WWC snapshot of http://www.alw.nih.gov/WWW/applications.html taken on Sat Jun 10 17:45:12 1995

Application Suite

Image Processing
Analyze (version 7.0)
is an interactive 3-D image display and analysis package for medical images developed at the Mayo Clinic. Analyze permits detailed investigation and evaluation of 3-D and 4-D biomedical images from CT, MRI, PET and other sources. The software includes integrated complimentary tools for fully interactive display, manipulation and measurement of multi-dimensional image data. Analyze has an intuitive graphical user interface which is easy to use with an on-line manual to assist the user. The large number of Analyze users at NIH attests to its popularity and ease of use. There is also a electronic mailing list (analyze@mayo.edu) for analyze users to ask technical questions dealing with the use of analyze. Users can be placed on this list by sending e-mail and requesting to be added to the mailing list.

Analyze is site licensed to NIH. All users and machines which plan to run Analyze are required to register their user ID and machine hostID. To register either an ALW machine or user id, contact the UNIX hotline at 496-UNIX.
Availability: all ALW platforms locally
Command: analyze

AVS (version 5.01)
software was developed as a general purpose, easy to use image processing tool. AVS is a package of data visualization software tools that allows researchers to analyze and view their scientific data. AVS can be used for a wide variety of applications such as fluid dynamics, computer-aided engineering, molecular modeling, medical imaging and geophysics. An AVS user constructs a network of modules which controls the flow of module execution. Modules are combinations of the standard modules and user modules. Standard modules are those which come with AVS such as "field to mesh" which transforms a 2D scalar field to a surface in 3D space, or "generate axes" which generates 3D geometric axes. User modules are those developed by the user. A graphical interface allows connecting these modules in an intuitive fashion.
Availability: all ALW platforms locally
Command: avs

Khoros (version 1.0)
is an integrated software development environment for information processing and visualization. Khoros components include a visual programming language, code generators for extending the visual language and adding new application packages to the system, an interactive user interface editor, an interactive image display package, an extensive library of image processing, numerical analysis, signal processing routines, and 2D/3D plotting packages.
Availability: all ALW platforms locally in /usr/local/khoros
Command: All programs found in /usr/local/khoros/bin*

SAOimage (version 1.06)
is the Smithsonian Astrophysical Observatory image utility which is an interactive color or halftone image display program. Designed primarily for astronomical images, its tools can be applied to other images as well. It is a simple tool and not designed for heavy duty image processing and analysis but is adequate for simple manipulations and viewing.
Availability: Sun and SGI locally and remotely on all other ALW platforms
Command: soaimage

Mathematics
Mathematica (version 2.2)
is a general system and computer language intended for mathematical and other applications. It can be used as a numerical and symbolic calculator, a visualization system for functions and data, a high level programming language, and a modeling and data analysis environment. Its computational functions can be divided into three categories; numerical, symbolic and graphical, which it handles in a unified way.
More information is available on the Mathematica WWW home page.
Availability: all ALW platforms locally
Command: math

MLAB (12/12/94 release)
is a mathematical modeling system originally developed at DCRT for the DEC-10 system. It has facilities for curve fitting, differential equation solving, linear algebra, statistics, and 2D and 3D graphics.
Availability: all ALW platforms remotely
Command: mlab

MATLAB (version 4.2)
is an interactive program that can be used for general matrix mathematics as well as aid in the study of system theory, statistical analysis, spectral analysis, and signal analysis. MATLAB is able to perform operations with real or complex numbers and polynomial equations. MATLAB can also be used to graph x-y plots, bar graphs, histograms, polar coordinates and plots with semi-log scales or log10-log10 scales. In addition to these functions, this software can graph 3-D surface plots and create contour graphs. Included with MATLAB is the Signal Processing Toolbox which provides additional functions specialized to signal processing.
More information is available on the Matlab WWW home page.
Availability: all ALW platforms locally
Command: matlab

Macsyma (version 419)
automates symbolic mathematics combining symbolic and numerical analysis into an automated approach to mathematical modeling. Some of the areas Macsyma can be applied are algebra, calculus, symbolic approximation methods, numerical analysis and graphics.
Availability: Suns locally and all others remotely
Command: macsyma

Statistics
SAS (version 6.09)
is an integrated software system providing complete control over data access, management, analysis and presentation. SAS on ALW comes with INSIGHT, a module providing a highly integrated graphical user interface for data analysis. Other modules included in the ALW implementation of SAS are: CONNECT, STAT, IML, FSP and GRAPH.
Availability: Suns locally and all others remotely
Command: sas

S-Plus (version 3.2)
is a statistical package based on the AT&T New S Language with enhancements such as a mouse-driven X-window based graphics, on-line help, and extended statistical functions.
More information is available on the S-Plus WWW home page.
Availability: Suns locally and all others remotely
Command: splus

SPSS (version 4.0)
is a comprehensive, integrated system for statistical data analysis. The Advanced Statistics option is included which allows high level statistical operations such as discriminant analysis, nonlinear and logistic regression analysis, and multivariate analysis of variance. Another included option is Tables, which allows presenting data in presentation quality tables and can tabulate multiple variables at once providing flexibility for displaying totals, percentages, and other statistics.
Availability: All but SGIs remotely
Command: spss

Prophet (version 4.0)
is an integrated system for statistical data analysis. There are also sequence analysis and molecular modeling modules which are still under development and not available in this version. The statistical analysis works by entering data into a spreadsheet- like table from where statistical analysis takes place as well as graphs generated. On-line help makes using Prophet for statistical analysis easy to use. Its ease of use makes it preferable for simple data analysis.

XLispStat (version 2.1)
is a statistical programming environment built on the XLISP programming language developed by David Betz. It is an experimental system developed at the University of Minnesota's School of Statistics. It has not been as extensively tested as commercial programs such as S-Plus and SAS and should not be used for casual statistics. On-line documentation is available.
Availability: Suns locally.
Command: xlispstat

Molecular Modeling
Quanta (version 4.0)
is comprised of a variety of applications that construct, model, and analyze molecular structures. This comprehensive set of tools accommodates all classes of molecular and macromolecular systems, including the particular requirements of small organic structures, proteins and peptides, polymeric systems, and crystals. Quanta provides you with a choice of using one of its applications to construct the desired molecular structure, or working with an existing structure which was created by an application external to Quanta. Once a structure is displayed, you are provided with full control to study and refine the structure for modeling purposes. The modeled structure is further refined and analyzed based on energy calculations obtained through QUANTA's local or remote access to CHARMm. Quanta only runs on SGI workstations with a limited number of floating licenses available.
Online help is available for Quanta via the WWW (use a WWW client like mosaic).
Availability: SGIs locally
Command: quanta

Sequence Analysis
The BIMAS section of the Distributed Systems Branch supports sequence analysis software on ALW Sun workstations.
More information is availalbe on the BIMAS supported sequence analysis packages.
Availability: Suns locally.

Office Automation
Asterix (version 2.1)
is a collection of document creation applications that can be used for writing letters and reports, creating illustrations and technical drawings, and performing data analysis. Asterix integrates word processing with spreadsheet and graphic packages into a user friendly working environment.
Availability: all ALW platforms locally
Command: asterix

FrameMaker (version 4)
is a desktop publishing software package which integrates full-featured word processing, graphics, page layout, structured document building, tables and equations editing. All elements in the document, including illustrations, tables and equations, can be viewed while editing. FrameMaker is file compatible across many hardware platforms.
Availability: Suns & HPs locally and all others remotely
Command: maker

LaTeX
is a command interface for the TeX document processing language that hides some of the complexity of TeX and allows the user to concentrate on document layout.
Availability: Suns locally
Command: latex

Lotus 1-2-3 (version 1.2)
is the Unix workstation version of the popular PC speadsheet program.
Availability: Suns locally, SGIs remotely.
Command: 123

Microsoft Excel
is the Mac version of the speadsheet package running on a Unix workstation with the Mac emulator, Quorum Equal.
Availability: near future
Command: excel

Microsoft Word
is the Mac version of the word processing package running on a Unix workstation with the Mac emulator, Quorum Equal.
Availability: near future
Command: word

Pine (version 3.89)
is a mail user agent for non-AMDS [messages] delivered mail, designed primarily for novice users, though it's full-featured enough for processing large amounts of mail. Pine has its own tightly integrated pager for scrolling though incoming messages and its own editor (Pico) for composing messages
Availability: SGI
Command: pine or pico

SoftWindows (version 1.0)
emulates a high specification IBM PC/AT or compatible, and is supplied with Windows 3.1 already installed and ready for use. Unix directories can be accessable with alternate drive letters (e.g. H: is your UNIX home directory).
Availability: SGIs locally
Command: softwindows or win or dos

Synchronize (version 1.2)
is a multi-user time management database program which allows the user to keep an on-line calendar, make appointments, write notes to himself, and send messages to other users. When scheduling a meeting with a group of people, the user can see the intersection of their available time graphically displayed. Synchronize also allows the user to maintain a "to-do" list of things to be done on a particular day.
Availability: all ALW platforms locally
Command: synchronize

WordPerfect (version 5.1)
is the Unix workstation version of the popular PC/Macintosh word processing package.
Availability: Suns locally and all others remotely
Command: wp

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