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Creating Realistic Animations of Nature

One of the most exciting areas that researchers use MSI for is computer-generated visualizations. Avery Musbach, a graduate student in the Department of Computer Science and Engineering , is the lead author on a paper that demonstrates the power of scientific computing to create visualizations. The...

Genomics, Metagenomics, and Transcriptomics of Fungal Pathogens of Invertebrates

Abstract: 
<h3 class="red">Genomics, Metagenomics, and Transcriptomics of Fungal Pathogens of Invertebrates</h3><p>Using a combination of next generation sequencing, phylogenomics, genetics, and natural products chemistry, the Bushley lab examines the evolution, diversity, and functions of fungal secondary metabolites. Current research projects utilizing MSI resources include:&nbsp;</p><ul><li>A comparative population genomic study of the evolution of NRPS secondary metabolites among strains of the beetle pathogen and cyclosporin producing fungus <em>Tolypocladium inflatum</em> using PacBio sequencing</li><li>A comparative genomic and transcriptomic analysis of interactions of insect pathogenic and endophytic fungi with both plant and insect hosts</li><li>A metagenomics study of fungal pathogens of the &nbsp;soybean cyst nematodes to elucidate patterns of distribution in natural and agricultural ecosystems and potential roles in mediating resistance to nematodes</li><li>Metagenomics analyses of tropical endophytic fungi of Papua New Guinea and potential anti-herbivore and anti-cancer activity.</li></ul><p>These research projects utilize HPC computing for de-novo genome sequencing and assembly, RNA-Seq, network analysis, large-scale phylogenomic analyses, and population genotyping.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/db501caadd84bb7ee4c9a6bebfa9ebed/10689">main page</a>.</p>
Group name: 
bushleyk

Geobiology of Sulfur Bacteria

Abstract: 
<h3 class="red">Geobiology of Sulfur Bacteria</h3><p><span style="background-color: rgb(255, 255, 255);">The activities of microorganisms have a profound influence on geological processes, such as the formation and dissolution of minerals and rocks. This lab primarily investigates the influences of sulfur bacteria on the geochemistry of marine systems and the precipitation and dissolution of certain minerals, some of which are of economic importance. These investigations require analysis of single-gene and whole-genome sequence data. The group&#39;s HPC usage is primarily focused on the assembly and analysis of several Illumina and PacBio sequence datasets that will be used to construct genomes and metagenomes for the organisms they study.</span></p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/78b3414177c45cb418191073e8d50198/10318">main page</a>.</p><p>&nbsp;</p>
Group name: 
baileyj

Orofacial Pain Neuroimaging

Abstract: 
<h3 class="red">Orofacial Pain Neuroimaging</h3><p>Chronic orofacial pain conditions presenting in the face/head (temporomandibular disorders (TMD)) or more localized to the mouth (persistent dentoalveolar pain disorder (PDAP)) cause significant societal burden. Underlying mechanisms are poorly understood with developing evidence suggesting peripheral nerve dysfunction and deficient pain modulation are involved. TMD patients were shown to have abnormal sensory/pain processing, as well as brain structural and functional differences, compared to painfree controls. Such research has yet to be explored with PDAP patients.</p><p>This project includes analysis of neuroimaging data using MSI&rsquo;s HPC resources. It uses currently available neuroimaging analysis software, e.g., FSL and Freesurfer, to process datasets. Post-processed neuroimaging datasets use significant amount of disk space, necessitating MSI&#39;s storage capabilities.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/68bc52332ac1be724d445b8237d0e40a/10823">main page</a>.</p>
Group name: 
moanae

Contact Information

Address and contact information: Minnesota Supercomputing Institute University of Minnesota 599 Walter Library 117 Pleasant Street SE Minneapolis, MN 55455 Phone: (612) 624-0528 Fax: (612) 624-8861 General support Systems Status Help Request Form Support Email: help@msi.umn.edu Helpline Phone: (612...

Geomicrobiology Lab

Abstract: 
<h3 class="red">Geomicrobiology Lab</h3><p>The overall goal of research in the Santelli Geomicrobiology Lab is to examine interactions between minerals and microorganisms, including fungi, to understand how biomineralization, biocorrosion, and metabolic activity influence the fate and distribution of metals, nutrients, and pollutants in the environment. The lab&#39;s specific research objectives are driven by conducting fundamental scientific research on environmentally relevant biogeochemical processes and key elements in nature that are further influenced by anthropogenic activities, such as mining and agriculture. In addition to answering key questions on the mechanisms, metabolic pathways, and geochemical impact of mineral-microbe interactions, the researchers seek to inform and improve strategies for remediating inorganic pollutants to improve the quality and health of water and soil environments.</p><p>The group is using MSI&rsquo;s HPC resources for analysis of large quantities of DNA sequences using a variety of software packages. Current and near future work will include whole genome assembly of fungal genomes, RNAseq analysis, microbiome, and metagenomics analysis. The group is also storing&nbsp;<span style="background-color: rgb(255, 255, 255);">sequence data for numerous fungal genomes.</span></p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/524b2770781067c7b193a2377a4d2d35/10871">main page</a>.</p>
Group name: 
santelli

February 2017 Maintenance

On Wednesday, February 1, 2017, from 8am - 4pm CDT, MSI staff will perform scheduled maintenance and upgrades to the network and various MSI systems. During this month's scheduled maintenance period, MSI will apply updates to prevent jobs from using more memory or CPU resources than what the job...

Deep Learning at MSI

Over the past year, MSI has been increasing resources available to researchers working in machine learning fields. Deep learning methods have been getting a great deal of attention due to recent advances in hardware and successful applications in the fields of image classification, computer vision...

This two part tutorial will first introduce you to the concept of interactive high performance computing, as distinct from batch computing. We will cover the Citrix (Windows) and NICE EnginFrame (Linux) interactive computing environments hosted by MSI.

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...

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