Research Software

 

 

Icon denoting software title is available for installation on your desktop computer.

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

ArcGIS

 
Checkmark
  licensed
Icon denoting software title is available for installation on your desktop computer.
Atlas.ti  
Checkmark
See our overview and comparison of Qualitative Analysis Software. licensed for 10 concurrent users
Gurobi Optimizer
Checkmark
    Licensed for research and instructional use only.
Julia
Checkmark
Checkmark
  open source or free
Mathematica
Checkmark
Checkmark
  licensed for CLA use
Matlab
Checkmark
Checkmark
  licensed for CLA use
Icon denoting software title is available for installation on your desktop computer.

 

NVivo  
Checkmark

 

See our overview and comparison of Qualitative Analysis Software.

licensed for CLA faculty, graduate students, and staff as well as CSOM Ph. D. candidates
Icon denoting software title is available for installation on your desktop computer.

 

Python/Anaconda
Checkmark
Checkmark
  open source or free
R
Checkmark
Checkmark
  open source or free
R Studio
Checkmark
Checkmark
  open source or free
SAS
Checkmark
Checkmark

Windows: available via wts.umn.edu

Linux: only available on loki.cla.umn.edu

licensed
SPSS and AMOS
Checkmark
Checkmark
AMOS is Windows only licensed for CLA use and only academic purposes
Icon denoting software title is available for installation on your desktop computer.

may install only on University-owned devices

Stata/IC  
Checkmark

 

Instructional use only and via AppsToGo; contact us to request access

licensed
Stata/SE
Checkmark
Checkmark
  licensed
Stata/MP
Checkmark
 

Our license is for 8 cores and 2 concurrent users

licensed
UCINET  
Checkmark
  licensed

 

Neuroimaging Analysis

Application Linux (compute.cla) Windows (wts.umn.edu) Notes License
AFNI (multiple versions)
Checkmark
    open source or free
ANTs
Checkmark
    open source or free
Freesurfer (multiple versions)
Checkmark
    open source or free
FSL (multiple versions)
Checkmark
    open source or free
MRIcron
Checkmark
    open source or free
SPM
Checkmark
    open source or free
SUMA
Checkmark
    open source or free

 

Genomic Analysis

Application Linux (compute.cla) Windows (wts.umn.edu) Notes                 License
GCTA
Checkmark
    open source or free
PLINK
Checkmark
    open source or free

 

Programming and Other

Application Linux (compute.cla) Windows (wts.umn.edu) Notes             License
cuda
Checkmark
    open source or free
gcc
Checkmark
    open source or free
gmp
Checkmark
    open source or free
jdk
Checkmark
    open source or free
Kepler
Checkmark
    open source or free
LaTeX
Checkmark
    open source or free
mpfr
Checkmark
    open source or free
Open MPI
Checkmark
    open source or free
Python/Anaconda
Checkmark
Checkmark
  open source or free
Python (Intel)
Checkmark
  Optimized versions of NumPy, SciPy, scikit-learn, and 20 other modules open source or free
Singularity
Checkmark
    open source or free

 

Software Descriptions

Data Analysis

ABBYY Finereader

Optical Character Recognition (OCR) software primarily used for converting scanned documents to computer-readable text.

ArcGIS

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.

Atlas.ti

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.

Gurobi Optimizer

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), mixed-integer quadratic programming (MIQP), and mixed-integer quadratically constrained programming (MIQCP).

Julia

Julia is a high-level, high-performance dynamic programming language for numerical computing. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library.

Mathematica

Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields, based on symbolic mathematics.

Matlab

MATLAB (matrix laboratory) is a multi-paradigm numerical computing environment and fourth-generation programming language.

Nvivo

Nvivo is a qualitative data analysis computer software package produced by QSR International. It has been designed for qualitative researchers working with very rich text-based and/or multimedia information, where deep levels of analysis on small or large volumes of data are required.

Python/Anaconda

Python is an interpreted high-level programming language for general-purpose programming

R

R is a free software environment for statistical computing and graphics.

R Studio

RStudio IDE is a powerful and productive user interface for R

SAS

SAS is a software suite developed by SAS Institute for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics.

SPSS and Amos

The IBM SPSS® software platform offers advanced statistical analysis, a vast library of machine-learning algorithms, text analysis, open-source extensibility, integration with big data and seamless deployment into applications.

Stata/IC

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 mid-size datasets (up to about 2000 variables, 2 billion observations)

Stata/SE

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

Stata/MP

The fastest version of Stata (can handle 120,000 variables, up to 20 billion observations)

UCINET

UCINET 6 for Windows is a software package for the analysis of social network data.

Neuroimaging Analysis

AFNI

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

ANTs extracts information from complex datasets that include imaging.  ANTs is popularly considered a state-of-the-art medical image registration and segmentation toolkit.

Freesurfer

An open source software suite for processing and analyzing (human) brain MRI images.

FSL

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

MRIcron

NIfTI viewer (Next generation of MRIcro)

SPM

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 time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG.

SUMA

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

GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by all genome-wide 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

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

Programming and Other

cuda

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 CUDA-enabled graphics processing unit (GPU) for general purpose processing.

gcc

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, Ada, and Go, as well as libraries for these languages (libstdc++, libgcj,...).

gmp

GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point 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.

jdk

The JDK is a development environment for building applications, applets, and components using the Java programming language.

Kepler

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

LaTeX is a high-quality 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.

mpfr

The main goal of MPFR is to provide a library for multiple-precision floating-point computation which is both efficient and has a well-defined semantics.

Open MPI

N/A

Python (Intel)

A version of Python distributed by Intel that has been optimized for faster performance with certain modules.

Singularity

Singularity is a free, cross-platform and open-source computer program that performs operating-system-level virtualization also known as containerization.  One of the main uses of Singularity is to bring containers and reproducibility to scientific computing and the high-performance computing.