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Mimics

Software Description: 
Mimics is useful for visualization and segmentation of CT / MR images and 3D rendering of objects. It also provides an interface to create FEM meshes.
MSI currently has the following modules
  • Mimics basic - Allows segmentation, registration and measurement on 3D object
  • STL+ - Allows creation of 3D object for rapid prototyping
  • FEM - Add material property, create FEM mesh and export files to standard FEM packages

 

Software Support Level: 
Secondary Support
Citrix Documentation: 

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

Start > All Programs > Materialise Software > Mimics x64 15.01 > Mimics

We only have two Mimics licenses. To use Mimics we ask that you reserve time on one the Mimics calendars, calendar one or calendar two using these instructions.  Reservations can be made on a calendar if you have a UMN Google account.  If you have problems, send an email to help@msi.umn.edu with a subject such as 'Add reservations to Mimics calendars'.

 
Running Mimics
Mimics is installed on our Citrix server. Follow the instructions for connecting with Citrix. Select the GPU node. You should see a Windows desktop. It may take a minute to come up. From there you should be able to run Mimics. Let us know if you feel the performance is too slow, there are things we can do to improve that.
 
Issues
We know of the following issues – none of them are show-stoppers, but people should be aware of them:
  • Mimics and 3-Matic may take several minutes to launch, but will start up successfully, given time.
  • When launching 3-Matic, a warning will pop up about a crash report directory. The program will launch normally after clicking OK.
  • Opening the Mimics ‘Options’ window for the first time will cause the program to hang for a minute or two before the window appears.
  • Mimics defaults to using the folder C:\MedData for projects. There is some example data in there to play with, but please save projects to your U: or G: drives, as C: drive space is limited, and files on the C: drive are not guaranteed to be preserved after logout.
  • If all licenses are in use, Mimics will go straight to a screen asking to configure a new license. If this happens, click “Cancel”.
Software Access Level: 
Open Access
Software Interactive/GUI: 
No

ProteinPilot

Software Description: 

ProteinPilot™ Software can perform protein identification and quantitation, along with prediction of hundreds of peptide modifications and non-tryptic cleavages simultaneously. The protein grouping algorithm helps in distinguishing protein isoforms and visualize peptide-protein associations and relationships. The new version can take in generic input for non-AB SCIEX instruments via .mgf format. Other features include : Automatic and Rigorous False Discovery Rate (FDR) Analysis; Improved Quantitation for iTRAQ Reagent-Based Workflows; Speed and Scalability Improvements; Extended Gel Workflow Support; Open Control of Parameter Settings; Extended Support for Instruments from Other Vendors; Improved Identification Quality; Command Line Control and Open Results.

Currently, MSI has only one ProteinPilot license. We ask that all users use the calendaring program to sign up for time on ProteinPilot. Please specify your name on the calendar. Prior to using the calendar for the first time please email help@msi.umn.edu to request access to the ProteinPilot calendar. Please limit your ProteinPilot reservation to less than 24 hours at a time. If you need additional time after your 24 hour session has ended and the license is not reserved you may reserve another 24 hour session.  If you are not able to reserve time on the calendar please email help@msi.umn.edu.

You can use the following links to see the ProteinPilot calendar and reserve the license: ProteinPilot Calendar

Follow the instructions at https://www.msi.umn.edu/calendar/instruction.html to add a reservation to the calendar.

 

Software Support Level: 
Secondary Support
Citrix Documentation: 

ProteinPilot™ Software v. 5.0 is available in the "Node-Locked Software" virtual desktop at xen.msi.umn.edu. Instructions for connecting to xen.msi.umn.edu are available here. There are many new features and performance improvements in this version. Please read the Release Notes carefully to make sure you are aware of the changes.

Restore Files
If you modify the Data Dictionary and Parameter Translation files on the Xen ProteinPilot 4.5 version you must restore these files to the Original Modification Parameters after you complete your search so that the next user can ensure that the Standard, Unmodified Parameters were in use for their own search. We urge everyone to adhere to this policy.

Modifications to these files can drastically affect results outcome, in some cases, depending on exactly what modifications were made.
 

Clean Up Your Files
The C: drive on Xen (with node-locked licenses for ProteinPilot 4.5 version and Scaffold) has been getting full with input MGF files, search databases and output search results. We request that users back up and copy their .group, .sf3, MGF and other files once the searches are complete. Users can back up data to U: drive or any other location. Once you have backed up your files, remove the files from the C: drive so that there is enough space available for any new searches.

 

ProteinPilot is also available on Galaxy-P (https://galaxyp.msi.umn.edu). A screencast for using ProteinPilot within Galaxy-P is available at: http://z.umn.edu/ppingp

A "viewer" version of the software is available on all other MSI Windows systems. Please note that this version of software can be used to view previously generated .group files. This version cannot be used for searching the data. For searching data, use ProteinPilot on the "Node-Locked Software" virtual desktop, or via Galaxy-P as mentioned above.

Some highlights in the new version:
  • Improved quantitation results for SILAC and other survey-level quantitation

  • Improved mass accuracy from better feature detection

  • Improved identification results

  • Support for new AB SCIEX instruments released in 2012, including the TripleTOF® 4600, TripleTOF® 5600+, QTRAP® 4500, and QTRAP® 6500 systems.

  • Peptide shared status is provided for better downstream use of ProteinPilot results with the MS/MSALL with SWATH™ Acquisition MicroApp 1.0 add-in for PeakView® Software (versions 1.2.0.3 or higher)

  • New Spectrum Summary export

  • Reduction in false singleton and blank ratios

A number of tutorial materials and webinars have been created for ProteinPilot users.   You can find a complete list here.

 
 
Software Access Level: 
Limited Licenses
Software Categories: 
Software Interactive/GUI: 
No

Computational Papyrology

An article featuring MSI Principal Investigator Lucy Fortson (Physics and Astronomy) recently appeared in the Summer 2012 edition of the College of Liberal Arts Reach magazine and was reposted on the College of Science and Engineering website . The project, called Ancient Lives , uses the help of...

MATLAB Distributed Compute Server Demo

posted on August 5, 2014 UPDATE (posted August 19, 2014): The demo license was extended until September 17. Contact Evan Bollig ( boll0107@umn.edu ) to participate in the demo. MSI has deployed a demo of the MATLAB Distributed Compute Server (MDCS), which allows MATLAB jobs to launch parfor and...

Extension to MATLAB Distributed Compute Server Demo

posted on August 19, 2014 The demo license for the MATLAB Distributed Compute Server (MDCS) has been extended to September 17! The MDCS allows MATLAB jobs to launch parfor and SIMD loops across multiple nodes on Itasca. With MDCS there is no need to run pbsdsh or another parallel shell environment...

Computational Modeling of Endovascular Deep Brain Simulation

Deep brain stimulation (DBS) is a surgical therapy used to treat many neurological disorders that are refractory to medication. Patients with severe Parkinson’s disease, dystonia, essential tremor, obsessive-compulsive disorder, and depression have all benefited from DBS. The therapy involves...

Molecular Reagents for Precision Optical Control of Neural Computations

Abstract: 
<h3 class="red">Molecular Reagents for Precision Optical Control of Neural Computations</h3><p>To understand how brain function emerges from the activities of ion channels in neuronal cell membranes is an overarching goal in neuroscience. Because &quot;how much of which ion channel type is expressed where&quot; determines the functional role of neurons within neural circuits, it is necessary to have a method for precise and dynamic perturbation of endogenous ion channels with subcellular resolution, in specific neural circuits, and in intact behaving organisms to achieve this goal. These researchers have begun to address this need by engineering rationally designed proteins (called lumitoxins) that can modulate the activity of endogenous ion channels and receptors with light. To improve this technology, they have developed an all-optical screening platform that they hope will scale to potentially millions of lumitoxin variants. Central to this screening platform is an Image Processing Workflow that detects functional lumitoxins and labels the neurons expressing them. This workflow is parallelizable and needs to operate in real time, making MSI resources useful.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/a6d4c04f25f4c7526a93d408ad5bfc14/10979">main page</a>.</p>
Group name: 
schmidtd

Tecplot

Software Description: 

Tecplot is a powerful interactive plotting program for visualizing and analyzing engineering and scientific data. It integrates XY plotting with two and three-dimensional surface data-visualization capabilities into a single easy-to-use program. Tecplot allows the user to create plots with contours,iso-surfaces, mesh lines, vectors, streamlines, light-source shaded surfaces, and scatter symbols.

Software Support Level: 
Secondary 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 > Tecplot 360 $VERSION  > Tecplot 360 $VERSION
$VERSION is the version number of the Tecplot installation. For more information and tutorials visit the tecplot documentation page.
Software Access Level: 
Open Access
Software Interactive/GUI: 
No
General Linux Documentation: 

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

module load tecplot
tec360

Under "Help" (far right on the menu bar) select "Tecplot Licensing..."
Select "Network License"
Under "License Server Name:", enter: tecplot-rlm.license.enet.umn.edu

Avizo

Software Description: 

Avizo software is a powerful, multifaceted tool for visualizing, manipulating, and understanding scientific and industrial data.

Software Support Level: 
Secondary 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 > Avizo > Avizo$VERSION

Software Access Level: 
Limited Licenses
Software Interactive/GUI: 
No
General Linux Documentation: 

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

isub -m 8GB
module load avizo
avizo

In order to run avizo 8.0 or higher, a minimum of 8 GB memory is required.

If you are trying to run Avizo remotely (via ssh or NX) please note that some versions of Avizo may not work well with NX. Let us know if you have problems. For version 9.0, you will see a message about the security context. Answer "n" to the question to get Avizo to run. We are working with the vendor to remove this question.

How do I create a key pair?

SSH keypairs are essential for accessing VMs You can access keypair options by going to the " Key Pairs" tab located at Project > Compute > Access & Security Create a new key pair to generate and download a new private key, or Import a key pair to upload an existing public key Every VM...

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