The Data Management, Analysis and Resources Dissemination Core (DMARD) will support all four Research Projects and the Technology Core by providing rapid, accurate and cost-effective data management, high throughput analysis and resource sharing and dissemination according to the Resource Sharing Plan. DMARD Core functions will be divided into three primary responsibilities;resource sharing, comprehensive data management and infrastructure to support high throughput analysis. Our GCID Program will rapidly release, pre-publication genomic and other data including metadata as detailed in the Resource Sharing Plan. Raw genome sequence will be submitted as rapidly as possible not exceeding 45 days from generation and data quality check to either the Trace Archive or, as appropriate, to the Short Read Archive at NCBI/NLM/NIH. Full and partial genome assemblies will be deposited in GenBank at NCBl after verification, no later than 45 days of being generated, followed by release to other web sites, as approved by NIAID. Single nucleotide polymorphisms (SNP) generated as part of the project, will be submitted as rapidly as possible to NCBl dbSNP and not later than 45 days from validation. Clinical data and other metadata will be deposited to the appropriate NIAID funded Bioinformatics Resource Centers or other public resources as appropriate. Metadata formats developed through the NIAID GSC-BRC collaborative efforts will be employed. Microbial strains employed in the JCVI GCID will be deposited to the NIAID BEI (Biodefense &Emerging Infections Research Resources Repository) or other approved public repositories. Informatics tools developed within the Program for processing or analyzing the data generated in the course of performing the Program's Research Projects will be placed in the public domain via SourceForge as open source. The DMARD will provide comprehensive data management for tracking metadata, samples, reagents, and data. The DMARD will work with Technology Core to provide Galaxy and Kepler based modular infrastructure for integrative analysis and interpretation. The DMARD will work with the Technology Core to provide ready to use tools and pipelines to the research community.

Public Health Relevance

The DMARD Core will provide resource sharing, sample tracking, metadata tracking, data management and integration, and analysis infrastructure to all GCID Projects. The DMARD Core services will be crucial for the success of GCID Projects, and equally important for GCID collaborators and the research community.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Program--Cooperative Agreements (U19)
Project #
1U19AI110819-01
Application #
8711786
Study Section
Special Emphasis Panel (ZAI1-EC-M (J1))
Project Start
Project End
Budget Start
2014-04-04
Budget End
2015-03-31
Support Year
1
Fiscal Year
2014
Total Cost
$360,741
Indirect Cost
$168,857
Name
J. Craig Venter Institute, Inc.
Department
Type
DUNS #
076364392
City
Rockville
State
MD
Country
United States
Zip Code
20850
Shao, Lulu; Fischer, David D; Kandasamy, Sukumar et al. (2016) Comparative In Vitro and In Vivo Studies of Porcine Rotavirus G9P[13] and Human Rotavirus Wa G1P[8]. J Virol 90:142-51
Rojas, Laura J; Wright, Meredith S; De La Cadena, Elsa et al. (2016) Initial Assessment of the Molecular Epidemiology of blaNDM-1 in Colombia. Antimicrob Agents Chemother 60:4346-50
Chavda, Kalyan D; Chen, Liang; Fouts, Derrick E et al. (2016) Comprehensive Genome Analysis of Carbapenemase-Producing Enterobacter spp.: New Insights into Phylogeny, Population Structure, and Resistance Mechanisms. MBio 7:
Rosas-Salazar, Christian; Shilts, Meghan H; Tovchigrechko, Andrey et al. (2016) Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection With Human Rhinovirus and Respiratory Syncytial Virus in Infancy. J Infect Dis 214:1924-1928
Nelson, Martha I; Stucker, Karla M; Schobel, Seth A et al. (2016) Introduction, Evolution, and Dissemination of Influenza A Viruses in Exhibition Swine in the United States during 2009 to 2013. J Virol 90:10963-10971
Schobel, Seth A; Stucker, Karla M; Moore, Martin L et al. (2016) Respiratory Syncytial Virus whole-genome sequencing identifies convergent evolution of sequence duplication in the C-terminus of the G gene. Sci Rep 6:26311
Shilts, Meghan H; Rosas-Salazar, Christian; Tovchigrechko, Andrey et al. (2016) Minimally Invasive Sampling Method Identifies Differences in Taxonomic Richness of Nasal Microbiomes in Young Infants Associated with Mode of Delivery. Microb Ecol 71:233-42
Chen, Rubing; Puri, Vinita; Fedorova, Nadia et al. (2016) Comprehensive Genome Scale Phylogenetic Study Provides New Insights on the Global Expansion of Chikungunya Virus. J Virol 90:10600-10611
Rosas-Salazar, Christian; Shilts, Meghan H; Tovchigrechko, Andrey et al. (2016) Nasopharyngeal Microbiome in Respiratory Syncytial Virus Resembles Profile Associated with Increased Childhood Asthma Risk. Am J Respir Crit Care Med 193:1180-3
Nelson, Martha I; Wentworth, David E; Das, Suman R et al. (2016) Evolutionary Dynamics of Influenza A Viruses in US Exhibition Swine. J Infect Dis 213:173-82

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