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New Information About Dark Matter

posted on April 20, 2015 MSI PI Liliya Williams, a professor at the Minnesota Institute for Astrophysics ( College of Science and Engineering ), was part of a team that has discovered dark matter interacting with a force other than gravity. The research, published in the journal Monthly Notices of...

How do I use Singularity on CentOS 7?

Background Docker containers have arrived at MSI for user testing. Beginning in early June 2018, the Singularity container runtime will be available for users on a subset of Mesabi compute nodes. Anyone submitting jobs to the "centos7" or "centos7gpu" job queues will have access to the singularity...

How do I use Docker on Stratus?

Docker is installed by default on all Stratus MSI-blessed images Download and run Docker Container Images from DockerHub ( https://hub.docker.com/ ) Try it out: docker run -it centos /bin/bash Or docker run -it biocontainers/samtools \ samtools --version

System Status

Network access to MSI systems is currently available only on-campus or through the University's VPN . GPUT Visualization features are now available through our Interactive HPC resources . The current version of the NX client can be downloaded from our NX FAQ page . Next Maintenance Day: Wednesday,...

Computational Biochemistry and Proteomics

Abstract: 
<h3 class="red">Computational Biochemistry and Proteomics</h3><p>This research group is involved in two major projects and uses MSI software resources for<span style="background-color: rgb(255, 255, 255);">&nbsp;routine applications.</span></p><ul><li>One project focuses on anti-cancer and antimicrobial drug design that target enzymes like the proteasome or integral membrane proteins like cell surface growth receptors and transporters. For example, inhibition of the proteasome leads to cancer cell apoptosis or programmed cell death. This project requires access to the molecular modeling and simulation resources to perform molecular docking (e.g., with AUTODOCK and DOCK) and QSAR studies (e.g., with Tripos Sybyl , GAUSSIAN, and the Cambridge Structural Database) to guide the synthesis of novel hybrid inhibitors with some similarity to known scaffolds. Similar methods will be applied to other anti-microbial compounds.</li><li>The second project is to identify the structure and function of a novel family of membrane-bound aspartyl proteases. This uses molecular modeling and simulation resources (e.g., Discovery Studio (Accelrys, Inc.) and PyMOL software packages) and will use structural biology resources (e.g., molecular dynamics software (Gromacs and NAMD) designed for biomolecular systems, biological force fields (CHARMm and AMBER), and docking software (AUTODOCK and DOCK)) in the future to perform docking studies in order to elucidate the preferred protein substrates for these proteases.&nbsp;<span style="background-color: rgb(255, 255, 255);">In addition, this lab collaborates with the Center for Mass Spectrometry and their data are being stored on shared MSI/Mass Spec resources. They use a variety of the proteomics software packages (e.g., MAXQUANT, TINT, X! TANDEM, MASCOT, Scaffold Q+,and ProteinPilot ) for analyzing mass spectrometry data to identify proteins cleaved by their proteases.</span></li></ul><p>In routine applications, the lab uses the Vector NTI software package for molecular biology and genetic engineering applications, the software for data analysis, curve fitting, and graphing (e.g., Origin Lab software and GraphPad Prism), and MATLAB and Mathematica for numerical computation.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/2b705f381197d48dfb423ae1934e86df/10155">main page</a>.</p>
Group name: 
johnsonj

R

Software Description: 

R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity.

Software Support Level: 
Primary Support
Citrix Documentation: 

To run this software under Windows, connect using instruction provided in our Windows systems page.  Once logged in, navigate to

Start > All Programs > R > R x64 $VERSION

$VERSION is the version number of the R installation. If you need to run long or memory-intensive jobs, use R on Linux instead. If you need more details, visit the official documentation.

We recommend that you install R packages in your home directory. It can be accomplished by typing the following in the R command prompt. You need to replace packagename with the actual package.

r <- getOption("repos");
r["CRAN"] <- "http://cran.rstudio.com/";
options(repos=r);
install.packages("packagename");

Some packages need external libraries such as gccgslfftw etc. You can find the requirements in the package documentation. These packages have to be loaded by using 'module load' command before using R. If you still experience issues, please contact help@msi.umn.edu.                          

Software Access Level: 
Open Access
PBS Example: 

Programs can be submitted to a queue using PBS script such as the one below.  You need to modify the parameters depending on the machine where the job is executed. By default, an R script runs only on one core.  If you need to use multiple cores and/or multiple nodes, use packages that are listed in the CRAN page on high performance computing. The most popular R parallel packages are snow, snowfall, Rmpi and parallel. 

#PBS -l nodes=1:ppn=8,mem=12gb,walltime=04:00:00
#PBS -m abe
cd /location/of/the/script
module load R
R CMD BATCH myscript.R
wait
Software Interactive/GUI: 
No
General Linux Documentation: 

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

module load R
R

Several versions of R are available, but the versions may be different on different platforms.To list all versions of R available on the machine, type

module avail R

We recommend that you install R packages in your home directory. It can be accomplished by typing the following in the R command prompt. You need to replace packagename with the actual package.

r <- getOption("repos");
r["CRAN"] <- "http://cran.rstudio.com/";
options(repos=r);
install.packages("packagename");

Some packages need external libraries such as gccgslfftw etc. You can find the requirements in the package documentation. These packages have to be loaded by using 'module load' command before using R. If you still experience issues, please contact help@msi.umn.edu.                          

 
 

November 2011

The Le Sueur River Basin in southern Minnesota is a major source of sediment in the Minnesota River and in Lake Pepin. Excess sediment can adversely affect the ecosystems of rivers and lakes. Assistant Professor Karen B. Gran (Geological Sciences, University of Minnesota Duluth) is studying...

Stata

Software Description: 

Stata is an integrated statistical package that provides extensive functionality for data analysis, data management, and graphics.

 

To use Stata you must be on the Stata user list. Contact MSI Help, help@msi.umn.edu, to be added to the Stata user list. We have two Stata-MP8 version 13 licenses. We ask that all users use the calendaring program to sign up for time on Stata. If someone is signed up in the spot that you want, use a different calendar. Up to two users can sign up for the same time slot, one user per calendar. Please specify your name on the calendar. You can use the following links to see the Stata calendars and reserve a license:

Stata Calendar for License One                                                                                                
Stata Calendar for License Two

 

Follow the instructions  to add a reservation to the calendar.

Software Support Level: 
Secondary Support
Software Access Level: 
RESTRICTED - Contact Helpdesk
PBS Example: 

An example "mystata.pbs":

#!/bin/bash -l 
#PBS -l nodes=1:ppn=1,mem=30gb,walltime=1:00:00 
#PBS -m abe 
cd myStataDir
module load stata 
stata -b do < mystata.do
Software Categories: 
Mesabi Documentation: 
To run this software interactively in command line mode in the Stata queue of Mesabi, use the option '-q stata'. For example:
   qsub -I -q stata -l walltime=1:00:00,nodes=1:ppn=24
To submit a Stata job into the queue, from login.msi.umn.edu ssh to Mesabi, then run:
   qsub -q stata jobscript.pbs
Lab Documentation: 
To run this software interactively with a graphical user interface in the Lab queue, use the commands:
isub -q stata
module load stata
xstata

 

To submit a Stata job into the queue, from login.msi.umn.edu ssh to lab.msi.umn.edu, then run:
qsub -q stata ./mystata.pbs
Software Interactive/GUI: 
No

How do I get API access with OpenStack RC v3?

Stratus is backed by many web service APIs that can be controlled directly To see API access options, locate the " API Access " tab, found at Project > Compute > Access & Security Click Download OpenStack RC File v3 to get your OpenStack RC file for the current project When sourced in...

WebViz: A Collaborative Visualization System

Thanks to the advancement of computing hardware, researchers in all fields are able to generate huge datasets. Data processing, including analysis and visualization, has to tackle the problem of large-data throughput. Both the software and hardware architectures of current computational science...

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