgement of their participation as part of a winning team will be recognized when results are announced. If you have a question about eligibility, please read the Challenge Specific Agreement Eligibility Rules section or use your Project Room to ask a question. Details on the specific eligibility criteria are listed in the Federal Register Notice (


The Single Cell Analysis Program (SCAP) is funded by the National Institutes of Health (NIH) Common Fund. The Common Fund began a decade ago to support collaborative programs with participation by all NIH Institutes and Centers. These programs must also be transformative, catalytic, synergistic, and unique. The overall goal of SCAP is to accelerate the discovery, development, and translation of cross-cutting, innovative approaches to analyzing the heterogeneity of biologically relevant populations of cells in situ. Through various grant mechanisms, SCAP currently supports multiple research projects including transcriptional profiling of single cells (U01), and development of new tools and technologies for single cell analysis (R21 and R01) (

The majority of current SCAP awardees are associated with academic institutions. This Challenge will strengthen and complement the existing SCAP grant portfolio by reaching out to a broader diverse population of innovators and solvers, including not only those who are from academic institutions, but also those who are from research and development communities in the private sector, and those who are outside biomedical disciplines. It is hoped that this Challenge will stimulate investment from both public and private sectors in single cell analysis research and product development, which will in turn lead to the development of more sensitive, more robust, and more cost-effective assay approaches, reagents, tools, and devices for basic research and clinical diagnosis.

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This Challenge is a Theoretical-Licensing Challenge, meaning that the Seeker is requesting non-exclusive rights to use the winning solution. By contrast, Theoretical-IP Transfer means that Solvers must relinquish all rights to the Intellectual Property (IP) for which they are awarded. For these forms of a Theoretical Challenge, Solvers that do not win retain the rights to their solution after the evaluation period is complete. The Seeker retains no rights to any IP not awarded.

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