Denotes licensed software available for installation on your desktop or laptop computer. Please contact [email protected] for more information.
Data Analysis
Application  Linux (compute.cla)  Windows (wts.umn.edu)  Notes  License 

ABBYY Finereader 

licensed for 5 named users, contact [email protected] to see if a license is available  

licensed


Atlas.ti 

See our overview and comparison of Qualitative Analysis Software.  licensed for 10 concurrent users  
Gurobi Optimizer 

Licensed for research and instructional use only.  
Julia 


open source or free  
Mathematica 


licensed for CLA use  
Matlab 


licensed for CLA use


NVivo 

See our overview and comparison of Qualitative Analysis Software. 
licensed for CLA faculty, graduate students, and staff as well as CSOM Ph. D. candidates


Python/Anaconda 


open source or free  
R 


open source or free  
R Studio 


open source or free  
SAS 


Windows: available via wts.umn.edu Linux: only available on loki.cla.umn.edu 
licensed 
SPSS and AMOS 


AMOS is Windows only  licensed for CLA use and only academic purposes
may install only on Universityowned devices 
Stata/IC 

Instructional use only and via AppsToGo; contact us to request access 
licensed  
Stata/SE 


licensed  
Stata/MP 

Our license is for 8 cores and 2 concurrent users. 
licensed  
UCINET 

licensed 
Neuroimaging Analysis
Application  Linux (compute.cla)  Windows (wts.umn.edu)  Notes  License 

AFNI (multiple versions) 

open source or free  
ANTs 

open source or free  
Freesurfer (multiple versions) 

open source or free  
FSL (multiple versions) 

open source or free  
MRIcron 

open source or free  
SPM 

open source or free  
SUMA 

open source or free 
Genomic Analysis
Application  Linux (compute.cla)  Windows (wts.umn.edu)  Notes  License 

GCTA 

open source or free  
PLINK 

open source or free 
Programming and Other
Application  Linux (compute.cla)  Windows (wts.umn.edu)  Notes  License 

cuda 

open source or free  
gcc 

open source or free  
gmp 

open source or free  
jdk 

open source or free  
Kepler 

open source or free  
LaTeX 

open source or free  
mpfr 

open source or free  
Open MPI 

open source or free  
Python/Anaconda 


open source or free  
Python (Intel) 

Optimized versions of NumPy, SciPy, scikitlearn, and 20 other modules  open source or free  
Singularity 

open source or free 
Software Descriptions
Data Analysis
Optical Character Recognition (OCR) software primarily used for converting scanned documents to computerreadable text.
ArcGIS is a geographic information system (GIS) for working with maps and geographic information. It is used for creating and using maps, compiling geographic data, analyzing mapped information, sharing and discovering geographic information, using maps and geographic information in a range of applications, and managing geographic information in a database.
The purpose of ATLAS.ti is to help researchers uncover and systematically analyze complex phenomena hidden in unstructured data (text, multimedia, geospatial). The program provides tools that let the user locate, code, and annotate findings in primary data material, to weigh and evaluate their importance, and to visualize the often complex relations between them.
The Gurobi Optimizer is a mathematical optimization solver for a wide variety of problem types, including: linear programming (LP), quadratic programming (QP), quadratically constrained programming (QCP), mixed integer linear programming (MILP), mixedinteger quadratic programming (MIQP), and mixedinteger quadratically constrained programming (MIQCP).
Julia is a highlevel, highperformance dynamic programming language for numerical computing. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library.
Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields, based on symbolic mathematics.
MATLAB (matrix laboratory) is a multiparadigm numerical computing environment and fourthgeneration programming language.
Nvivo is a qualitative data analysis computer software package produced by QSR International. It has been designed for qualitative researchers working with very rich textbased and/or multimedia information, where deep levels of analysis on small or large volumes of data are required.
Python is an interpreted highlevel programming language for generalpurpose programming
R is a free software environment for statistical computing and graphics.
RStudio IDE is a powerful and productive user interface for R
SAS is a software suite developed by SAS Institute for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics.
The IBM SPSS® software platform offers advanced statistical analysis, a vast library of machinelearning algorithms, text analysis, opensource extensibility, integration with big data and seamless deployment into applications.
Stata is for data science needs. Obtain and manipulate data. Explore. Visualize. Model. Make inferences. Collect your results into reproducible reports. Stata/IC is for midsize datasets (up to about 2000 variables, 2 billion observations)
Stata is for data science needs. Obtain and manipulate data. Explore. Visualize. Model. Make inferences. Collect your results into reproducible reports. Stata/SE is for large datasets (up to about 33,000 variables, 2 billion observations) to SE
The fastest version of Stata (can handle 120,000 variables, up to 20 billion observations)
UCINET 6 for Windows is a software package for the analysis of social network data.
Neuroimaging Analysis
AFNI (Analysis of Functional NeuroImages) is a leading software suite of C, Python, R programs and shell scripts primarily developed for the analysis and display of anatomical and functional MRI (FMRI) data.
ANTs extracts information from complex datasets that include imaging. ANTs is popularly considered a stateoftheart medical image registration and segmentation toolkit.
An open source software suite for processing and analyzing (human) brain MRI images.
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
NIfTI viewer (Next generation of MRIcro)
The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or timeseries from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG.
SUMA is a program that adds cortical surface based functional imaging analysis to the AFNI suite of programs. It allows viewing 3D cortical SUrface models, and MApping volumetric data onto them.
Genomic Analysis
GCTA (Genomewide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by all genomewide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits.
PLINK is a free, opensource whole genome association analysis toolset, designed to perform a range of basic, largescale analyses in a computationally efficient manner.
Programming and Other
CUDA is a parallel computing platform and application programming interface (API) model created by Nvidia.[1] It allows software developers and software engineers to use a CUDAenabled graphics processing unit (GPU) for general purpose processing.
The GNU Compiler Collection includes front ends for C, C++, ObjectiveC, Fortran, Java, Ada, and Go, as well as libraries for these languages (libstdc++, libgcj,...).
GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floatingpoint numbers. There is no practical limit to the precision except the ones implied by the available memory in the machine GMP runs on. GMP has a rich set of functions, and the functions have a regular interface.
The JDK is a development environment for building applications, applets, and components using the Java programming language.
Kepler is designed to help scientists, analysts, and computer programmers create, execute, and share models and analyses across a broad range of scientific and engineering disciplines.
LaTeX is a highquality typesetting system; it includes features designed for the production of technical and scientific documentation. LaTeX is the de facto standard for the communication and publication of scientific documents.
The main goal of MPFR is to provide a library for multipleprecision floatingpoint computation which is both efficient and has a welldefined semantics.
N/A
A version of Python distributed by Intel that has been optimized for faster performance with certain modules.
Singularity is a free, crossplatform and opensource computer program that performs operatingsystemlevel virtualization also known as containerization. One of the main uses of Singularity is to bring containers and reproducibility to scientific computing and the highperformance computing.