home Bioinformatics, Funding, Life Science Topics, Sequencing Call for Proposals: 2019 FICUS JGI-NERSC-KBase Biological Data Science

Call for Proposals: 2019 FICUS JGI-NERSC-KBase Biological Data Science

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Source: FICUS JGI-NERSC-KBase – DOE Joint Genome Institute

I am copying some of the announcement below:

The Biological Data Science call will enable users to perform state-of-the-art computational research to explore the wealth of genomic and metagenomic data generated worldwide and translate sequence information into biological discovery. Users will have access to resources and capabilities through two DOE Office of Science User Facilities, the Joint Genome Institute (JGI) and the National Energy Research Scientific Computing Center (NERSC), as well as the DOE Systems Biology Knowledgebase (KBase). The call aims to help users perform large-scale computational analyses of genomics and related omics data to solve problems relevant to the DOE missions in bioenergy and the environment.’

Projects are encouraged that relate to:

  • Large-scale data mining for genes, genomes, metabolic and biosynthetic pathways, and regulatory motifs of interest
  • Large scale computations for large datasets exploring the power of High Performance Computing
  • Developing explainable scalable machine learning and artificial intelligence based methods for sequence classification, gene calling or gene functional annotation leveraging high performance computational tools such as HipMCL, MetaHipMer, etc.
  • Developing new analysis and/or visualization tools for Terabyte (TB)-sized multi-omics data that can be deployed in KBase, IMG, or MycoCosm
  • Distributing resulting data products through IMG/JGI portals or KBase

DOE JGI, NERSC and KBase core capabilities available through this call include:

  • Up to 2 million CPU hours on the Cori supercomputer (128GB memory per node, 32 cores)
  • Access of up to 100TB of high-performance storage on the NERSC parallel file system and burst buffer to overcome I/O bottlenecks
  • The expertise of DOE JGI, NERSC and KBase staff
  • The Integrated Microbial Genomes & Microbiomes (IMG/M) database, the largest publicly available integrated resource of assembled metagenomic sequences and isolate microbial genomes
  • The MycoCosm portal, the largest collection of fungal genomes
  • An integrated software and data platform, KBase, for metabolic modeling of microbes or microbial communities, custom processing of microbial and fungal genomes and metagenomes and state-of-the-art computational workflows, narratives, and pipelines
  • Comparative analyses (e.g. large or complex queries) of the IMG system that are not available through the web interface.
  • Gene/protein family-centric analysis of IMG or KBase data’

For more information see FICUS JGI-NERSC-KBase – DOE Joint Genome Institute

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