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RECON is software for automated de novo identification of repeat families from genomic sequences. This software was originally developed by the Eddy lab . A newer version that fixes several bugs is available from the RepeatMasker webpage.

MSI Exhibits at SC08

The University of Minnesota's Supercomputing Institute showcased the University's research efforts at this year's Supercomputing Conference held November 15-21, 2008 in Austin, TX. The SC Conference is the premier international conference for high performance computing (HPC), networking, storage...

Dell Town Hall Meeting, September 4

posted on September 3, 2013 As part of the ongoing selection process for the next HPC system at MSI, MSI has invited top high performance computing vendors to present their high performance computing portfolios and roadmaps to users in a open discussion setting. Dell Computing will be at MSI on...


DRMAA (Distributed Resource Management Application API) is a specification developed by a working group in the Global Grid Forum (GGF). The intention is to provide an API specification for the submission and control of jobs to one or more Distributed Resource Management (DRM) systems.

Gene expression profiling human ovarian carcinoma


Gene Expression Profiling in Human Ovarian Carcinoma Using Primary Tumorgrafts

These researchers have developed primary patient ovarian carcinoma tumorgrafts for the purpose of defining gene expression signatures linked to outcome and therapeutic response. A number of these models have been analyzed by DNA microarray. The next step is to analyze these arrays in conjunction with publicly available datasets via the appropriate Microarray Data Analysis Software (primary and ancillary). The number of arrays being analyzed simultaneously requires MSI's HPC hardware. 

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Fungal Gut Microbiomes


Fungal Gut Microbiomes

The Gale lab studies the fungal gut microbiome in a variety of human and mouse subjects. Fungal sequencing is performed by the University of Minnesota Genomics Center using a next-generation sequencer from Illumina. Data generated by sequencing is analyzed using MSI's HPC systems due to the massive amounts of output from the sequencing experiments. 

This PI’s research was featured in an MSI Research Spotlight in April 2015.

Return to this PI’s main page.

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UMII UMGC Analysis Pipelines

Custom analysis pipelines developed with support from the UMGC and UMII. Pipelines include RNA-Seq analysis, 16s amplicon sequence analysis, and whole-genome shotgun resequencing alignment and variant calling.


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Full documentation for the pipelines is available at this website:


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This software is available to any MSI user.
SW Category

Cyber Enabled Discovery and Innovation

The research group of Professor Steven Girshick ( MSI Fellow ; Mechanical Engineering ) uses MSI to support their development of computational models of gas plasmas in which nanoparticles nucleate and grow. These plasmas have industrial applications, such as semiconductor processing and materials...