Research Software

ABINIT

www.abinit.org
ABINIT is a software package that allows you to find the total energy, charge density, and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a plane wave basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors. Excited states can be computed within the Time-Dependent Density Functional Theory (for molecules), or within Many-Body Perturbation Theory (the GW approximation). In addition to the main ABINIT code, different utility programs are provided. Abinit is distributed under the GNU General Public License.

Accessing ABINIT

To request access to ABINIT, send email to hpc@nyu.edu.

To start ABINIT, type the following on the command line: module load abinit
To execute serial ABINIT, type: abinit
To execute parallel ABINIT under MPT on the ALTIX operating system, type: mpirun -np <number of CPU> 'which ainip'

ADF

http://www.scm.com/
ADF software is used for first-principles electronic structure calculations. It is widely used in the research areas of homogeneous and heterogeneous catalysis, inorganic chemistry, heavy element chemistry, various types of spectroscopy, and biochemistry.

Accessing ADF

To request access to ADF, send email to hpc@nyu.edu.

Amber 9

http://amber.scripps.edu/
Amber is a set of mechanical force fields for the simulation of biomolecules and also a package of molecular simulation programs. The force fields are in the public domain and can be used with molecular simulation codes other than the Amber codes. The Amber codes are licensed and distributed by the University of California, San Francisco, and use the Amber force fields as well as other force fields.

A user's manual for Amber 9 containing tutorials is available on the Amber website.

Sander is the Amber module that carries out energy minimumization, molecular dynamics, and NMR refinements. Only Sander-based executables are parallelized.

Accessing Amber

To request access to Amber, send email to hpc@nyu.edu.

To start Amber, type the following on the command line: module load amber
To execute serial Sander, type: sander
To execute parallel Sander, type: sander.MPI
(Note: One of the above can be added to the shell script.)

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Amos

www.spss.com/amos/
Amos is a powerful, easy-to-use structural equation modeling (SEM) software program that enables you to create more realistic models than if you used standard multivariate statistics or multiple regression models alone. You can easily incorporate Amos into your SPSS workflow.

Accessing Amos

NYU-licensed copies of Amos software are available for purchase by NYU faculty, administrators, staff, and matriculated graduate students. See the Research Software Licenses page for more information. Amos is also available for use on several ITS-owned computers; send email to data.service@nyu.edu to request access.

ArcGIS, ArcIMS & ArcPad

www.esri.com/products.html
ArcGIS
ArcGIS and other ESRI products are the premier suite of Geographical Information System (GIS) tools used at NYU. Free ArcGIS licenses are now available for distribution at NYU. ArcView, the most popular desktop mapping product will still be available at every ITS student computer lab and classroom, but in addition, NYU faculty and researchers may now obtain a free license for ArcGIS. Many other ESRI tools such as Spatial Analyst and 3D Analyst are also included in the DVD. In addition, ITS' new license allows faculty to obtain a one-year timed version to be distributed free to their entire class. This will allow students full functionality of ArcGIS and to take ESRI Virtual Campus classes at home. Faculty may request that an entire class be enrolled in a monitored web introduction to ArcView mapmaking or in many other self-paced courses.

For more information and to obtain the software from ITS, please attend one of our GIS Clinics or send email to data.service@nyu.edu. Additional information about ArcGIS is available on the ArcGIS website.

ArcIMS
ArcIMS, ESRI's Internet Map Server, is used to create and manage server-based GIS applications that share GIS functionality and data on the Internet (see Connect Magazine for a case study). ArcIMS was used at NYU for the Aphrodisias archeological dig in Turkey during the summer of 2006. Click here to visit the test website.

ArcPad
ArcPad is an ESRI package designed for field tasks that uses Global Positioning signals to allow data collection to create maps. It runs on hand-held and portable computers such as Pocket PCs, laptops, and tablet PCs.

Accessing ESRI Software

Copies of the ESRI software packages described above are available at no cost to NYU faculty and their students, and are installed on ITS systems. To obtain copies, attend a GIS Clinic, send email to data.service@nyu.edu or call 212-998-3398.

ATLAS.ti

www.atlasti.com/
ATLAS.ti is a powerful workbench for the qualitative analysis of large bodies of textual, graphical, audio and video data. It offers a variety of tools for accomplishing the tasks associated with any systematic approach to "soft" data—i.e., material which cannot be sufficiently analyzed using formalized, statistical approaches. (Source)

Accessing ATLAS.ti

ATLAS.ti is available for use on ITS systems; to request access, send email to data.service@nyu.eduor call 212-998-3398.

Freeware

ITS provides and/or supports the following freeware packages. Contact hpc@nyu.edu for more information.

For Text Writing & Editing

• emacs
• xemacs

For Compiling Code

• g++
• GCC
• GSL

Graphics Packages

• xmgrace
• Xephem
• Kpl
• Blender
• xsane

Image Viewers (for Molecular Modeling):

• Cactus
• Chime
• ICM
• Jmol
• Picasa
• rasmol
• Swiss PDB viewer
• Tinker
• Vmd
• Yasara

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CPMD

www.cpmd.org/cpmd_download.html
CPMD code is a parallelized plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.

Accessing CPMD

To request access to CPMD, send email to hpc@nyu.edu.

GAMESS -UK

www.cfs.dl.ac.uk
GAMESS -UK is a general purpose ab initio molecular electronic structure program. It can compute wavefunctions including RHF, ROHF, UHF, GVB, and MCSCF (with CI and MP2 energy corrections available for some).

Accessing GAMESS -UK

To request access to GAMESS -UK, send email to hpc@nyu.edu.

To start GAMESS -UK, type the following on the command line:
module load gamess
<submission script> [options] input_file

Gaussian 03

www.gaussian.com
Gaussian uses basic quantum mechanic electronic structure programs. This software is capable of handling proteins and large molecules using semi-empirical, ab initio molecular orbital (MO), density functional, and molecular mechanics calculations.

Accessing Gaussian 03

To request access to Gaussian 03, send email to hpc@nyu.edu.

To start Gaussian 03, type the following on the command line:
module load g03
<submission script> [options] input file

GaussView

www.gaussian.com/gv_plat.htm
GaussView is a graphical user interface for Gaussian 03 (see above).

Accessing GaussView

To request access to GaussView, send email to hpc@nyu.edu.

To start GaussView, type the following on the command line:
module load GaussView
xgv

GeoLytics

www.geolytics.com/
GeoLytics provides demographic data, census demographics, market research data, and geocoding for social researchers. It offers built-in mapping capabilities for spatial display of demographic information such as population estimates, population projections, and GIS data.

Accessing GeoLytics

GeoLytics is available for use on ITS systems; to request access, send email to data.service@nyu.eduor call 212-998-3398.

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GRASS

GROMACS

www.gromacs.org
GROMACS is a classical molecular dynamics package. It simulates the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since it is extremely fast at calculating nonbonded interactions (which usually dominate simulations), it is also used for research on non-biological systems such as polymers.

Accessing GROMACS

To request access to GROMACS, send email to hpc@nyu.edu.

To start GROMACS, type the following on the command line:
module load gromacs
gromacs

Hierarchical Linear and Nonlinear Modeling (HLM)

www.ssicentral.com/hlm/
For use with hierarchical data, the HLM program can fit models to outcome variables that generate a linear model with explanatory variables that account for variations at each level, utilizing variables specified at each level.

Accessing HLM

HLM is available for use on ITS systems; to request access, send email to data.service@nyu.eduor call 212-998-3398.

Insight II

www.accelrys.com/products/insight/
Insight II is a molecular modeling environment that provides a graphical interface for algorithms for molecular dynamics, homology modeling, de novo design and electronics. The package includes Biopolymer, Discover, CHARMm, and Delphi. Each of these modules can be accessed from the graphical interface or run independently.

Accessing Insight II

To request access to Insight II, send email to hpc@nyu.edu.

To initialize Insight II, type the following on the command line: source /local/msi/cshrc
To start Insight II, type:
insightII

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JChem

www.chemaxon.com/jchem/intro/
JChem is a tool for the development of applications that allow for the search of mixed structural and non-structural data. JChem works with variety of database systems (Oracle, MS SQL Server, DB2, Access, etc) with web interfaces and offers fast substructure, similarity, exact, and superstructure search engine using 2D hashed fingerprints. The system includes Marvin, a Java-based chemical editor and viewer.

Accessing JChem

To request access to JChem, send email to hpc@nyu.edu.

LISREL

www.ssicentral.com/lisrel/
The LISREL software package is often used by researchers in the social sciences, management sciences, behavioral sciences, biological sciences, educational sciences and other fields to empirically assess theories using structural equation modeling (SEM). The package also offers a number of statistical capabilities, including data manipulations and basic statistical analyses, hierarchical linear and non-linear modeling, generalized linear modeling, formative inference-based recursive modeling for categorical response variables, and formative inference-based recursive modeling for continuous response variables.

Accessing LISREL

LISREL is available for use on ITS systems; to request access, send email to data.service@nyu.eduor call 212-998-3398.

MapInfo

www.mapinfo.com/
MapInfo Professional is an easy-to-use GIS package. See the MapInfo website for more information about this package.

Accessing MapInfo

MapInfo is available for use on ITS systems; to request access, send email to data.service@nyu.eduor call 212-998-3398. NYU also has a very liberal MapInfo license which allows for temporary installation on student laptop computers and for deployment on an instructor's single computer for the purposes of development of their curriculum.

Maple

www.maplesoft.com
Maple is a software tool that offers high performance mathematics capabilities with integrated numerics and symbolics. The most recent update is Maple11, which can be used from the command line or with a graphical interface. Helpful documentation to assist with the use of Maple is available upon request to hpc@nyu.edu.

Accessing Maple

A permanent license for Maple is shared by ITS and the Courant Institute of Mathematical Sciences, and is available from accounts on NYU CIMS Computers and CDs are available for all platforms by request: hpc@nyu.edu.

To initialize Maple11 (for both the command line and the graphics interface), type:
Cd /local/maple11/bin
For command line operation of Maple, type: ./maple
For the Maple graphical interface, type: ./xmaple

Marvin

www.chemaxon.com/product/marvin_land.html

Marvin software is free for academic use and combines three packages:

• MarvinSketch: Structure, query and reaction editor
• MarvinView: Structure, query and reaction viewer
• MarvinSpace: 3D structure viewer

There are 28 plugins for the above packages developed in seven functional areas: calculations in protonation, electrostatics, molecular dynamics, isomers, conformation, Huckel anlysis, geometry and topology. For a full list of plugins and instructions, send email to hpc@nyu.edu

Accessing Marvin

To request access to Marvin, send email to hpc@nyu.edu.

Mathematica

www.wolfram.com
Mathematica is a general computing environment with organizing algorithmic, visualization, and user interface capabilities. The many mathematical algorithms included in Mathematica make computation easy and fast.

Accessing Mathematica

NYU has a campus-wide site license for Mathematica 6 which permits qualified faculty, staff and post doctoral students to purchase discounted annual licenses to use the software on University-owned computers. Network and single user licenses are available for all platforms. The Physics Department, Courant Institute, Center for Neural Sciences, Politics, ITS, and the ITS Multimedia Center have network licenses. Single user licenses can be purchased from ITS. A home-use license is provided free of charge to purchasers of single licenses. Network managers can obtain home-use licenses for some network users. See the Research Software Licenses page for more information.

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Matlab

www.mathworks.com
Matlab is a technical computing environment for high performance numeric computation and visualization. Matlab integrates numerical analysis, matrix computation, signal processing, and graphics in an easy to use environment without using traditional programming. Typical uses include general purpose numeric computation, algorithm prototyping, and special purpose problem solving with matrix formulations that arise in disciplines such as control theory, statistics, and digital signal processing.

Matlab features a family of application specific solutions called Toolboxes. The Toolboxes available, and the number of each are: Bioinformatics (26), Compiler (25), Control Toolbox (6), Data Acquisition (5), Database (2), Financial (3), GADS (2), Image Acquisition (6), Instrument Control (6), Identification (25), Image (20), Mapping (6), Builder for Java (1), Neural Network (1), Optimization (25), PDE (2), Robust Toolbox (2), Simulink Control Design (2), Signal (25), Symbolic (25), Statistics (37), and Wavelet (1).

Accessing Matlab

NYU has a permanent network license for Matlab which is shared by CIMS and ITS. The latest version installed is 19. The software is available on computers at CIMS, Physics, Politics, Economics, and the ITS Multimedia Center. Single User CDs are available by request to hpc@nyu.edu, or the software can be downloaded from the Matlab website: www.mathworks.com. Send email to hpc@nyu.edu to request an installation key for single user usage. NYU's license allows up to 145 simultaneous Matlab sessions; since NYU has a network license, all users must check out a license from the license server (hilbert.acs.its.nyu.edu). For assistance with using an ITS/CIMS license, send email to hpc@nyu.edu.

National Algorithms Group (NAG)

www.nag.co.uk
The National Algorithms Group (NAG) is the largest collection of algorithms for mathematical, statistical, and data mining problems. The subroutines can be incorporated into code in all languages and used on all platforms. Compilers for Fortran and C are available.

A Fortran Library of routines is available for the following (and others):

• Complex Arithmetic
• Optimization
• Solution of Ordinary and Partial Differential Equations
• Roots of Nonlinear Equations
• Solution of Linear and Nonlinear Least Squares Problems
• Special Functions
• Eigenvvalue and Eigenvector Problems
• Sparse Linear Algebra
• Simple Calculations and Statistical Data
• Correlation and Regression Analysis
• Random Number Generators
• Operations Research
• Sorting

The IRIS Explorer Package has subroutines for visualization.

Accessing NAG

A license for NAG software is shared by ITS and the Courant Institute of Mathematical Sciences; it includes the Parallel Library and all the Fortran and C Libraries. The software is installed on the CIMS computers; to request access, send an email request to hpc@nyu.edu.

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National Center for Atmospheric Research (NCAR)

www.ncar.ucar.edu
NCAR Graphics is a Fortran- and C-based software package for scientific visualization. The plot package is incorporated during code compilation, and plot instructions are included in the code and in a manual available upon request. The ncargf77 and ncargf90 utilities can be used for codes written in Fortran. The ncargcc utility is used for C codes.

Accessing NCAR

NCAR software is available on CIMS computers and on some of ITS' computers. For information on how to access NCAR, send an email request to hpc@nyu.edu.

nQuery Advisor

www.statsol.ie/html/nquery/nquery_home.html
The nQuery Advisor software package helps you find the most efficient sample size to use in your research studies. It can also help you to specify the standard deviation and effect sizes for sample size and power computations, and to produce protocol-ready sample size statements in accordance with FDA/ICH guidelines.

Accessing nQuery Advisor

nQuery Advisor is available for use on ITS systems; to request access, send email to data.service@nyu.eduor call 212-998-3398.

Numerical Recipes

Numerical Recipes: The Art of Scientific Computing is a book published by the Cambridge University Press that includes about 200 mathematical subroutines. For each subroutine, the code (in Fortran or C) and a discussion is included. The code (available electronically) can be incorporated in a user's program as a subroutine.

Typical topics are: Solutions of linear algebraic equations, interpolation and extrapolation, special functions, random numbers, root finding, eigenvalues, Fourier transforms, statistical descriptions of data, integration of Ordinary Differential Equations (ODE), 2-point boundary value problems, and Partial Differential Equations (PDE).

Accessing Numerical Recipes

A copy of this book is available through ITS. Send an email request to hpc@nyu.edu for more information.

NWChem

www.emsl.pnl.gov/docs/nwchem/nwchem.html
NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as on conventional workstations and clusters. NWChem provides many methods to compute the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction and/or density to perform classical molecular dynamics and free energy simulations. These approaches may be combined to perform mixed quantum-mechanics and molecular-mechanics simulations.

Accessing NWChem

To request access to NWChem, send email to hpc@nyu.edu.

R

www.r-project.org/
R is a highly extensible language and environment that provides a wide variety of statistical (linear and nonlinear modeling, classical statistical tests, time-series analysis, classification, clustering) and graphical techniques. It is a GNU project which is similar to the S language and environment.

Accessing R

R is available for use on ITS systems; to request access, send email to data.service@nyu.eduor call 212-998-3398.

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Remark Office OMR

www.gravic.com/remark/officeomr/
Remark Office OMR is a popular Windows-based forms-processing software package for surveys and tests. The software recognizes optical marks (bubbles and checkboxes) and barcodes. It allows you to design your own forms using any word processor, print them out, scan and recognize data with your image scanner, and then analyze the data or export it to the application of your choice!

Accessing Remark Office OMR

Remark Office OMR is available for use on ITS systems; to request access, send email to data.service@nyu.eduor call 212-998-3398.

SAS

www.sas.com
SAS is a predictive analytics software package. Along with SPSS, it is the most popular statistical software package at NYU. For additional information about using SAS, see the Statistics Publications page of this website, or attend a free ITS workshop.

Accessing SAS

NYU-licensed copies of SAS software are available for purchase by NYU faculty, administrators, staff, and matriculated graduate students. See the Research Software Licenses page for more information. SAS is also available for use on several ITS-owned computers; send email to data.service@nyu.eduto request access.

Schrodinger

www.schrodinger.com
Schrodinger enables the solving of problems in Pharmacology, Biotechnology, and Material Science.

The Molecular Modeling modules included in the Schrodinger package and available within Maestro are listed below. Any of these modules can be started within Schrodinger's GUI.

• Prime - Accurate protein structure prediction
• Glide - Accurate, rapid ligand-receptor docking
• Liason - Predicts binding affinity
• Qsite - Reaction Mechanisms within a protein active site (QM/MM)
• Phase - Ligand based pharmacophore modeling
• QikProp - ADME properties prediction of drug candidates
• LigPrep - Rapid 2D to 3D conversion program
• Jaguar - High-performance ab initio quantum mechanics application

  This software is useful for studying large molecular systems. Jaguar now uses Maestro as a common graphical user interface.

  To start Jaguar's GUI, type:
  module load schrodinger
  maestro

  To run Jaguar from the command line, type:
  Jaguar run <filename>.in
  (Note: The suffix .in must be added to the end of the input filename, e.g., mysystem.in)

• Macromodel - Molecular Modeling
• Strike - Chemically aware statistical package

Accessing Schrodinger

To request access to Schrodinger, send email to hpc@nyu.edu.

To start Schrodinger, type the following on the command line: module load schrodinger
To start Schrodinger's GUI, type: maestro

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Scientific Word

www.mackichan.com/
Scientific Word can be used to compose mathematical, scientific, and technical documents using natural mathematical notation; the documents can then be published on the Web using HTML or PDF or in print, with or without LaTeX (the industry standard for mathematics typesetting).

Accessing Scientific Word

Scientific Word is available for use on ITS systems; to request access, send email to data.service@nyu.eduor call 212-998-3398.

Sequin

www.ncbi.nlm.nih.gov/Sequin/
Sequin is a program developed by Professor Nadrian C. Seeman of the NYU Department of Chemistry. It is an interactive procedure which assigns sequences for the design of nucleic acid secondary structures. The primary goal is to facilitate macromolecular architecture studies through the design of branched nucleic mono- and ologo-junction constructs in a convenient fashion. See the following paper for a full description of the method: "De Novo Design of Sequences for Nucleic Acid Structural Engineering," Journal of Biomolecular Structure and Dynamics, ISSN 0739-1102, Volume 8, Number 3 (1990), Adenine Press (1990).

Accessing Sequin

To request access to Sequin, send email to hpc@nyu.edu.

The code sequin.f is written in Fortran and can be compiled to obtain the executable file. A Macintosh version is also available. The code is interactive and has a HELP command which lists all the available commands. A description of the instructions appears in the file sequin.book. Two files, MOLDES.DAT and RSITES.DAT are required to run the program.

SPSS

www.spss.com
SPSS is a predictive analytics software package. Along with SAS, it is the most popular statistical software package at NYU. For additional information about using SPSS, see the Statistics Publications page of this website, or attend a free ITS workshop.

Accessing SPSS

NYU-licensed copies of SPSS software are available for purchase by NYU faculty, administrators, staff, and matriculated graduate students. See the Research Software Licenses page for more information. SPSS is also available for use on several ITS-owned computers; send email to data.service@nyu.eduto request access.

SPSS Text Analysis

www.spss.com/textanalysis_surveys/
SPSS Text Analysis is natural language processing software that facilitates categorization and import of text responses to open-ended survey questions. The software offers both automated and manual techniques, and allows you to import data from SPSS for Windows, Microsoft¨ Excel, ODBC-compliant databases and SPSS' Dimensions survey research products. Results can be exported as categories or dichotomies for further analysis in SPSS, mrTables, or Excel.

Accessing SPSS Text Analysis

SPSS Text Analysis is available for use on ITS systems; to request access, send email to data.service@nyu.eduor call 212-998-3398.

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Stata

www.stata.com
Stata is a statistical package used for data analysis, data management, and graphics.

Accessing Stata

Stata is available for use on ITS systems; to request access, send email to data.service@nyu.eduor call 212-998-3398.

SUDAAN

www.rti.org/sudaan/
The SUDAAN software package offers nine analytic procedures for analyzing complex data sets, and is often used in conjunction with SAS and SPSS.

Accessing SUDAAN

SUDAAN is available for use on ITS systems; to request access, send email to data.service@nyu.eduor call 212-998-3398.

Tecplot 360

www.tecplot.com/products/360/360_main.htm
Tecplot 360 is a software package that combines advanced plotting and data visualization. It enables you to analyze and explore complex datasets, arrange multiple XY, 2- and 3-D plots, and create high-quality animations.

Accessing Tecplot 360

A license for Tecplot 360 is shared by ITS and CIMS, and is available for download from the hilbert.acs.its.nyu.edu license server. This license allows up to five Tecplot 360 sessions to be used simultaneously. For assistance with using an ITS/CIMS license, send an email request to hpc@nyu.edu. Tecplot 360 is also available on the Chemistry machine: tosca.chem.nyu.edu. This license allows up to five simultaneous Tecplot 360 sessions .

To start Tecplot 360, type the following on the command line:
source /local/tec360/cshrc
tecplot

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