Elizabeth Thomson

Elucidation of seventeen human peripheral blood B-cell subsets and quantification of the tetanus response using a density-based method for the automated identification of cell populations in multidimensional flow cytometry data

Advances in multiparameter flow cytometry (FCM) now allow for the independent detection of larger numbers of fluorochromes on individual cells, generating data with increasingly higher dimensionality. The increased complexity of these data has made it difficult to identify cell populations from high‐dimensional FCM data using traditional manual gating strategies based on single‐color or two‐color displays.

ImmPort: disseminating data to the public for the future of immunology

The immunology database and analysis portal (ImmPort) system is the archival repository and dissemination vehicle for clinical and molecular datasets created by research consortia funded by the National Institute of Allergy and Infectious Diseases Division of Allergy, Immunology, and Transplantation. With nearly 100 datasets now publicly available and hundreds of downloads per month, ImmPort is an important source for raw data and protocols from clinical trials, mechanistic studies, and novel methods for cellular and molecular measurements. To facilitate data transfer, templates for data representation and standard operating procedures have also been created and are also publicly available. ImmPort facilitates transparency and reproducibility in immunology research, serves as an important resource for education, and enables newly generated hypotheses and data-driven science.

FCSTrans: An open source software system for FCS file conversion and data transformation

IN flow cytometry (FCM) experiments, investigators usually rely on instrument manufacturers and ‘‘black box’’ commercial software to transform cellular marker expressions into cell populations on 2D dot plots. Techniques behind these systems and their limitations have not been sufficiently addressed or disclosed. Currently, a Flow Cytometry Standard (FCS) file can be FCS2.0 or FCS3.0 (N.B. Newer standards like FCS3.1 and ACS1.0 have been proposed and might be generated by some manufacturers in the

ImmPort: Shared research data for bioinformatics and immunology

Researchers are applying a wide variety of assay methods to explore the complex and dynamic human immunology system. There are a number of initiatives to encourage sharing of results, the standardization of terminology, and the reanalysis of data to improve reproducibility and ensure scientific rigor. The ImmPort project is an example of a NIH resource to collect, curate, and share immunological research. We describe the ImmPort project resources available to encourage an exploration of the tools and skill sets needed for analyzing shared immunological data, including clinical and mechanistic studies, analysis tools, and example analysis code. There is an ongoing effort to annotate the shared data with standardized terms from ontologies, make these curated data sets available in formats amenable to bioinformatic tools, and provide examples of how to access and analyze the data sets.