FICUS JGI-NERSC

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About FICUS

The “Facilities Integrating Collaborations for User Science” (FICUS) initiative was established in 2014 to encourage and enable researchers to more easily integrate the expertise and capabilities of multiple user facilities stewarded by the Department of Energy Office of Science into their research. In recognition of the increasingly collaborative and multidisciplinary nature of DOE mission science projects, this initiative aims to encourage innovative research exploiting a range of capabilities.

About FICUS JGI-NERSC

The mission of the Department of Energy Joint Genome Institute (DOE JGI), as set forth in its 10-year strategic vision, is to serve the scientific community as a user facility pioneering functional genomics to solve the most relevant bioenergy and environmental problems. The mission of the National Energy Research Scientific Computing Center (NERSC) is to accelerate scientific discovery at the DOE Office of Science through high performance computing (HPC) and data analysis. To support both these missions, and to expand upon their highly successful past collaborations, the DOE JGI and NERSC are issuing a call for proposals in microbiome data science as part of the Facilities Integrating Capabilities for User Science (FICUS) initiative.

2017 FICUS JGI-NERSC Microbiome Data Science Call for Proposals (CLOSED)

The Microbiome Data Science call will enable users to perform state-of-the-art computational genomics and metagenomics research and help them translate sequence information, generated by the DOE JGI or elsewhere, into biological discovery. The call aims to help users perform large-scale computational analyses of sequence data to solve problems relevant to the DOE missions in bioenergy and the environment. It capitalizes on existing unique resources available through the DOE JGI including:

• The Integrated Microbial Genomes & Microbiomes (IMG/M) database, the largest publicly available integration of assembled metagenomic sequences and isolate genomes
• State-of-the-art computational workflows and pipelines
• The expertise of DOE JGI personnel to mine and analyze the integrated data
• The HPC capabilities provided by NERSC through Cori
• The expertise of NERSC staff to optimize algorithms and workflows for the HPC environment

DOE JGI and NERSC will combine the power of data science and HPC to enable users to explore the wealth of genomic and metagenomic data generated worldwide and address DOE relevant questions that require massive-scale data and computing capabilities.

Examples of work that could be requested include but are not limited to:

• Mining all isolate genome and metagenome data for genetic features of interest, such as studying the presence and diversity of a certain enzyme or metabolic pathway
• In-depth analysis of large sets of relevant metagenomes, including analysis of taxonomic composition using multiple phylogenetic markers, reassembly and binning using state-of-the-art tools
• Multi-genome analysis of taxonomic clades including identification of species, computation of ortholog families and phylogenomic detection of gene signatures associated with certain lifestyles

DOE JGI and NERSC Capabilities available through this call include:

• Custom data processing
  1. Assembly and annotation of multiple isolates and/or metagenomes sequenced outside the DOE JGI
  2. Binning of individual genomes from a set of metagenomes
  3. Gene expression analysis of transcriptomes and/or metatranscriptomes using reference genomes in IMG/M or using custom reference genomes
• Comparative analysis
  1. Pangenome technology: developing a pangenome for a selected list of isolate genomes or single cells
  2. Microbial species delineation including, but not limited to, Average Nucleotide Identity (ANI) computation and ANI-based clustering for a group of microbial isolates
  3. Identification of shared or unique genes within a group of isolate genomes and/or metagenomes
  4. Phylogenomic analysis to identify “incongruent phylogeny”, e.g., limited phylogenetic distribution candidates for delineating host-microbe interactions
• Gene/protein family centric analysis
  1. Identification of all genes/proteins across all isolate genomes and/or metagenomes, for a specific query gene/protein/model
  2. Compilation and curation of known biomarker sets for various biogeochemical processes, and development and assessment of novel biomarkers based on protein clusters
• Quantitative Ecology
  1. Large-scale metagenome mining for biogeographic distribution of a target organism, phylogenetically coherent group, or phylum of interest
  2. Comparative analysis of matched iTag, metagenome, and/or metatranscriptome data to elucidate abundance profiles within a microbial community. Includes targeted assembly of 16S ribosomal RNA gene sequences from metagenome and metatranscriptome data
  3. Global fragment recruitment for single-cell amplified genomes (SAGs) or genomes from metagenomes (GFMs)
  4. Co-occurrence analysis of phylotypes and/or genomes across metagenomes of interest to predict patterns of co-occurrence
  5. Identification of viral contigs from a set of metagenomes and host identification where possible

Proposals will be reviewed for feasibility, scientific excellence and DOE mission relevance by scientific experts in microbial genomics and HPC. All relevant data must be available at the time of submission; proposals requesting sequencing will be rejected without peer review. Applications should be submitted at proposals.jgi.doe.gov. Inquiries about the program should be directed to Susannah Tringe, mailto:sgtringe@lbl.gov.

Proposal Schedule

2017 proposals will only be accepted electronically and should be submitted at http://proposals.jgi-psf.org/ between January 9 and March 17, 2017.

The full schedule is below:

Calls for proposals issued	January 9, 2017
Proposals received	March 17, 2017
Technical and scientific review	May 25, 2017
Approval and rejection notices sent	June 16, 2017