David Brown

High-throughput sequence analysis for communities and environmental sample metagenomics

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Christopher Oehmen

Project type

Capability Research

Metagenomes and multiple genome samples include environmental samples from soil and water, community samples involving multiple species (such as human or termite gut) and others. DOE has recognized…

PLFS Testing on Chinook

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

David Brown

Many HPC Applications do periodic checkpointing to save state after each itteration of a simulation. Sometimes the scientific application creates I/O patterns that do not fit Chinook very well. In an…

Introducing Parallel Computing to Undergraduate Students

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Kevin Glass

Parallel computing is growing in importance in both the scientific and commercial computing worlds. Part of this growth can be attributed to changes in computer architecture such as multicore…

Understanding Biomass Conversion within Thermophilic Communities and Isolates

Lead Institution

Lawrence Berkeley National Laboratory

Principal Investigator

Steven Singer

Project type

Large-Scale EMSL Research

Efficient deconstruction of lignocellulose into monomeric sugars is a key step in the development of renewable and sustainable liquid transportation fuels from biomass. The DOE Joint BioEnergy…

Reverse Methanogenesis: Validating the Hypothesis with Lineage-Resolved Environmental Proteomics

Lead Institution

University of British Columbia

Principal Investigator

Steven Hallam

Project type

Large-Scale EMSL Research

In marine sediments three known lineages of anaerobic methane oxidizing archaea (ANME-1, 2 and 3) filter up to ~384 Tg of the greenhouse gas methane annually, greatly reducing methane flux from ocean…

Innovative Molecular Imaging Using Spatially Controlled Ionization Combined with High Performance FT-ICR Mass Spectrometry

Lead Institution

Maastricht University

Principal Investigator

Ronald Heeren

Project type

Scientific Partner

The objective of this proposed 3 year EMSL-FOM institute AMOLF partnership is to incorporate C60 SIMS and MALDI ionization techniques with a 9.4 Tesla FT-ICR mass spectrometer to enable and enhance…

Development of the Integrated MetaPROteomics Viewer (IMPROV) Software Toolkit

Lead Institution

University of British Columbia

Principal Investigator

Steven Hallam

Project type

Scientific Partner

Beyond the periphery of our senses exists an infinitely diverse microbial world. This microcosm extends into every imaginable habitat, thrives under powerful extremes, and helps create and sustain…

Soybean Proteomics

Lead Institution

University of Missouri - Columbia

Principal Investigator

Gary Stacey

Project type

Large-Scale EMSL Research

The USA is the world's largest producer of soybean (Glycine max) according to the UN food and agriculture organization with a production of 83.9 million metric tons per year. Soybean is an…

Comparative metaproteomics and metametabolomics of the biomass-degrading microbial community that inhabits the cow rumen

Lead Institution

University of California, Davis

Principal Investigator

Matthias Hess

Project type

Large-Scale EMSL Research

Lignocellulosic plant material is one of the most promising sources of sustainable liquid transportation fuels but the recalcitrant nature of the plant cell wall and the cost of biomass-degrading…

Development of computational pipeline to integrate protein structure/function discovery with genome scale model

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Marat Valiev

The project is focused on developing a computational pipeline that connects genome scale model to protein structure/function at the molecular level. It addresses an immediate need of the Subcellular…

Collaborative Access Team: Pacific Northwest Cryo-EM Center (PNCC)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

PNNL will create and operate the Pacific Northwest Center for Cryo-EM (PNCC), a state-of-the-art national center for cryo-electron microscopy (Cryo-EM) that will rapidly and efficiently collect and…

Event-driven Instrument Data Processing

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Kurt Maier

Automate pipelines for data processing and/or analysis codes based on EMSL instrument data using the computational framework integrated with the Pacifica code base that underlies MyEMSL,…

Lustre Scalability Research

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Evan Felix

We propose to continue the work of proposal 20909 by using a raid0 dataset on the cluster

Petascale Institute Virtualized Lustre Scalability Research

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Robert Farber

Project type

Limited Scope

For the following proposal, our plan is to run during MPP2 downtimes to not affect other users. Achieving aggregate bandwidth scaling of storage devices with parallel-distributed file systems is a…

Understanding I/O behavior of Scientific Applications

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

David Brown

The future of High Performance File Systems are being written now. To better understand how those file systems are being used and what usage patterns to optimize for is important for file system…

Lustre Scalability Research

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

David Brown

This project will be using the Lustre parallel file system during a scheduled down time to test scalability and performance limitations of Lustre and Chinook.

Projects