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361459-191001-021000
20-NGI3-112
N/A
10/1/2020
2022-9-30 0:0:0
Active
$188,063.00
Advancing Bioinformatics Infrastructure with Standards, Workflows, and Databases
Thompson
Luke
MSU
Mickle
Paul
MSU
EM-DM
OAR
‘Omics and bioinformatics tools support marine systems studies, NOAA missions, and the sustainable use of ocean resources. Scientists with expertise in these areas are building a foundation of infrastructure (adapting traditional and cloud HPC systems for bioinformatics), competence (cultivating bioinformatics skills in scientists), capacity (high-throughput analysis and improved standards, workflows, and databases), and application (analysis of ‘omics datasets). Infrastructure includes documentation of cloud computing strategy and development of genomic databases and repositories for bioinformatics code and ‘omics protocols. Workforce includes hosting ‘omics meetings on topics of broad interest, technical workshops (Python, QIIME 2, metagenomics), and bioinformatics tutorials. Capacity includes development of reference databases and software to query them, environmental DNA (eDNA) metadata standards, quality control workflows, workflows for amplicon and shotgun sequence data, and a cloud-based eDNA and omics analysis platform. Application includes collection and analysis of fish eDNA datasets and eDNA data from the mesopelagic zone, analysis of harmful algal bloom datasets, and analysis of microbial communities from pelagic (metagenomes for hydrocarbon degradation potential) and benthic (gut microbiomes from methane ice worms) environments. This effort builds upon the earlier development of an ‘Omics Data Management Plan, data and metadata standards (https://microbiomedata.org/); data analysis tutorials (https://github.com/aomlomics/tutorials); and an updated Tourmaline amplicon DNA sequence analysis workflow (https://github.com/aomlomics/tourmaline).
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