Page not found

Call for Proposals - Allocations on Blue Waters HPC System

The Great Lakes Consortium for Petascale Computation (GLCPC) has issued a Call for Proposals for allocations on the Blue Waters system. The Call for Proposals can be found on the GLCPC website . Proposals should focus on the scale and unique capabilities of the Blue Waters system. Projects that...

Discovery and Study of Microbial Peptide Natural Products

Abstract: 

Discovery and Study of Microbial Peptide Natural Products

Since the discovery of penicillin in the 1920s, natural products have had an unmistakable impact on our health and have inspired us with their intricate chemical structures and fascinating underlying metabolic pathways. Historically, biochemical and genetic studies in these systems have focused on free-living, fast growing terrestrial organisms due to technological and laboratory constraints. However, the past 10-15 years have seen an explosion of new DNA sequencing technologies and molecular biological techniques that have, for the first time, allowed genetic access to more subtle and intricate ecosystems.

This lab's work focuses on the discovery and heterologous expression of pathways and genes involved in the biosynthesis of metabolites from unique microbial sources. The researchers use cutting-edge and classical techniques in biochemistry, microbiology, metagenomics, and mass spectrometry to investigate unconventional peptide-based metabolites and pathways invoking radical-mediated chemistry. MSI resources crucial to this group's success include computing power and software for de novo peptide identification from LC-MS data as well as data management and analysis of sequenced microbial genomes. All in all, this research aims to tackle the exponentially expanding genomic universe for the discovery of new enzymology and therapeutics.

Return to this PI's main page.

Group name: 
freeman0

Understanding the Role of Transposable Elements in Maize Abiotic Stress Response

Abstract: 

Understanding the Role of Transposable Elements in Maize Abiotic Stress Response

Abiotic stress, such as extreme temperatures or drought, severely limits agricultural productivity. These researchers have evidence that certain families of transposons can confer stress responsive expression patterns to nearby genes in maize. The first aim of this project is to define the role of transposons in gene expression responses to abiotic stress in several different tissues and genotypes. The focus of the second aim is to determining the mechanism by which transposons influence the stress-responsive expression of nearby genes. The third aim of this project will document natural variation for insertion sites of the transposons that confer stress-responsive gene expression and will attempt to identify protocols to mobilize these elements to generate novel allelic diversity in maize. This project will provide novel understanding of the molecular processes that underlie gene expression responses to abiotic stress. MSI is used for NGS data analysis and other downstream computationally intensive tasks.

Return to this PI's main page.

Group name: 
hirschc3

SciTegic Pipeline Pilot

Pipeline Pilot, Accelrys' scientific informatics platform, was designed for scientists by scientists. It aggregates and provides immediate access to the volumes of disparate research data locked in silos, automates the scientific analysis of that data, and enables researchers to rapidly explore, visualize and report research results.

What does job exit status XX mean?

The exit_status attribute reported by "qstat -f <jobId>" can help users identify why a job failed. Successful runs report exit_status=0. Non-zero status (positive or negative) implies job failure, but the exact meaning of exit codes varies by software. For jobs submitted to PBS, negative...

How do I create a new virtual machine / instance?

The easiest way to boot a VM is through Horizon ( https://stratus.msi.umn.edu ) Go to Project > Compute > Instances and click Launch Instance Horizon provides a Wizard to help you launch VMs. Look for stars (*); those are required fields and can only be set before instance creation! To begin...

If you are new to bioinformatics this is the best place to start.

This hands-on tutorial will help a new user understand how to use the the Galaxy platform to analyze NGS data by working though the quality control steps needed for Illumina sequencing data.

Stratus Protected Data Cloud

MSI is building a local research compute cloud environment called Stratus ( https://stratus.msi.umn.edu ) , which is designed to store and analyze protected data, such as dbGaP. Stratus is a subscription-based infrastructure as a service that enables users to operate within their own self-service...

Simulations in Chemical and Condensed Matter Physics

Abstract: 

Simulations in Chemical and Condensed Matter Physics

This group studies a variety of complex many body systems providing insight at many length and time scales into the collective phenomena of interest. A current focus is on abstracted models of interacting polymer systems far from equilibrium in which they are accumulating data on the statisitcal distribution of chemical morphologies and dynamics. These models are intended to provide better understanding of how dynamic metastable states  involving large molecules can emerge from a starting configuration of small molecules as is believed to have occurred in the origin of life. The researchers have studied a "well mixed reactor" version of such a model and are currently studying an extension in which spatial heterogeneity and diffusion can occur. Studies of the detailed morphological and dynamic character of the well mixed model also continue.  Simulations using more chemically realistic descriptions of the atomic level are also planned.

A second focus is on the behavior of  oxide water interfaces using in-house self consistent tightbinding codes. There is tremendous current interest  in oxides as electrodes in a variety of technologies using aqueous electrolytes including fuel cells, batteries and electrolysers. Water-oxide interfaces are also a key component in corroding metal surfaces so such studies are also relevant to attempts to understand and inhibit corrosion. In one project the researchers are simulating at titania water interfaces with particular emphasis on new methods for calculating surface energies to understand the propensity of titania water interfaces to dissociate water. This project is a collaboration with former student Patrick Schelling, now an associate professor at the University of Central Florida, and his students. A second project in this category is a simulation of the magnetite water interface. In addition to its obvious corrosion relevance, the study is intended to provide better understanding of the mechanisms of water dissociation at a magnetite water interface, as occurs in experiments which the group is doing on the use of magnetite electrodes in electrolysers for production of gaseous hydrogen as an energy storage medium. This project is a collaboration with Professor Melissa Eblen of the Carleton College Physics Department, the Natural Resources Research Institute in Duluth, and high school physics teacher Jon Huber, who worked with the Halley Group in the Research Experiences for Teachers program at Minnesota in summer 2015 and continues experiments with students in Burnsville. In a third related project the researchers are beginning molecular dynamics simulations of membrane proteins in water at various solid aqueous interfaces. The aim is to  explore the possible use of such membrane proteins to solve certain technical problems associated with the behavior of lithium-based electrodes in water in applications to batteries. This is a preliminary exploratory collaboration with Jonathan Sachs of the Department of Biomedical Engineering.

Thirdly the group simulates quantum fluid phenomena. A current emphasis is on condensate mediated transmission using Diffusion Monte Carlo methods to obtain informaton about excited scattering states in the  strongly interacting helium four superfluid. The methods are unique and were developed in this group. They have published results in Physical Review B using a guiding wave function which did not conserve particle current. The current project is to use an improved guiding wave function which removes that defect. The project is relevant to an experiment they proposed more than a decade ago and which has been tried in various laboratories, still without a definitive result, to observe the condensate mediated transmission effect. Another quantum fluids project, carried on at a low intensity level, is the exploration of effects of disorder, and in particular of disorder induced pairing, in superconductors.

Return to this PI's main page.

Group name: 
halleyjw

Pages