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Comsol is specifically designed to easily couple transport phenomena, including computational fluid dynamics (CFD) as well as mass and energy transport to chemical-reaction kinetics and process-related modeling. Licensed Modules include: MultiPhysics, Chemical Engineering, Acoustics, Structural Mechanics, Script.
Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.
Cubit
CUBIT is a Geometry and Mesh Generation Toolkit
Desmond
Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems.
FFmpeg
FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video. It includes libavcodec - the leading audio/video codec library.
FE-Safe
The Abaqus add-on product FE-Safe is a highly effective tool for fatigue analysis of Finite Element models.
Gromacs
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.
It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
Platform Computing, Inc.'s LSF (Load Sharing Facility) software is a distributed load sharing and batch queuing suite of applications that can dispatch user requests to compute nodes in accordance with a Tufts-defined policy. It manages, monitors, and analyzes resources and load on the cluster. Platform LSF is layered in a way that allows it to sits on top of and extend the operating system services, speaking to the competing needs of resource management on the cluster. LSF commands must be used to submit batch jobs and assign interactive jobs to processors. bsub and lsrun are the usual command tools for this. It's important to note that cluster compute nodes are the only targets under LSF control. Jobs are not submitted to computers outside of the cluster. For more information about LSF command usage and job submission, you can read the man pages (example: type man lsrun at the cluster prompt). Most commands begin with the letter 'b' such as: bsub, bkill, lsrun, and bjobs.
MATLAB is a high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numerical computation. Using MATLAB, you can solve technical computing problems faster than with traditional programming languages, such as C, C++, and Fortran. Extensive documentation and tutorials are provided within Matlab. The following Matlab toolboxes are licensed, however for an up to date list, type ver within Matlab's command line:
MATLAB, Simulink,Control System,Curve Fitting,Distributed Computing,Financial,Fuzzy Logic,Image Processing,MATLAB Compiler,Neural Network,Optimization,Partial Differential Equation,Real-Time Workshop,Signal Processing,Simulink Control Design,Simulink 3D Animation,Spline,Statistics,Symbolic Math,System Identification,Virtual Reality,Wavelet Toolbox,Bioinformatics,Simbiology
The MATLAB Compiler Runtime (MCR) is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components without using MATLAB licensing. This is useful for running a large number of jobs that might exceed the license counts.
PetSc
PetSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for parallelism. Note, another useful link to visit. PetSc has a complex build environment that allows one to include various applications. We encourage interested users to build the suite of interest in their home directory. Installation instructions for a particular set of applications can be found here
RATS
RATS(Regression Analysis of Time Series) is a leading econometrics and time-series analysis software package.
R is a widely available object oriented statistical package. The current list of installed packages, to numerous to list, can be found in directory
/opt/shared/R/2.15.0-rhel6/lib64/R/library/.
This represents an augmented base installation suitable for most routine tasks, however not all available packages as found on the R web site are installed. If some other R package is needed, please make a software installation request as outlined above. However, for many people use of RStudio will allow for local installations in your home directory. Extensive user documentation and tutorials are available on the R web site. There are many texts as well, here is nice example
Note BioConductor and many genetics related R packages are installed as well.
RStudio
RStudio is a free and open source integrated development environment(IDE) for R.
Stata SE is an integrated statistical package for Windows, Macintosh, and Unix platforms. More than just a statistical package, Stata is also a full data-management system with complete statistical and graphical capabilities. It features both X-window and text user interfaces.
SAS
Sas is general purpose statistics package. Installed is the Education Analytical Suite of programs. These include:
• Base SAS
• SAS Bridge for ESRI
• SAS Enterprise Guide
• SAS Integration Technologies
• SAS/ACCESS
• SAS/AF
• SAS/ASSIST
• SAS/CONNECT
• SAS/EIS
• SAS/ETS
• SAS/FSP
• SAS/GRAPH
• SAS/IML
• SAS/INSIGHT
• SAS/LAB
• SAS/OR
• SAS/QC
• SAS/SECURE 168-bit
• SAS/SHARE
• SAS/STAT
SAS Enterprise Guide
SAS/Genetics
Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes.
Namd
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.
Maple is a well known environment for mathematical problem-solving, exploration, data visualization, and technical authoring. In may ways it is similar to Mathematica and Matlab.
MCCE (Multi-Conformation Continuum Electrostatics) is a biophysics simulation program combining continuum electrostatics and molecular mechanics.
WPP is a parallel computer program for simulating time-dependent elastic and viscoelastic wave propagation, with some provisions for acoustic wave propagation. WPP solves the governing equations in displacement formulation using a node-based finite difference approach on a Cartesian grid. WPP implements substantial capabilities for 3-D seismic modeling,
Mathematica, advertised as a one stop for technical work that integrates a numeric and symbolic computational engine, graphics system, programming language, documentation and advanced connectivity to other applications. Not only does this application have parallel functionality built into it from the ground up. The Wolfram Mathematica web site has extensive documentation, including numerous detailed tutorials.
ImageMagick® is a software suite to create, edit, and compose bitmap images. It can read, convert and write images in a variety of formats (over 100) including DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG, and TIFF. Use ImageMagick to translate, flip, mirror, rotate, scale, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves.
FFmpeg
FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video. It includes libavcodec - the leading audio/video codec library.
ParaView is a multi-platform visualization application designed to visualize large data sets.
gnuplot
Gnuplot supports many types of plots in either 2D and 3D. It can draw using lines, points, boxes, contours, vector fields, surfaces, and various associated text. It also supports various specialized plot types.gnuplot
Gnuplot supports many types of plots in either 2D and 3D. It can draw using lines, points, boxes, contours, vector fields, surfaces, and various associated text. It also supports various specialized plot types.
ggobi
GGobi is an open source visualization program for exploring high-dimensional data. It provides highly dynamic and interactive graphics such as tours, as well as familiar graphics such as the scatterplot, barchart and parallel coordinates plots. Plots are interactive and linked with brushing and identification.
Gromacs
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.
It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
GMT
GMT is an open source collection of ~60 tools for manipulating geographic and Cartesian data sets.
ImageMagick® is a software suite to create, edit, and compose bitmap images. It can read, convert and write images in a variety of formats (over 100) including DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG, and TIFF. Use ImageMagick to translate, flip, mirror, rotate, scale, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves.
Platform Computing, Inc.'s LSF (Load Sharing Facility) software is a distributed load sharing and batch queuing suite of applications that can dispatch user requests to compute nodes in accordance with a Tufts-defined policy. It manages, monitors, and analyzes resources and load on the cluster. Platform LSF is layered in a way that allows it to sits on top of and extend the operating system services, speaking to the competing needs of resource management on the cluster. LSF commands must be used to submit batch jobs and assign interactive jobs to processors. bsub and lsrun are the usual command tools for this. It's important to note that cluster compute nodes are the only targets under LSF control. Jobs are not submitted to computers outside of the cluster. For more information about LSF command usage and job submission, you can read the man pages (example: type man lsrun at the cluster prompt). Most commands begin with the letter 'b' such as: bsub, bkill, lsrun, and bjobs.
MATLAB is a high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numerical computation. Using MATLAB, you can solve technical computing problems faster than with traditional programming languages, such as C, C++, and Fortran. Extensive documentation and tutorials are provided within Matlab. The following Matlab toolboxes are licensed, however for an up to date list, type ver within Matlab's command line:
MATLAB, Simulink,Control System,Curve Fitting,Distributed Computing,Financial,Fuzzy Logic,Image Processing,MATLAB Compiler,Neural Network,Optimization,Partial Differential Equation,Real-Time Workshop,Signal Processing,Simulink Control Design,Simulink 3D Animation,Spline,Statistics,Symbolic Math,System Identification,Virtual Reality,Wavelet Toolbox,Bioinformatics,Simbiology
The MATLAB Compiler Runtime (MCR) is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components without using MATLAB licensing. This is useful for running a large number of jobs that might exceed the license counts.
Maple is a well known environment for mathematical problem-solving, exploration, data visualization, and technical authoring. In may ways it is similar to Mathematica and Matlab.
MCCE (Multi-Conformation Continuum Electrostatics) is a biophysics simulation program combining continuum electrostatics and molecular mechanics.
Mathematica, advertised as a one stop for technical work that integrates a numeric and symbolic computational engine, graphics system, programming language, documentation and advanced connectivity to other applications. Not only does this application have parallel functionality built into it from the ground up. The Wolfram Mathematica web site has extensive documentation, including numerous detailed tutorials.
NGSPICE
Spice is a general-purpose electric circuit simulation program for nonlinear dc, nonlinear transient and linear ac analysis.
NCAR
(The NCAR Command Language (NCL), a product of the Computational & Information Systems Laboratory at the National Center for Atmospheric Research (NCAR) and sponsored by the National Science Foundation, is a free interpreted language designed specifically for scientific data processing and visualization.
Namd
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
PetSc
PetSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for parallelism. Note, another useful link to visit. PetSc has a complex build environment that allows one to include various applications. We encourage interested users to build the suite of interest in their home directory. Installation instructions for a particular set of applications can be found here
ParaView is a multi-platform visualization application designed to visualize large data sets.
RATS
RATS(Regression Analysis of Time Series) is a leading econometrics and time-series analysis software package.
R is a widely available object oriented statistical package. The current list of installed packages, to numerous to list, can be found in directory
/opt/shared/R/2.15.0-rhel6/lib64/R/library/.
This represents an augmented base installation suitable for most routine tasks, however not all available packages as found on the R web site are installed. If some other R package is needed, please make a software installation request as outlined above. However, for many people use of RStudio will allow for local installations in your home directory. Extensive user documentation and tutorials are available on the R web site. There are many texts as well, here is nice example
Note BioConductor and many genetics related R packages are installed as well.
RStudio
RStudio is a free and open source integrated development environment(IDE) for R.
Stata SE is an integrated statistical package for Windows, Macintosh, and Unix platforms. More than just a statistical package, Stata is also a full data-management system with complete statistical and graphical capabilities. It features both X-window and text user interfaces.
SAS
Sas is general purpose statistics package. Installed is the Education Analytical Suite of programs. These include:
• Base SAS
• SAS Bridge for ESRI
• SAS Enterprise Guide
• SAS Integration Technologies
• SAS/ACCESS
• SAS/AF
• SAS/ASSIST
• SAS/CONNECT
• SAS/EIS
• SAS/ETS
• SAS/FSP
• SAS/GRAPH
• SAS/IML
• SAS/INSIGHT
• SAS/LAB
• SAS/OR
• SAS/QC
• SAS/SECURE 168-bit
• SAS/SHARE
• SAS/STAT
SAS Enterprise Guide
SAS/Genetics
TecPlot
Tecplot 360 is a numerical simulation and CFD visualization software that combines vital engineering plotting with advanced data visualization into one tool. It allows you to quickly plot and animate all your data exactly the way you want, as well as analyze complex data, arrange multiple layouts, and communicate your results with professional images and animations.ggobi
GGobi is an open source visualization program for exploring high-dimensional data. It provides highly dynamic and interactive graphics such as toursway you want, as well as familiar graphics such as the scatterplot, barchart and parallel coordinates plots. Plots are interactive and linked with brushing and identification.
NGSPICE
Spice is a general-purpose electric circuit simulation program for nonlinear dc, nonlinear transient and linear ac analysis.
GMT
GMT is an open source collection of ~60 tools for manipulating geographic and Cartesian data sets.
NCAR
(The NCAR Command Language (NCL), a product of the Computational & Information Systems Laboratory at the National Center for Atmospheric Research (NCAR) and sponsored by the National Science Foundation, is a free interpreted language designed specifically for scientific data processing and visualization.
Cubit
CUBIT is a Geometry and Mesh Generation Toolkitanalyze complex data, arrange multiple layouts, and communicate your results with professional images and animations.
Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes.
WPP is a parallel computer program for simulating time-dependent elastic and viscoelastic wave propagation, with some provisions for acoustic wave propagation. WPP solves the governing equations in displacement formulation using a node-based finite difference approach on a Cartesian grid. WPP implements substantial capabilities for 3-D seismic modeling,
Public domain Matlab Toolboxes
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