Secondary Support

Globus Command Line Interface

Globus is a data transfer service designed for convenient, fast file transferes between computer systems. More information about using Globus on MSI can be found here.  These command line tools provide an alternative interface to the Globus functionality.

PyPy Python

Python is a high level programming language that aims to combine remarkable power with very clear syntax. PyPy is an alternative implementation of the Python language that uses a Just-in-Time (JIT) compiler to run certain types of code much faster than the standard implementation.


SPADE: Spanning Tree Progression of Density Normalized Events

SPADE is a visualization and analysis tool for high-dimensional flow cytometry data. SPADE is implemented as an R package.


BCFtools are meant as a faster replacement for most of the perl VCFTools commands.


AbokiaBLAST is a parallel implementation of NCBI BLAST created by the inventors of the open-source mpiBLAST project. AbokiaBLAST inherits the super-scalable architecture from mpiBLAST but is re-factored and re-engineered to offer production quality. With intelligent task parallelization and I/O optimization, AbokiaBLAST enables users to massively accelerate large-scale BLAST search on clusters or supercomputers with a single command.

Due to the license, AbokiaBLAST is only installed in Itasca so far.


Python is a high level programming language that aims to combine remarkable power with very clear syntax. Anaconda is a free cross-platform Python distribution from Continuum Analytics. It comes built in with various scientific Python packages such as NumPy, SciPy, Pandas, Matplotlib, Numba, etc.


mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST.  mpiBLAST takes advantage of distributed computational resources, i.e., a cluster, through explicit MPI communication and thereby utilizes all available resources unlike standard NCBI BLAST which can only take advantage of shared-memory multi-processor computers. The primary advantage to using mpiBLAST versus traditional NCBI BLAST is performance.

SciTegic Pipeline Pilot

Pipeline Pilot, Accelrys' scientific informatics platform, was designed for scientists by scientists. It aggregates and provides immediate access to the volumes of disparate research data locked in silos, automates the scientific analysis of that data, and enables researchers to rapidly explore, visualize and report research results.


LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.