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Software

Provided Applications

The following table lists the third-party software which we have installed on our systems. Additional software may be available on request. Please contact if you are interested in the availability of software not shown in this list.

Data science, data analysis, and statistical software

Software

Description

Webpage

Anaconda

 distrution of Python and R designed for big data processing and analytics  Anaconda
R
R is a free software environment for statistical computing and graphics. R
Python
Python is a great object-oriented, interpreted, and interactive programming language Python
Julia
dynamic programming language for high performance computing
 Julia
HDF5
a data model and library for storing and managing data
HDF5
MATLAB
Global Optimization Toolbox, Optimization Toolbox, 
Parallel Computing Toolbox, Statistics and Machine Learning Toolbox
MATLAB
NetCDF
Network Command Data Form: Software libraries for sharing array-oriented scientific data
NetCDF
RapidMiner
software for business analytics, data and text mining, machine learning, and predictive analysis
RapidMiner
Hadoop
is a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models. Hadoop
Octave
open source software similar to MATLAB
 Octave
SQL
is a special-purpose programming language designed for managing data held in a relational database management system, or for stream processing in a relational data stream management system. Multiple Implementation

Continuum Mechanics and Computational Fluid Dynamics

Software

Description

Webpage

 OpenFoam

 is a C++ toolbox for the development of customized numerical solvers, and pre-/post-processing
utilities for the solution of continuum mechanics problems, including computational fluid dynamics.

 OpenFoam

Math Libraries

Software

Description

Webpage

 Intel Math Kernel Library
(MKL)

BLAS, LAPACK, Statistics, Fast Fourier Transforms, Data fitting optimized for Intel processors
Intel-MKL
ATLAS
local optimized version of BLAS including some LAPACK function
ATLAS
BLAS
perform scalar, vector, vector matrix operations, LU factorization
BLAS
LAPACK
Solving systems of linear equations, matrix factorizations, linear least squares, eigenvalue problems, 
singular value decomposition
LAPACK
ScaLAPACK
implementation of lapack for parallel distributed architectures
ScaLAPACK

Compilers

Software

Webpage

 C, C++

gcc
C++ (intel)
C++ (Intel)
Fortran
Fortran
Java
Java
Julia
Julia
MATLAB
MATLAB
Perl
Perl
Php
PHP
Python
Python
R
R
Ruby
Ruby

Bioinformatics and Genomic Data Analysis

Software

Description

Webpage

BLAST

 Basic Local Alignment Search Tool used for comparing biological sequences  BLAST
Bioconductor
Bioconductor provides tools for the analysis and comprehension of
high-throughput genomic data.
Bioconductor
Bowtie
is an ultrafast, memory-efficient short read aligner. It aligns short DNA
sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour.
Bowtie
Bowtie2

is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters,
and particularly good at aligning to relatively long (e.g. mammalian) genomes.

Bowtie2
Tophat
is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to
mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
Tophat
DSSP
a database of secondary structure assignments for all protein entries in the Protein Data Bank
 DSSP
HMMER
Biosequence analysis using profile hidden Markov models
HMMR
HyPhy
Hypothesis testing using Phylogenies
HyPhy
MATLAB Bioinformatics
Toolbox
provides algorithms and apps for Next Generation Sequencing (NGS), microarray analysis,
mass spectrometry, and gene ontology
MATLAB Bioinformatics Toolbox
Trinity
assembles transcript sequences from Illumina RNA-Seq data. Trinity
TransDecoder
software that identifies candidate coding regions within transcript sequences
 TransDecoder
SAMtools
provide various utilities for manipulating alignments in the SAM format, including
sorting, merging, indexing and generating alignments in a per-position format.
SAMtools
VarScan
The advent of massively parallel sequencing technologies has fundamentally changed
the study of genetics.
VarScan
RSEM
RNA-Seq by Expectation-Maximization, software for estimating gene and isoform expression
levels from RNA-Seq data
 RSEM

Chemical Biology, Drug Design, and Molecular Modeling

Software

Description

Webpage

Autogrow

is an evolutionary algorithm that optimizes candidate ligands for predicted binding
affinity and other drug like properties.
 Autogrow
AutoDock
is a suite of automated docking tools. It is designed to predict how small molecules, such
as substrates or drug candidates, bind to a receptor of known 3D structure.
Autodock
CARMA3
Taxonomic classification of metagenomic shotgun sequences
 CARMA3
I-TASSER
is a hierarchical approach to protein structure and function prediction. I-TASSER
PyRx
is a Virtual Screening software for Computational Drug Discovery that can be used to
screen libraries of compounds against potential drug targets.
PyRx
Gromacs
is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian
equations of motion for systems with hundreds to millions of particles.
Gromacs
PyMOL
A molecular visualization system on an open source foundation PyMOL
MATLAB: SimBiology 
Toolbox
provides an app and programmatic tools to model, simulate, and analyze dynamic
systems, focusing on pharmacokinetic/pharmacodynamic (PK/PD) and systems biology applications.
MATLAB: SimBiology Toolbox
OpenFoam: Molecular dynamics solvers    

Quantum Physics

Software

Description

Webpage

VASP
is a computer program for atomic scale materials modelling, e.g. electronic structure
calculations and quantum-mechanical molecular dynamics, from first principles.
 VASP
QuantumWise
are used by over 300 leading companies, government labs and universities around
the world to enhance R&D capabilities in a wide range of application areas.
QuantumWise

Quantum Chemistry and molecular dynamics

Software

Description

Webpage

NWChem
aims to provide its users with computational chemistry tools that are scalable both in their ability 
to treat large scientific computational chemistry problems efficiently, and in their use of available
parallel computing resources from high-performance parallel supercomputers to conventional
workstation clusters.
NWChem
ORCA
is a modern electronic structure program package written by F. Neese, with contributions from 
many current and former coworkers and several collaborating groups. The binaries of ORCA
are available free of charge for academic users for a variety of platforms.
ORCA
Q-Chem
is a comprehensive ab initio quantum chemistry package for accurate predictions of molecular structures, 
reactivities, and vibrational, electronic and NMR spectra
Q-Chem

MPI/Parallel software

 

Software

Description

Webpage

openmpi
is an open sourceMessage Passing Interface implementation that is developed and 
maintained by a consortium of academic, research, and industry partners.
openmpi
mpich
is a high performance and widely portable  implementation of the Message Passing Interface (MPI) standard.
mpich
mpi4pyton
a message passing interface built for use with python
mpi4python
Parallel 
Computing
Toolbox
 lets you solve computationally and data-intensive problems using multicore processors, 
GPUs, and computer clusters.
Parallel Computing Toolbox

 

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