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How do I get started with NX?

What is NX? For years the X11 Window System (Xwin32/Putty on Windows, X11/Terminal on Mac) has been the defacto standard for remotely displaying a graphical user interface from an MSI workstation or cluster on your local client. The aged X11 technology provides a solid starting point for simple and...

Interactive queue use with isub

Notes on isub Use The command isub is an MSI-written wrapper to ssh and qsub, designed specifically for interactive use. When isub is run with default options, it will ssh to a compute node in a pool of nodes reserved for interactive use. These nodes are the lab back-end, so when your shell starts...

FLUENT

FLUENT uses a finite volume numerical procedure to solve the differential equations governing fluid flow, as well as conservation of energy and chemical species therein. Both compressible and incompressible flows can be modeled, as can turbulence by way of the k-e turbulence model.

Partek Genomics Suite

Partek Genomics Suite (Partek GS) is a software suite of statistics and interactive data visualization designed to extract biological signals from noisy data. Partek GS is able to support microarray and next generation sequencing technologies including DGE and gene expression, RNA-seq and alternative splicing, copy number and association, ChIP-chip, ChIP-seq, and microRNA.

SGA - String Graph Assembler

From the SGA GitHub repository: Overview SGA implements a set of assembly algorithms based on the FM-index. As the FM-index is a compressed data structure, the algorithms are very memory efficient. An SGA assembly has three distinct phases. The first phase corrects base calling errors in the reads. The second phase assembles contigs from the corrected reads. The third phase uses paired end and/or mate pair data to build scaffolds from the contigs. Example real-data assemblies can be found here. Error Correction The first stage of the assembly. An FM-index of the sequence reads is constructed...

Modeling Hydrogen Bond Arrays

The research group of Professor Steven Kass ( MSI Fellow , Chemistry ) uses MSI resources in their investigations into hydrogen bond networks. The goal of this research is to understand enzyme catalysis and develop hydrogen bond catalysts, novel acids and bases, and molecular anion receptors. By...

Investigating the Maize Transcriptome

In the course of the history of agriculture, humans have tried to change the properties of the crops they raise. Maize (corn) is a very valuable and widely grown crop, and researchers are able to trace how modern maize has been developed from its wild ancestor, a plant called teosinte ( Zea mays...

Modeling Polymer Structures and Dynamics

Polymers, which many people think refer only to plastic, are actually a large group of natural and man-made materials. They have many uses in industry and as consumer products. Some of these include the super-absorbant polymers used in disposable diapers, the heat-stable materials used for non-...

Investigating Proteins With Crystallography

The research group of Professor Carrie Wilmot in the Department of Biochemistry, Molecular Biology, and Biophysics concentrates on understanding the synthesis and function of novel organic, organometallic, and metal-ion cofactors in proteins. (A cofactor is a chemically reactive protein...

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