LS&A Contributed Software
The following list of software is available on the Flux cluster contributed by the College of Literature Science and the Arts. To access any of these packages, use the module load modulename command; for more information on the module command see our module documentation page.
Many of these packages have multiple versions, to see available versions, type module avail.
| Module Name | Versions | Description | Additional Information | ||
| GAMESS | 20120501 | The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. | Flux Documentation Vendor Website Manual |
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| ImageMagick | 6.7.2 6.8.4 |
ImageMagick is a software suite to create, edit, compose, or convert bitmap images. | Vendor Website |
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| Q-chem | 3.2 3.2p 4.0p Experimental |
Qchem is a quantem chemistry software package | Vendor Website |
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| armadillo | 2.4.6 3.2.4 |
ARMADILLO is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. The syntax is deliberately similar to Matlab. | Vendor Website |
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| astro-fits-cfitsio | 1.08 1.09 |
ASTRO-FITS-CFITSIO is a Perl interface to William Pence's CFITSIO subroutine library | Vendor Website |
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| atk | 2.4.0 | ATK is a handy library of accessability functions. | Vendor Website |
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| autodocksuite | 4.2 | designed to predict how small molecules bind to receptors | Vendor Website |
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| biogeme | 2.2 | ERROR:105: Unable to locate a modulefile for 'biogeme' | |||
| catdcd | 4.0 | CATDCD is a tool much like the UNIX 'cat' that concatenates DCD files into a single DCD file | Vendor Website |
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| cfitsio | 3.29 3.31 |
cfitsio is a set of libraries to manipulate FITS image files | Vendor Website |
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| cns | 1.3 | Crystallography & NMR System (CNS) is the result of an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Highlights include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data. | Vendor Website |
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| cyana | 2.1 | CYANA is a NMR Structure Calculator. Thread support is enabled. | Vendor Website |
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| dri2proto | 2.8 | DRI2PROTO - DRI2 Protocol Headers. | Vendor Website |
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| eclipse | 4.2 | ECLIPSE is a development environment for C/C++/Fortran. | Vendor Website |
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| epd | 7.3 | The Enthought Python Distribution provides scientists with a comprehensive set of tools to perform rigorous data analysis and visualization. Python, distinguished by its flexibility, coherence, and ease-of-use, is rapidly becoming the programming language of choice for researchers worldwide. EPD extends this capacity with a powerful collection of Python libraries to enable interactive technical computing and cross-platform rapid application development. This module also includes pymc. | Vendor Website |
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| feff | 9 | FEFF is an automated program for ab initio multiple scattering calculations of X-ray Absorption Fine Structure (XAFS), X-ray Absorption Near-Edge Structure (XANES) and various other spectra for clusters of atoms. The code yields scattering amplitudes and phases used in many modern XAFS analysis codes, as well as various other properties. | Vendor Website |
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| ffmpeg | 1.0 | FFMPEG is a complete, cross-platform solution to record, convert and stream audio and video. | Vendor Website |
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| fftw | 2.1.5 | FFTW is a C/Fortran subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions | Vendor Website Manual |
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| freesurfer | 5.1.0 | ERROR:102: Tcl command execution failed: setenv FSL_DIR $::env(FSLDIR) | |||
| fsl | 4.1.9 | FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. | Vendor Website |
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| ftgl | 2.1.3-rc5 | FTGL is a free cross-platform Open Source C++ library that uses Freetype2 to simplify rendering fonts in OpenGL applications. | Vendor Website |
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| garli | 1.0 2.0 |
GARLI, Genetic Algorithm for Rapid Phylogenetic Inference is a program for inferring phylogenetic trees. | Vendor Website |
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| gdk-pixbuf | 2.26.4 | GDK-PIXBUF is an image loading library used with GTK. | Vendor Website |
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| gerris | 120906 | GERRIS is a program for the solution of the partial differential equations describing fluid flow. | Vendor Website |
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| gfsview | 120706 | GFSVIEW is a tool written specifically to visualise Gerris simulation files. | Vendor Website |
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| glib | 2.32.4 | GLIB - GTK+ is built on top of GLib. GLib provides the fundamental algorithmic language constructs commonly duplicated in applications. | Vendor Website |
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| glproto | 1.4.16 | GLPROTO - X.org GLProto protocol headers. | Vendor Website |
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| gtk | 2.24.13 | GTK is a multi-platform toolkit for creating graphical user interfaces. | Vendor Website |
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| gtkglext | 1.2.0 | GTKGLEXT is an OpenGL extension to GTK+. | Vendor Website |
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| gts | 120706 | GTS is a library intended to provide a set of useful functions to deal with 3D surfaces meshed with interco nnected triangles | Vendor Website |
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| haddock | 2.1 | High Ambiguity Driven biomolecular DOCKing based on biochemical and/or biophysical information. | Vendor Website |
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| harminv | 1.3.1 1.3.1 1.3.1 |
Harminv is a program (and library) to solve the problem of harmonic inversion given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids. | Vendor Website |
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| icm | 3.7-2d | ICM-Pro is an application that studies molecular structure and function. | Flux Documentation Vendor Website Manual |
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| idl-astro-libs | 2010.02 | A collection of low-level astronomy routines for IDL | Vendor Website |
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| igraph | 0.5.5 | igraph is a free software package for creating and manipulating undirected and directed graphs. It includes implementations for classic graph theory problems like minimum spanning trees and network flow, and also implements algorithms for some recent network analysis methods, like community structure search. | Vendor Website |
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| jags | 2.2.0 3.2.0 |
JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation | Vendor Website |
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| java | 1.7.0 | Java is a general-purpose, concurrent, class-based, object-oriented language that is specifically designed to have as few implementation dependencies as possible. | Vendor Website |
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| knitro | 8.1.1-z | knitro is a program. | |||
| lapack | 3.4.1 3.4.1 |
LAPACK is written in Fortran 90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems | Vendor Website |
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| libctl | 3.2 3.2 3.2 |
LIBCTL is a free Guile-based library implementing flexible control files for scientific simulations. | Vendor Website |
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| libdrm | 2.4.39 | LIBDRM - Direct Rendering Manager libraries for Mesa. | Vendor Website |
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| libffi | 3.0.11 | LIBFFI - A Portable Foreign Function Interface Library. | Vendor Website |
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| libpciaccess | 0.13.1 | LIBPCIACCESS - Generic PCI access library. | Vendor Website |
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| libxcb | 1.9 | LIBXCB - Headers and libraries for XCB. | Vendor Website |
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| llvm | 3.0 | LLVM is a collection of modular and reusable compiler and toolchain technologies. | Vendor Website |
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| lumerical-FDTD_Solutions | 6.5.11 7.0.1 8.0.7 |
finite-difference time-domain (FDTD) solver for optical design problems | Vendor Website |
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| magma | 2.18-7 | Magma is a large, well-supported software package designed for computations in algebra, number theory, algebraic geometry and algebraic combinatorics. | Vendor Website |
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| mason | 16 | Mason is a simulation library for Java simulations. | Vendor Website |
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| meep | 1.2 1.2 |
A free finite-difference time-domain (FDTD) simulation software package to model electromagnetic systems | Vendor Website |
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| mesa | 9.0 | MESA is an open-source implementation of the OpenGL specification. | Vendor Website |
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| mlpack | 0.2 1.0.1 |
mlpack (Machine Learning PACK) is an open-source, intuitive, fast, and scalable C++ machine learning library, meant to be a machine learning analog to LAPACK. It aims to implement a wide array of machine learning methods and function as a "swiss army knife" for machine learning researchers. | Vendor Website |
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| mmtsb_toolset | 2012.04.13 | Multiscale Modeling Tools for Structural Biology | Vendor Website |
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| molpro | 2012.1 | molpro is a quantem chemistry software package | Vendor Website |
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| mrbayes | 3.1.2 3.1.2-no-readline |
MrBayes is a program for the Bayesian estimation of phylogeny | Vendor Website |
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| ncl | 2.1.15 | The Nexus Class Library (NCL) is a C++ library for interpreting data files created according to the NEXUS file format used in phylogenetic systematics and molecular evolution. | Vendor Website |
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| netlogo | 5.0.3 5.0.4 |
NetLogo is a programmable modeling environment for simulating natural and social phenomena. This installation of NetLogo includes the BehaviorSearch extension. | Vendor Website |
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| neuron | 7.3 | NEURON is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for conveniently building, managing, and using models in a way that is numerically sound and computationally efficient. It is particularly well-suited to problems that are closely linked to experimental data, especially those that involve cells with complex anatomical and biophysical properties. | Vendor Website |
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| openbugs | 3.2.2 | OPENBUGS is a software package for performing Bayesian inference Using Gibbs Sampling | Vendor Website |
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| optpp | 2.4 | OPT++ is a library of nonlinear optimization algorithms written in C++. | Vendor Website |
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| phenix | 1.7.3 1.8 |
//www.phenix-online.org/download/ | |||
| raxml | 7.0.4 7.2.8a |
RAXML (Randomized Axelerated Maximum Likelihood) is a program for sequential and para llel Maximum Likelihood based inference of large phylogenetic trees. | Vendor Website |
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| rdock | 2006.2 | rDock is a suite of tools developed and tested over a number of years initially at RiboTargets, then Vernalis, before moving more recently to the York Structural Biology Laboratory (YSBL) at the University of York. rDock is a program for docking small molecules to protein and RNA targets. It can be used for molecular docking | Vendor Website |
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| root | 5.34.01 | ROOT provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. | Vendor Website |
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| siesta | 3.1 | //www.icmab.es/siesta-joomla/Create-an-account | |||
| stata | 12 | Stata is a complete, integrated statistical package that provides everything you need for data analysis, data management, and graphics. | Flux Documentation Vendor Website Manual |
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| vina | 1.1.2 | AUTODOCK VINA is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use. | Vendor Website |
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| xcbproto | 1.8 | XCBPROTO - is part of the X protocol C-language Binding (XCB) library. | Vendor Website |
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| xmgrace | 5.1.22 | XMGRACE is a WYSIWYG 2D plotting tool for the X Window System and M*tif | Vendor Website |
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| xspec | 12 | An X-Ray Spectral Fitting package for reducing XRay data from a variety of different orbital instrumentation | Vendor Website |
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| yasm | 1.2.0 | YASM is a complete rewrite of the NASM assembler. | Vendor Website |
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