User:ImmPort/sandbox

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This is a draft of the ImmPort Database wiki page

The Immunology Database and Analysis Portal (ImmPort) system was developed under the Bioinformatics Integration Support Contract (BISC) Phase II by the Northrop Grumman Information Technology Health Solutions team for the National Institutes of Health (NIH), National Institute of Allergy and Infectious Diseases (NIAID), Division of Allergy, Immunology, and Transplantation (DAIT).

The goals of the ImmPort system are to:
 * Accelerate a more collaborative and coordinated research environment
 * Create an integrated database that broadens the usefulness of scientific data and advances hypothesis-driven and hypothesis-generating research
 * Advance the pace and quality of scientific discovery while extending the value of scientific data in all areas of immunological research
 * Integrate relevant data sets from participating laboratories, public and government databases, and private data sources
 * Promote rapid availability of important findings, making new discoveries available to the research community for further analysis and interpretation
 * Provide analysis tools to advance immunological research

The ImmPort system provides advanced information technology support in the production, analysis, archiving, and exchange of scientific data for the diverse community of life science researchers supported by NIAID/DAIT. It serves as a long-term, sustainable archive of data generated by investigators funded through the NIAID/DAIT. The core component of the ImmPort system is an extensive data warehouse containing an integration of experimental data supplied by NIAID/DAIT-funded investigators and genomic, proteomic, and other data relevant to the research of these programs extracted from a variety of public databases. The ImmPort system also provides data analysis tools and an immunology-focused ontology. The functionality of the ImmPort system will be expanded continuously over the life of the BISC contract to accommodate the needs of the NIAID/DAIT-funded research community. The analytical tools created and integrated as part of the BISC contract are available to any researcher within ImmPort after registration and approval by DAIT. Additionally, the data provided by NIAID/DAIT funded researchers in ImmPort will be available to all registered users after the appropriate embargo time.

Public Data

The ImmPort data repository houses a variety of data types in the areas of both clinical and basic research. Data types include study protocols, case report forms, clinical assessments and lab tests as well as mechanistic data such as ELISA, ELISPOT, flow cytometry, gene expression, virus neutralization and viral titer. Each public study is labeled with a Data Completeness level which identifies the extent to which the study data has been annotated and curated. Access to these data is facilitated by user-friendly web interfaces for data query, import, export and analysis.

NIAID-funded research programs currently submitting data to ImmPort are:


 * Atopic Dermatitis Research Network(ADRN)
 * Collaborative Network for Clinical Research on Immune Tolerance Network
 * Enhanced Protective Immunity Against Filariasis
 * Human Immunology Project Consortium(HIPC)
 * Immune Function and Biodefense in Children, Elderly, and Immunocompromised Populations
 * Modeling Immunity for Biodefense
 * NIAID Centers of Excellence for Influenza Research and Surveillance(CEIRS)
 * Population Genetics Analysis Program

Analysis Tools

Flow Cytometry Data Management and Analysis

Recent advances in flow cytometry (FCM) instrumentation combined with the availability of new staining reagents have resulted in the ability to assess cell samples based on the quantification of many individual molecular characteristics simultaneously. Historically, investigators have analyzed FCM data manually by utilizing gating strategies and visualization of two-dimensional dot plots to identify specific cell populations within samples. The ImmPort flow cytometry module facilitates management of flow cytometry files and analysis of those files with an automated population identification algorithm, FLOCK.

Data management

ImmPort flow cytometry file data management supports:
 * Upload one or more flow cytometry data files for future analysis
 * View and edit the uploaded .txt files, e.g., adding sample information, renaming markers.
 * Put mutiple .txt files into a data set that can be used either in batch FLOCK runs or Cross Sample Comparison
 * View and edit the created dataset, e.g., adding/removing files, adding information for files in the dataset

The uploaded data file can be in either .fcs or .txt format. ImmPort automatically converts .fcs files to .txt files when the upload includes only .fcs files. The .txt files can be created using third party tools including Tree Star FlowJo™ on MacOS.

Channels, such as forward scatter width (FSC-W), can distort FLOCK analysis result if included together with forward scatter height (FSC-H) in the .fcs data file. Selection or exclusion of channels is supported by the user interface.

The ImmPort FCS conversion component, FCSTrans, uses logicle transformation for all flow files. FCSTrans generates a data matrix output from FCS2.0 and FCS3.0 binary files which can be used by immunologists and bioinformaticians to perform lab-specific analysis and customized visualization of their FCM data. Within the ImmPort flow cytometry module sll uploaded .fcs files are converted by FCSTrans to a data format suitable for FLOCK analysis without further action on the part of the user. For more details see the FCSTrans publication: FCSTrans: An open source software system for FCS file conversion and data transformation Qian Y, Liu Y, Campbell J, Thomson E, Kong YM, Scheuermann RH. 2012. Cytometry Part A. 81A(5) doi.org/10.1002/cyto.a.22037 (FCSTrans) FCSTrans code is available on SourceForge (SourceForge/ImmPort)

FLOCK

FLOCK,(FLOw Clustering without K) was developed by Max Qian and members of the University of Texas Southwestern Medical School as a system for automated population discovery in multidimensional FCM. FLOCK has been designed to specifically take into account the unique features of FCM data and produce an objective segregation of cell populations. Flow Cytometry data analysis within ImmPort employs theFLOCK algorithm.

FLOCK publications:
 * 1) The Polyfunctionality of Human Memory CD8+ T Cells Elicited by Acute and Chronic Virus Infections Is Not Influenced by Age Lelic A, Verschoor CP, Ventresca M, Parsons R, Evelegh C, et al. PLoS Pathogen 2012. 8(12): e1003076. doi:10.1371/journal.ppat.1003076
 * 2) Heterogeneity of Multifunctional IL-17A Producing S. Typhi-Specific CD8+ T Cells in Volunteers following Ty21a Typhoid Immunization McArthur MA, Sztein MB. 2012. PLoS ONE 7(6):e38408.doi:10.1371/journal.pone.0038408]
 * 3) Advances in human B cell phenotypic profiling Kaminski DA, Chungwen W, Qian Y, Rosenberg AF, Sanz I. 2012. Front. Immunol. 3:302. doi: 10.3389/fimmu.2012.00302
 * 4) FCSTrans: An open source software system for FCS file conversion and data transformation Qian Y, Liu Y, Campbell J, Thomson E, Kong YM, Scheuermann RH. 2012. Cytometry Part A. 81A(5) doi.org/10.1002/cyto.a.22037
 * 5) 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 Qian Y, Wei C, Eun-Hyung Lee F, Campbell J, Halliley J, Lee JA, Cai J, Kong YM, Sadat E, Thomson E, Dunn P, Seegmiller AC, Karandikar NJ, Tipton CM, Mosmann T, Sanz I, Scheuermann RH. Cytometry B Clin Cytom. 2010;78 Suppl 1:S69-82.

Cross Sample Analysis

summary of Cross Sample goes here


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