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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

Abstract: 
<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="https://www.msi.umn.edu/pi/18730a36f92cc324c13d78a3ef324130/10898">PI&#39;s main page</a>.</p>
Group name: 
topczews

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

Abstract: 
<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="https://www.msi.umn.edu/pi/93cbdb0867d546668b1cec64d34ac20c/10968">main page</a>.</p>
Group name: 
hirschc3

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...

3D Printing on Skin

MSI PI Michael McAlpine ( Mechanical Engineering ) led a group of researchers who successfully used a 3D printer to print electronics on the back of a real human hand. This research could be used by soldiers, who could get temporary sensors to detect biological or chemical agents or solar cells to...

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...

breseq

Software Description: 

From the breseq manual pages:

breseq (pronounced: breeze-seq) is a computational pipeline for the analysis of short-read re-sequencing data (e.g. 454, Illumina, SOLiD, etc.).
 
It uses reference-based alignment approaches to predict mutations in a sample relative to an already sequenced genome. breseq is intended for microbial genomes (<10 Mb) and re-sequenced samples that are only slightly diverged from the reference sequence (<1 mutation per 1000 bp).
 
breseq‘s primary advantages over other existing software programs are that it can:
Predict new sequence junctions, such as those associated with mobile element insertions, from single-end read data.
 
Reliably identify short indel mutations by appropriately masking the ends of read alignments.
Produce annotated output describing biologically relevant mutational events.
breseq is available on the lab cluster.
 

 

Software Support Level: 
Secondary Support
Software Access Level: 
Open Access
Software Categories: 
Lab Documentation: 
module load breseq

This loads breseq, bowtie and R.

Example command:

>>>breseq -r NC_012967.gbk SRR030257_1.fastq SRR030257_2.fastq
 
The first named argument (-r) is the reference sequence. If you had multiple reference sequences, you could input multiple ones (e.g., -r NC_012967.gbk -r plasmid.gbk).
 
The unnamed arguments at the end of the command line are the read files. You can input as many as you need to and mix FASTQ files from different sequencing technologies (Illumina and 454).
 
Software Interactive/GUI: 
No

libsequence

Software Description: 

libsequence is a C++ library designed to aid writing applications for genomics and evolutionary genetics. A large amount of the library is dedicated to the analysis of "single nucleotide polymorphism", or SNP data. The library is intended to be viewed as a "BioC++" akin to the bioperl project, although the scope of libsequence is limited in comparison. Much of the bioperl project concerns parsing the output of various bioinformatics programs, and the management of databases of biological data. perl is a good language for such things, and libsequence tries not to re-invent the wheel. Rather, the focus is on biological computation, such as the analysis of SNP data and sequence divergence, and the analysis of data generated from coalescent simulation.

Software Support Level: 
Secondary Support
Software Access Level: 
Open Access
Software Categories: 
Software Interactive/GUI: 
No
General Linux Documentation: 

To use this software in an interactive Linux environment, run the commands:

module load libsequence

Documentation for libsequence can be found here

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