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Network Effects on Human Health and Intervention Optimization

<h3 class="red">Network Effects on Human Health and Intervention Optimization</h3><p>This project investigates how the network structure formed by human interactions influences population health and the implications this has for health interventions. The structure of contact networks influences the spread of infectious agents and the likelihood of an epidemic, while social networks allow for the spread of lifestyle habits and health attitudes that may also influence the health of a population. Using concepts from graph theory, optimization, and epidemiology, the goal of this project is to quantify the impact of particular network features on the spread of disease and develop methodologies that leverage knowledge of the network structure to target health interventions such that the overall health of the population is maximized. This work requires computational resources for intensive data analysis and large-scale simulation modeling.&nbsp;</p><p>Return to this PI&#39;s <a href="">main page</a>.</p><p>&nbsp;</p>
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Reduced-Complexity Air Quality Model Development and Application

<h3 class="red">Reduced-Complexity Air Quality Model Development and Application</h3><p>Outdoor air pollution kills approximately three million people per year. Air quality models are commonly used to understand and manage air quality. Chemical transport models (CTMs) are the most accurate of these models but are too computationally intensive for many applications. Reduced complexity models can be used to augment CTM simulations. These researchers have developed a reduced complexity air pollution modeling framework (InMAP, the Intervention Model for Air Pollution) and have created implementations of the model for the continental US for the years 2005 and 2030. They are using MSI resources to create additional implementations of the model: one that is specific to China, one that is specific to India, and a worldwide version.</p><p>Research Spotlights about this work appeared on the MSI website in <a href="">September 2014</a> and <a href="">February 2015</a>.</p><p>Return to this PI&rsquo;s <a href="">main page</a>.</p>
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Treatment for Clostridium difficile Infections

MSI PIs Dan Knights ( Computer Science and Engineering - College of Science and Engineering ) and Michael Sadowsky ( Soil, Water, and Climate - College of Food, Agricultural, and Natural Resource Sciences ), are co-authors on a recent study supporting the value of fecal transplantation for the...

Mechanistic Investigation of Allylic Azides

<h3 class="red"><span style="line-height: 1.5em;">Mechanistic Investigation of Allylic Azides</span></h3><p>Allylic azides have been known to undergo spontaneous rearrangement to form an equilibrating mixture of branched and linear azides. Although the mechanism for such an event has been speculated in the past, detailed investigations have not been done yet to elucidate key intermediates or favorable energetic pathways. Experimentally, it has been shown that substituents on the allylic azide can affect the reaction equilibrium and subsequently the ratio of the equilibrating mixture. This equilibrium may also be influenced by interactions like hydrogen bonding of the substrate, however no experimental evidence substantiates these claims.</p><p>Computational studies can go a long way in gaining mechanistic insights of these reactions by identifying favorable transition states and/or reactive intermediates and role of various non-covalent binding events. These researchers envision that mechanistic analysis of the allylic azide rearrangement will provide insights for optimization of current reaction conditions. With these insights, the allylic azides can be synthetically converted to value added precious materials like chiral amines, which are important moieties in various substances like drugs, natural products, and more.</p><p>Return to this <a href="">PI&#39;s main page</a>.</p>
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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...

Understanding the Role of Transposable Elements in Maize Abiotic Stress Response

<h3 class="red">Understanding the Role of Transposable Elements in Maize Abiotic Stress Response</h3><p>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.</p><p>Return to this PI&#39;s <a href="">main page</a>.</p>
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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...

Stratus Protected Data Cloud

MSI is building a local research compute cloud environment called Stratus ( ) , 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...

How do I create a new virtual machine / instance?

The easiest way to boot a VM is through Horizon ( ) 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...


Software Description: 

The molecular ADF program can be applied to gas phase molecules, solvated molecules, and molecules in protein environments. It can treat all elements of the periodic table, and contains state-of-the-art relativistic methods (ZORA and spin-orbit coupling) to treat heavy nuclei.

Software Support Level: 
Secondary Support
Web Documentation: 

A graphical user interface for ADF is available on the machine

ssh -Y

module load adf


Software Access Level: 
Open Access
Software Categories: 
Software Interactive/GUI: 
General Linux Documentation: 

To run this software interactively in a Linux environment run the commands:

module load adf

adf < input_file

A graphical user interface for ADF is available on the machine 

ssh -Y
module load adf/2016.103

MSI's ADF license also permits users to install the graphical user interface on their own computers. Interested users should contact about adding their machine to the MSI license.