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Three-dimensional computer reconstructions of histological brain preparations and neural network analysis


Three-Dimensional Computer Reconstructions of Histological Brain Preparations and Neural Network Analysis

The growing success and widespread acceptance of deep brain stimulation (DBS) for Parkinson’s and essential tremor has opened up the possibilities for applying brain stimulation for other neurological disorders and conditions. The Lim lab pushes to develop new neural prostheses for hearing restoration and tinnitus suppression. This research requires parallel experiments in animals and in humans to understand the various ways in which we can electrically stimulate different brain regions to restore normal auditory function in patients suffering from hearing loss and debilitating tinnitus. For the animal experiments, special electrode arrays are implanted into different brain regions and stimulated with various parameters to characterize the corresponding activation effects on neural coding and perception. After each experiment, histological slices are used to reconstruct three-dimensional computational brain models using Rhinoceros software to identify the locations of our electrode arrays. The researchers also perform extensive spiking pattern analysis and correlations across locations to identify how specific brain regions are related to different electrical stimulation brain activation patterns. These results not only help characterize different brain regions but will also help to identify optimal locations for implanting neural implants in future patients. The large data files used to create these brain reconstructions and neural analyses require the high-performance computers available at MSI to ensure effective and efficient creation and manipulations of the various brain and network models. 

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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.

Python is a modern general purpose programming language that is popular in scientific computing for its readable syntax and extremely rich ecosystem of scientific and mathematical modules.

Computational Astrophysics

The physics of diffuse, ionized gases - plasmas - and gravity in deep space are of great interest to researchers investigating how the early universe developed. The use of high-performance computing allows computational astrophysicists to create simulations that extend over cosmic times and...

MSI Users Bulletin - September 2016

The Users Bulletin provides a summary of new policies, procedures, and events of interest to MSI users. It is published quarterly.

To request technical assistance with your MSI account, please contact

1. Accounts for Non-UMN MSI Users: MSI is transitioning from using sponsored accounts for non-UMN affiliated users to a “Person of Interest (POI)” designation. This change will create a greater level of security for accounts.

MSI is no longer accepting sponsored accounts as valid UMN Internet IDs for new users. As of January 1, 2017, sponsored accounts will no longer be allowed to log in to MSI resources. PI groups who have users with sponsored accounts must convert the accounts to POI. PI groups will need to get POI status for any external user they wish to add to their group. See the FAQ for more information.

The MSI Tech Support staff ( will assist non-University affiliated PIs with creating POIs. University-affiliated PIs are authorized to set up POIs with the University.

2. High Performance Storage (Panasas) Expansion:  MSI staff and Panasas expanded the Panasas high-performance storage system on September 7, 2016. Ten new AS20 shelves with 10 TB drives, expanded SSDs, and improved director blades will replace ten of the original AS14 storage shelves. In net, the high-performance storage system capacity will expand by 1 PB to a total of 4.5 PB.    

3. Overclocked Returned to Interactive Lab Queue Resources: MSI has worked with the vendor, LiquidCool Solutions, to return the four Overclocked nodes to the interactive queue. The processors and GPUs have been upgraded to the Intel Xeon 5698/4.4GHz and Nvidia Tesla M2090s. The nodes each have 2 physical cores, 24 GB of memory, and 2 x 120 GB SSDs. The nodes are available via the oc queue.  

4. Annual Account Renewal Deadline, December 1: The deadline for annual MSI account renewals is December 1. PIs and Group Administrators will receive email notification when the renewal period is open, which will be on or about November 1. Renewals are submitted using the myMSI portal. Renewal by December 1 ensures continued MSI access through the following calendar year.

5. MSI Beta: MSI’s website now includes a page that describes projects that are part of our MSI Beta program. MSI Beta is a way for MSI staff and users to explore new technologies without hindering ongoing research. Instructions for participating in these programs can be found on the page.

6. Research Ethics: The Office of the Vice President for Research (OVPR) has launched a University-wide research ethics campaign. This campaign is intended to emphasize our collective responsibility to uphold the highest ethical standards. An article appears in the OVPR’s Inquiry blog that describes the campaign and upcoming symposiums and other events concerning research ethics.

OVPR also maintains a Research Ethics webpage.

7. Fall Tutorials: The list of upcoming tutorials for the fall has been posted on the MSI website. See the list on the MSI website.

8. Job Available at MSI:

a. Biological Mass Spectrometry Analyst

9. Useful Webpages: Looking for help with using MSI? One of these pages may have the information you need:

a. Services available at MSI

b. Getting Started (includes Quickstart Guides)

c. MSI Systems

d. Help and Documentation

e. Staff Listing and Areas of Expertise

f. Upcoming Events and Tutorials

g. Proposal Support


A New Computer Model for Air Pollution

Scientists studying air pollution use powerful computer models to simulate how various types of pollution spread in the atmosphere. Among these models are Eulerian Chemical Transportation Models (CTMs), which are able to simulate the effectiveness of pollution-reduction efforts. This provides...


Definitions Allocation period The allocation period corresponds to the calendar year, January 1 to December 31. Group Members of a PI group High Performance Computing Includes not only traditional input and output from supercomputing systems operated by the Institute, but also other activities in...


The basic philosophy behind Molcas is to develop methods that will allow an accurate ab initio treatment of very general electronic structure problems for molecular systems in both ground and excited states. This is not an easy task. Our knowledge about how to obtain accurate properties for single reference dominated ground states is today well developed and MOLCAS contains a number of codes that can perform such calculations (MP2, CC, CPF, CCSD(T) etc.). All these methods treat the electron correlation starting from a single determinant (closed or open shell) reference state. Such codes are...

Using Computational Chemistry to Solve Energy Challenges

The challenge of finding “green” energy resources to replace non-renewable fossil fuels is a topic of great interest for researchers. Chris Cramer (Distinguished McKnight Professor of Chemistry ; MSI Fellow ) and his research group and collaborators are among those who are using high-performance...

MSI Supporting DOE Grants in Computational Chemistry

MSI is proud to spotlight some of our researchers in a new series of articles that are aimed both at highlighting their research and illustrating how MSI facilitates it. Christopher Cramer’s group uses supercomputing resources to push the limits of present-day computational chemistry tools in order...