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Last checked or modified: Oct. 17, 1997

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Snapix

A set of tools designed for the creation of interactive applications under Unix, X and Motif. It consists of an editor, an interpreter/compiler, a driver and an object oriented language. The editor makes it easy to define the visual appearance of an application, with all the tasks associated with specifying an interface (e.g. designing input forms and dialog boxes, selecting fonts, etc.) quick and simple. The driver is supplied with over 20 pre-defined classes including some high-level classes like menus, and it can also handle user-defined classes. The language is complete, typed, structured, event driven and object oriented. Additional features include the possibility of modular application design, manual code generation with a standard editor or automatic code generation using an interactive editor, version management under SCCS, code maintainability and rapid modification, pre-compilation for fast run times and source protection, use of C-like syntax, and integration of user defined C functions using standard calls. A Linux version is freely available and comes with 110+ page manual in PostScript format. [http://sunsite.unc.edu/pub/Linux/X11/devel/builders/]

 

snd

A sound editor based loosely on Emacs and a PDP-10 sound editor named Dpysnd which is currently an X/Motif application. It can accomodate any number of sounds at once, each with any number of channels. Each channel of each sound is displayed in its own window with its own cursor, edit history, and marks. Each sound as a control panel to try out various changes quickly, and an expression parser usedly mainly during searches. There is an overall stack of regions which can be browsed and edited, and channels and sounds can be grouped together during editing. Edits can be undone and redone without limit and snd can be customized using an Elisp-like syntax. It can also be extended with user-supplied editing or display functions loaded at run time. Snd is available as source code or as a binary for SGI and Linux Intel platforms. It is written in ANSI C and requires the Motif widget set for compilation. It is documented in a user's manual in HTML format which is included in the distribution. This is useful by itself but can also be used with the CLM package.

[http://www-ccrma.stanford.edu/CCRMA/Software/snd/snd.html]

 

SNDAN

A package of signal analysis, graphics, modification, and synthesis routines for UNIX systems. One group of programs performs analysis and converts sound files into analysis files which contain data for the amplitudes and frequences of components within the file. Another group contains programs for viewing the data in either signal or analysis format. Another group contains programs to modify the analysis data, and the final group programs to synthesize signal files from the analysis data. The programs assume that sound files are in monaural NeXT sound file format, although the SoX package can be used to convert other formats to this. Graphics files are output in EPS format. The programs available in SNDAN include: sp, which graphs sound files; sextract, which extracts individual sounds from a sound file containing a sequence of sounds and puts them in separate files; pvan, which performs phase vocoder analysis; mqan, which performs spectral tracking analysis; monan, which combines the activities of parameter viewing, modification, and additive synthesis.

A source code distribution of SNDAN is available. It is written in C and has been compiled successfully on several systems including Linux Intel.

[http://cmp-rs.music.uiuc.edu/cmp/software/sndan.html]

 

SNePS

The Semantic Network Processing System is a system for building, using, and retrieving from propositional semantic networks. A semantic network can be thought of as a labeled directed graph in which nodes represent entites, arc labels represent binary relations, and an arc labeled R going from node n to node m means that n bears the relation R to m. SNePS is a propositional semantic network because every proposition represented in the network is represented by a node and not by an arc. The core of SNePS is a system for building nodes in the network, retrieving nodes that have a certain pattern of connectivity to other nodes, and performing housekeeping tasks like dumping a network to a file or loading a network from a file. The major components which comprise SNePS are:

• SNIP (SNePS Inference Package), which interprets certain nodes as representing reasoning rules called deduction rules and supports a variety of specially designed propositional connectives and quantifiers and performs a kind of combined forward/backward inference called bi-directional inference;
• SNeBR (SNePS Belief Revision System), which recognizes when a contradiction exists in the network and interacts with the user when it detects the user operating in a contradictory belief space;
• SNaLPS (SNePS Natural Language Processing System), which consists of a morphological analyzer, a morphological synthesizer, and a Generalized Augmented Transition Network (GATN) Grammar interpreter and compiler, all of which allow natural language interfaces for SNePS to be built;
• SNePSUL, (SNePS User Language), the standard command language for SNePS which resembles Lisp;
• XGinseng, an X Window-based graphical editing and display environment for SNePS networks which can be used to build and edit networks; and
• SNePSLOG, a logic programming interface to SNePS which provides direct access in a predicate logic notation to almost all of the facilities provided by SNePSUL.

A source code distribution of SNePS is available. It is written entirely in Common Lisp and has been used successfully with both CLISP and CMUCL. It may also work with AKCL and Allegro CL. The program and its use are documented in a 94 page user's manual available in PostScript format.

[http://www.cs.buffalo.edu/pub/sneps/WWW/]

 

snes

An emulator for the Super Nintendo Entertainment System (SNES) for Linux SVGA and X. It is currently (5/98) under development but plans on including features such as SuperFX support, sound digital FIR filter and echo, sound pitch modulation, mouse and multi-tap support, 8- and 16-bit color screen modes, transparency, hi-res and interlaced screen modes, improved ROM detection routines, and more. An older version is available at the second URL. [http://www.euronet.nl/users/jkoot/snes9x/]
[http://sunsite.unc.edu/pub/Linux/system/emulators/ ]

 

Sniffit

A packet sniffer which supports both Ethernet and PPP. See the related TOD. [http://reptile.rug.ac.be/~coder/sniffit/sniffit.html]

 

SNLS1E

A Fortran 77 subroutine package which solves nonlinear least squares problems, i.e. it minimizes a sum of squares of M nonlinear functions of N variables. It also contains programs for solving systems of nonlinear equations which can be used separately. The package consists of:

• SNLS1, which minimizes the sum of the squares of M functions in N variables using a modification of the Levenberg-Marquardt algorithm with the user providing a subroutine to calculate the functions (and optionally the full Jacobian);
• SNLS1E, an easy-to-use version of SNLS1;
• SNSQ, which finds a zero of a system of N nonlinear equations in N variables using a modification of the Powell hybrid method with the user supplying a subroutine to calculate the functions (and optionally to calculate the full Jacobian);
• SNSQE, an easy-to-use version of SNSQ; and
• SOS, which solves a system of N simultaneous nonlinear equations in N unknowns based on an iterative method which is a variation of Newton's method using Gaussian elimination in a manner similar to the Gauss-Seidel process.

A source code distribution of SNLS1E is available. All of the routines are written in Fortran 77 and are documented via comment statements contained within each source code file. This is part of CMLIB.

[http://sunsite.doc.ic.ac.uk/public/computing/general/statlib/cmlib/]

 

SNMP

The Simple Network Management Protocol is a protocol for Internet network management services. It facilitates communication between a managed device, i.e. a device with an SNMP agent, e.g. a router, and an SNMP manager or management application. Communication is via SNMP protocol data units (PDUs) typically encapsulated in UDP packets, with various operations permitted between managers and agents to either handle objects on the managed device or notify the manager about events occurring on the device. An SNMP manager obtains information about the available objects on a managed device via Management Information Base (MIB) modules. An MIB file contains a description of the object hierarchy on the managed device as well as the name, syntax, and access priveleges for each variable in the MIB, i.e. only the types of objects are specified and not the specific objects. It is basically an enormous tree which provides a map for locating information. There is only one official SNMP MIB, although other kinds of MIBs exist which are extensions to the official SNMP MIB.

The standard implementation of SNMP for Linux platforms is CMU SNMP, much more about which can be found in the User's Guide to SNMP for Linux . Programs for SNMP administration include btng, OSIMIS, Scion, Scotty, SNMX, and WILMA. The available literature on SNMP is vast, e.g. see Black (1995), Comer (1991), Comer and Stevens (1991), Comer and Stevens (1993), Feit (1994), Griffith and Hein (1994), Halsall (1996), Leinwand and Fang (1993), Miller (1993), Perkins and McGinnis (1997), Rose (1994), Rose and McCloghrie (1995), Stallings (1993), Stevens (1994), Taylor (1996), and Townsend (1995).

 

SNMPY

An interface to SNMP for Python. [http://alumni.dgs.monash.edu.au/~anthony/snmpy/snmpy.html]

 

SNMX

The Simple Network Management eXecutive is a self-contained SNMP manager, extensible SNMP agent, scripting language, and development environment which allows users to rapidly create SNMP applications. The program provides a shell-like command line interface which presents the SNMP MIB as a series of virtual directories which can be traversed using standard cd commands and listed with the ls command. The scripting language can be used to create SNMP interactive and background applications including SNMP agent processes. SNMX can be used as:

• an administrative tool, i.e. it is a full-featured MIB browser providing numerous functions allowing users to explore the structured management information on a device;
• an element configurator since it allows an entire MIB to be listed to a disk file, potentially edited, and then put back on the network device;
• a network scanner useful for making comparative measurements of network devices, e.g. a built-in agent table (as part of its private MIB) allows a variety of scanning and charting operations; and
• a network configurator, i.e. multiple network devices and be updated with a single commmand.

Scripts can be constructed to poll devices, check network performance, and issue traps when network anomalies are detected. Agent scripts can be built to provide SNMP compatibility with existing systems or processes including such applications as instrumenting queues and controlling network graphical systems.

SNMX is freely available to individuals and organizations with the base distribution containing an SNMX interpreter, a MIB compiler, and several examples of management and agent scripts. Extensive documentation is provided in several large manuals in ASCII format.

[http://www.cpro.com/cpro/html/cpro_snmx.html]

 

SNNAP

The Simulator for Neural Networks and Action Potentials is a tool designed for the rapid development and simulation of realistic models of single neurons and small neural networks. The electrical properties of individual neurons are described with Hodgkin-Huxley type voltage- and time- dependent ionic currents. The connections among neurons can be made by either electrical or chemical synapses. The chemical synaptic connections are capable of expressing several forms of plasticity, such as homo- and heterosynaptic depression and facilitation. SNNAP also includes mathematical descriptions of intracellular second messengers and ions. The synthesis of second messengers can be driven by either synaptic inputs or by externally applied transmitters. The accumulation of an ion can be driven by any specified voltage- and time- dependent ionic current(s). The intracellular concentrations of ions and/or second messengers, in turn, can be linked to one or more ionic conductances and/or mechanisms contributing to chemical synaptic transmission. Thus, SNNAP can simulate the modulation, either enhancement or inhibition, of membrane currents and synaptic transmission. SNNAP also can simulate current flow in multicompartment models of neurons by using the equations describing electrical coupling. The features of SNAPP include: the specifics of all intrinsic neuron properties, network structures, and simulation properties can be controlled using editors in a GUI framework; the capability of simulating common experimental manipulations, e.g. the injection of external currents into multiple cells, the removal of individual conductances to simulate pharmacological agents, etc; and the modular organization of all input files, i.e. the equations and related parameters are passed to SNNAP via files generated by the graphical editors which allows for the creation of a library of modules for describing different aspects of neural networks.

A source code distribution of SNNAP is available. It is written in ANSI C using Xlib functions and is thus portable to most UNIX/X11 environments. A user's manual is available in PostScript format.

[http://nba19.uth.tmc.edu/~snnap/home.htm]

 

SNNS

The Stuttgart Neural Net Simulator is a software simulator for neural nets which runs on UNIX workstations. The goal of the project is to create an efficient and flexible simulation environment for research on and the application of neural networks. SNNS consists of a simulator kernel and a graphical interface. The simulator kernel operates on the internal network data structures of the neural nets and performs all operations of learning and recall, and it can also be used as an embedded program in custom applications. It supports arbitrary network topologies and can be extended by the user with user-defined activation functions, output functions, site functions, and learning procedures which are written as C programs and linked to the kernel. The graphical interface controls the kernel during the simulation and gives 2- and 3-D representations of the networks being simulated. The network architectures and learning procedures included in SNNS include: backpropagation (BP) for feedforward networks (i.e. vanilla BP, BP with a momentum term and flat spot elimination, and batch BP), counterpropagation, quickprop, backpercolation 1, RProp, generalized radial basis functions (RBF), ART1 and ART2, ARTMAP, cascade correlation, recurrent cascade correlation, dynamic LVQ, backpropagation and quickprop through time (for recurrent networks), self-organizing (Kohonen) maps, time-delay networks (TDNN) with backpropagation, Jordan networks, Elman networks and extended hierarchical Elman networks, and associative memory. A genetic algorithm tool called Enzo is separately available which allows the evolutionary optimization of neural networks. A tool called snns2c automatically generates C code from nets built interactively.

The source code for SNNS is available. It is written in C and has been tested on Sun SunOS, DEC Ultrix and Alpha, IBM AIX, HP-UX, SGI IRIX, and Linux Intel platforms. The huge user's manual is available in either PostScript or HTML format.

[http://www.informatik.uni-stuttgart.de/ipvr/bv/projekte/snns/snns.html]

 

Snob

A package which uses the Minimum Message Length (MML) principle to to mixture modeling, which concerns modeling a statistical distribution by a mixture (or weighted sum) of other distributions and is also known as unsupervised concept learning, intrinsic classification, clustering, and numerical taxonomy. Snob can use several distributions, e.g. normal (i.e. Gaussian), discrete multi-state (i.e. Bernoulli or categorical), Poisson, and von Mises distributions, and can also handle missing data. The source code for Snob, written in Fortran 77, is available. It is documented in a ASCII user's guide as well as in several papers and technical reports available in PostScript format. See also AutoClass C.

[http://www.cs.monash.edu.au/~dld/Snob.html]

 

SNOBOL

The StriNg Oriented symBOLic language is an unconventional programming language based on logical principles of pattern matching to solve string manipulation problems. It features a powerful collection of string processing and pattern matching functions. SNOBOL was developed at Bell Labs in 1962 to develop applications in symbolic formula manipulation. Improved versions called SNOBOL3 (1966) and SNOBOL4 (1969) were later developed, with active development on the language stopping with SNOBOL4. It was initially developed for formula manipulation but was extended to perform graph processing and text manipulation tasks, with the primary objective being to provide a general purpose language for the manipulation of non-numerical scientific data that can be naturally represented by strings of characters. Another significant design criteria was to develop a language suitable for use by non-programmers. An available compiler is SNOBOL4. [http://www.tiac.net/users/philb/snobol.html]

 

SNOBOL4

A port of Macro SNOBOL4 (i.e. the original Bell Labs implementation written in SIL macros) to machines with 32-bit C compilers. It supports the full SNOBOL4 language plus extensions from Catspaw SNOBOL4+, SPITBOL, and SITBOL. All aspects of the language are implemented except the trapping of arithmetic exceptions and the dynamic use of LOAD() platforms not using the a.out executable format. It has been tested on most UNIX flavors. See Gimpel (1976), Griswold et al. (1971), Griswold (1972), and Griswold (1975). [http://www.tiac.net/users/philb/src.html]

 

SNP

The SemiNonParametric software is a package for multivariate nonparametric time series analysis by maximum likelihood polynomial expansion which permits uneven weighting, non-normality, and nonlinearity. An extensive user's manual is available in PostScript format. [http://lib.stat.cmu.edu/general/]

 

SOAR

Soar is an AI programming language which implements a theory of cognition as a set of principles and constraints on cognitive processing, i.e. it provides a cognitive architectural framework within which cognitive models can be constructed. It can be considered as an integrated architecture for knowledge-based problem solving, learning, and interacting with external environments. It incorporates problem spaces as a single framework for all tasks and subtasks to be solved, production rules as the single representation of permanent knowledge, objects with attributes and values as the single representation of temporary knowledge, automatic subgoaling as the single mechanism for generating goals, and chunking as the single learning mechanism. Soar is used by AI researchers to construct integrated intelligent agents and by cognitive scientists for cognitive modeling. Soar is written in C and versions are available for both UNIX and Mac systems. There is quite a bit of documentation available, including several tutorials and manuals in PostScript format. Quite a bit of ancillary software has also been developed. Browse the several Soar sites to see what's available.

[http://www.isi.edu/soar/soar.html]

 

Socket Script

A simple scripting language for accessing sockets. Socket Script was designed to provide users with a quick and easy way to make powerful networking applications without needing to learn C or complicated socket code. It can be used for such tasks as retrieving web pages or creating an IRC bot, a web server, an ICMP water, a network monitor tool, online forms, etc. It consists of over 80 commands, some simple and some highly complex. It can be compiled into text only, Xt graphics, or GTK graphics modes. The Socket Script distribution consists of an interpreter, a compiler, and a C library of Socket Script functions for those who wish to program in C. Documemtation is a bit sparse but available in various ASCII text files within the distribution.

[http://devplanet.fastethernet.net/sscript.html]

 

SOCKS

An open Internet standard for performing network proxies at the transport layer. This is also known as authenticated firewall traversal (AFT) and is described in RFC-1928. SOCKS is a networking proxy protocol which enables hosts on one side of a SOCKS server to gain full access to hosts on the other side of the server without having to create a direct IP connection. The server authenticates and authorizes the requests, establishes a proxy connection, and relays the data. It is most commonly used as a network firewall which enables those behind it to gain full access to the Internet and prevents unauthorized access from the outside. There are two major versions: SOCKS V4 and V5, with the latter supporting authentication methods and UDP proxy and the former not. Newer features also allow SOCKS to be used as:

• a network enabler which allows an unstructured and unsecured enterprise network to safely use the Internet;
• a network broker supporting a wide range of security mechanisms; a network folder which can collect a group of networks and represent them as a single node;
• a network keeper which provides a centralized network access point that facilitates administration; and
• a network master which, as a generic internetworking proxy mechanism becomes the master of a network.

This (i.e. the NEC) reference implementation of SOCKS supports all the requirements of RFC-1928 and includes additional features like a shared library for UNIX clients, ping and traceroute proxy, SOCKS Server-to-Server proxy, address resolution proxy, Ident name proxy, preforking and threading, and Kerberos-based Server-to-Server proxy. These features allow SOCKS users to build virtual private networks (VPN) over the Internet which offer: one-time sign on, user-based authentication, encrypted communication channels, transparent access across the entire VPN, centralized network access control and audit, localization of network administration, and the masking of the VPN computing environment.

The UNIX SOCKS5 package contains a socks server, static and unshared client libraries, and some popular client applications. It is available in source code format or in binary format for several UNIX flavors. Extensive documentation is available at the site and in the distribution. This is also covered in Garfinkel and Spafford (1996).

[http://www.socks.nec.com/]

 

SoftFloat

A free, high-quality implementation of the IEC/IEEE Standard for Binary Floating-point Arithmetic. It is completely faithful to the IEEE Standard and relatively fast. All functions dictated by the standard are supported except for conversions to and from decimal, and both single (32 bits) and double (64 bits) precision are implemented. All required rounding modes, exception flags, and special values are supported. SoftFloat is written in ISO/ANSI C and should compile on any machine with an ISO-conformant C compiler, e.g. gcc. The package has been tested using gcc on Intel 386, SPARC, MIPS and HP Precision Architecture processors. The SoftFloat distribution includes the source code and documentation. A test program called FloatTest is also supplied. [http://HTTP.CS.Berkeley.EDU/~jhauser/arithmetic/SoftFloat.html]

 

Software ChipSet

A collection of reusable software components written in C. The goal is to provide small, general, production quality off-the-shelf solutions to common problems faced by programmers. The name comes from an analogy to components used in the development of integrated circuits. The components of the ChipSet are intended to be general enough to use in a wide variety of applications. This goal is reached by providing generalized interfaces and programmability, with the former permitting the components to be used with arbitrary data types and the latter permitting the application to tune the components to its data types and performance requirements at runtime. The components are also programmable in that they can be composed into larger components. The components of the ChipSet are:

• btree, a in-memory B-tree implementation;
• dupkey, which generalizes in-memory unique key index structures (i.e. btree and list) to allow redundant keys;
• list, an in-memory doubly-linked list; and
• readln, a component for safe text line input which supports lines of arbitrary length.

A source code distribution is available. All components are written in C for maximum portability.

[http://www.sander.cupertino.ca.us/source.html]

 

SOLVATE

A program for constructing atomic solvent environment models for given atomic macromodule models (solutes) used in molecular dynamics simulations. The capabilities of SOLVATE include:

• generation of irregularly shaped solve volumes adapted to a given solute's structure;
• efficient computation of boundary forces as required in molecular dynamics simulations;
• a guaranteed minimal solute boundary distance;
• specification of a minimum solvent surface curvature to avoid flat surface regions;
• generation of disordered (i.e. fluid) water rather than a grid of water molecules, i.e. ice;
• local minimization of the positions of all water molecules;
• optional placement of salt ions obeying a Debye-Hückel distribution;
• optional placing and marking of buried water molecules; and
• compatibility with X-PLOR and CHARMm with output in PDB/PSF format.

A source code distribution of SOLVATE is available. It is written in Fortran and can be compiled on most generic UNIX platforms. A user's manual is included in PostScript format.

[http://www.mpibpc.gwdg.de/abteilungen/071/solvate/docu.html]
[ftp://ftp.osc.edu/pub/chemistry/software/SOURCES/FORTRAN/solvate/ ]

 

SOMA

Stefan's Own Mail Application is a mail reader (i.e. a mail user agent) for Linux under X11 based on the XView library which provides an OpenLook user interface. [http://sunsite.unc.edu/pub/Linux/system/mail/mua/]

 

SoPlex

The Sequential Object-oriented simPLEX class library is a C++ library of primal and dual simplex algorithms for solving linear programming problems. It consists of elementary classes for general purposes, linear algebra classes providing basic data types for regular and sparse linear algebra computations, and algorithmic classes implementing a wide variety of algorithms for solving numerical problems and subproblems. The elementary classes include Array, CmdLine, DataArray, DataHashTable, DataSet, IdElement, IdList, IsElement, IsList, NameSet, Random, and Timer classes as well as classes for data objects and sorting functions. The linear algebra classes include those for dynamic index sets, dynamic sparse vectors, dynamic vectors, index sets, LP columns, sets of LP columns, sets of LP rows, semi-sparse vectors, parts of semi-sparse vectors, sparse vectors, sparse vector sets, sparse unit vectors, vectors with updates, and dense vectors.

The algorithmic classes are divided into several categories including general, pricer, ratio test, simplifier, start basis, and linear system solver classes. The general classes include:

• LPSOlver, an interface class for LP solvers;
• CacheLPSolver, an LP solver with result caching;
• SoPlex, a sequential object-oriented simplex solver;
• SPxBasis, a simplex basis;
• SPxSolver, a preconfigured SoPlex LP solver;
• SPxLP_SPxColId, IDs for LP columns;
• SPxLP_SPxRowId, IDs for LP rows;
• SPxLP_Id, generic IDs for LP rows or columns;
• SPxLP, for saving LPs in a form suitable for SoPlex; and
• SPxTCL, a TCL interpreter for SoPlex.

The pricer classes include:

• SPxPricer, a SoPlex pricer base class;
• SPxWeightPR, for weighted pricing;
• SPxSteepPR, a steepest edge pricer;
• SPxDefaultPR, a default pricer;
• SPxParMultPR, for partial multiple pricing; and
• SPxHybridPR, a hybrid pricer for SoPlex.

The ratio test classes are:

• SPxRatioTester, a SoPlex ratio test base class;
• SPxDefaultRT, a textbook ratio test for SoPlex;
• SPxHarrisRT, for Harris pricing with shifting; and
• SPxFastRT, a fast shifting ratio test.

The simplifier classes are:

• SPxSimplifier, an LP simplification base class;
• SPxScale, for LP scaling;
• SPxRedundantSM, to remove redundant rows and columns;
• SPxRem1SM, an LP simplifier for removing singletons;
• SPxAggregateSM, to remove redundant rows and columns; and
• SPxGeneralSM, for general LP preprocessing.

The start basis classes include:

• SPxStarter, a SoPlex start basis generation base class;
• SPxSumST, a simple heuristic SPxStarter;
• SPxWeightST, a weighted start basis; and
• SPxVectorST, a solution vector based start basis.

The linear system solver classes are

• SLinSolver, a sparse linear solver virtual class base; and
• SLUFactor, a sparse LU factorization class.

A source code distribution of SoPlex is available. It is written in C++ and includes a user's guide in PostScript format. It is available by filling in an interactive form at the site.

[http://www.zib.de/Optimization/Software/Soplex/index.html]

 

sound

There are many packages for synthesizing, editing, annotating, and doing various other things with sound. Sound synthesis packages include

• CMIX,
• CLM,
• CM,
• CMIX,
• Csound,
• Nyquist,
• saolc, and
• Sapphire.

Sound editors include:

• DAP,
• GOM,
• MiXViews,
• OSS,
• snd, and
• Studio.

Music notation editors include:

• CMN,
• LilyPond,
• MusicTeX,
• MusiXTeX,
• Rosegarden, and
• Vivace.

Available MIDI software includes:

• JAZZ,
• KeyKit,
• midikb,
• Tclmidi, and
• TiMidity.

Miscellaneous other available sound-related software includes:

• BashFest,
• Cecilia,
• Cthugha,
• CyberRadio,
• Drumachine,
• Midi2Cs,
• OSS,
• Q-SeeMe,
• SFS,
• SNDAN,
• Space,
• SoX, and
• SPKit.

[http://www.bright.net/~dlphilp/linux_soundapps.html ]
[http://www.digiserve.com/ar/linux-snd/ ]

 

SoX

Sound Exchange is a sound file converter which also does sample rate conversion and some sound effects. The sound file formats understood by SoX include various binary formats, raw textual data, Microsoft Windows .WAV files, MAUD files, Sound Blaster .VOC files, IRCAM SoundFile files, SUN Sparcstation .au files, DEC .au files, Apple/SGI AIFF files, CD-R (music CD format), Macintosh HCOM files, Sounder files, NeXT .snd files, SUN ADPCM (compressed) .au files, Soundtool (DOS) files, and Psion (palmtop) A-law files. The sound effects include changing the sample rate, adding echo delay lines, applying low-, high, and band-pass filtering, examining sample loops and grabbing the looped parts, translating between stereo and monophonic channels reversing a sample, adding masking noise to avoid buzzing voices, and the Fender Vibro effect. A source code distribution of SoX is available. It is written in C and should compile on most UNIX platforms. Its use is documented on the site as well as in the distribution.

[http://www.spies.com/Sox/]

 

SP

An SGML system conforming to International Standard ISO 8879. It is a free, object-oriented toolkit for SGML parsing and entity management. The features of SP include:

• nsgmls, a program which parses and validates an SGML document whose entity is specified by system identifiers and prints to standard output a simple text representation of its Element Structure Information Set (ESIS);
• spam, a markup stream editor;
• sgmlnorm, a normalizer which focuses on producing the same ESIS rather than preserving details of the markup;
• access to all the information about an SGML document, e.g. to DTD and SGML declarations as well as document instance, to markup as well as abstract document, etc., sufficient to recreate an identical copy of any SGML document;
• support for almost all optional SGML features, e.g. arbitrary concrete syntaxes, SHORTTAG, OMITTAG, RANK, SUBDOC, LINK, etc.;
• a sophisticated entity manager which supports ISO/IEC 10744 Format System Identifiers, SGML Open catalogs, and WWW and can be used independently of the parser;
• support for multi-byte character sets, e.g. ISO/IEC 10646 Unicode, Japanese character sets (Shift-JIS, EUC), etc.; and
• production quality tested using several SGML test suites.

The SP distribution is available as source code. It is written in C++ which can be compiled using gcc 2.7.2 or later. Binary versions are also available for MS-DOS, Linux Intel, DEC Alpha, Sun Solaris, and Windows NT and 95 platforms.

[http://ftp.jclark.com/sp/]

 

Space

A program which spatializes sound using a script by placing and moving mono sound files using 3-D coordinates. It will render the same script in stereo, Ambisonics, or in crude mono. The features of Space include:

• the use of delay lines to correspond to the distance the sound is from the listener;
• the use of low-pass filtering and the inverse-square law to further process the signal as it travels long distances;
• the capability for sounds to stay motionless, move in straight lines, or in long arcs;
• the capability of mixing in pre-spatialized sound files which are in the same format as the output;
• the use of Angled Cardiod Virtual Microphones to record the two signals used for stereo;
• the inclusion of Ambisonic decoding equations so the system can be modified to produce a four speaker feed; and
• the reflection of sounds off of configurable walls within a simple room model to generate early reflection images or cruder echoes.

A source code distribution of Space is available. Compilation requires C, Yacc, and Lex and it works by creating a shell and using the Csound package to process output.

[http://www.muse.demon.co.uk/Csound.html]

 

SPAK

Send PACket is a collection of tools that can be used to generate and send arbitrary packets to a UNIX socket. It was originally written as part of a firewall testing project, and is designed to be modular and allow maximal control over the design of the packet. SPAK consists of several programs including: makeip, which makes an IP packet; maketcp, which makes a TCP packet; makeudp, which makes a UDP packet; and sendpacket, which sends a packet to a socket. A source code distribution of SPAK is available. It is written in C and can be compiled on most UNIX flavors. [http://www.cs.purdue.edu/homes/steinkf/software/spak/]

 

spinne

A program that superimposes colored graphs onto 2-D plots of results of various projection methods as principal components analysis (PCA), nonlinear mapping (NLM), and self organizing maps (SOM) that are used for analyzing multidimensional data via dimensional reduction. The colors of the graph edges encode the original high dimensional distances between the connected points, allowing the distortions produced by the projection methods to be viewed. Spinne can handle input data in four different ASCII formats and can output results in PosScript format. Binary versions of spinne are available for MS-DOS, NextSTEP, SGI IRIX, and Linux Intel platforms. A user's manual is supplied in PostScript format.

[http://www2.organik.uni-erlangen.de/Bruno_Bienfait/Spinne/]

 

SPKit

The Sound Processing Kit is an object-oriented class library for audio signal processing which includes classes for various signal processing tasks written in C++. SPKit contains more than 20 classes including signal routing and processing modules such as a multiplexer, an amplifier, a signal inverter, sum units, delay lines, and a set of filters. The SPKit classes are divided into several categories. A sound input/output classes include:

• SPKitReader, which reads audio files in 16 bit linear NeXt/SUN format; and
• SPKitWriter, which writes files in the same format.

The basic signal processing classes are:

• SPKitAmp, an amplifier class which multiplies input samples by a gain value;
• SPKitInverter, which outputs an input signal in opposite phase;
• SPKitMult, which multiplies two input signals with each other; and
• SpKitRectifier, which outputs absolute values of input signals.

A dynamics processing class includes:

• SPKitCompressor, a signal amplitude compressor class which scales the amplitude of input signals by a user-specified compression ratio;
• SPKitGate, which compares the input signal amplitude with the threshold level and scales the amplitude to zero if the former is less than the latter;
• SPKitLimiter, which scales the amplitude of an input signal to match a maximum output level indicated by a threshold value; and
• SPKitCompressorLimiter, which feeds the input signal through a compressor followed by a limiter.

The filtering classes are:

• SPKitBWLowPassFilter, a Butterworth low-pass filter;
• SPKitBWHighPassFilter, a Butterworth high-pass filter;
• SPKitBWBandPassFilter, a Butterworth band-pass filter;
• SPKitBWBandRejectFilter, a Butterworth band-reject filter; and
• SPKitResonator, a second-order all-pole band-pass filter.

The delay and reverberation class includes:

• SPKitDelay, a delay line class;
• SPKitFBDelay, a delay line class specialized for use in a feedback loop;
• SPKitSchroederReverb, a reverberator class;
• SPKitAllPassNetwork, an implementation of an allpass network or filter;
• SPKitComb, a comb filter class; and
• SPKitCombLowPass, a comb low-pass filter class.

A distortion class contains

• SPKitWaveShaper, a waveshaping or non-linear distortion class.

A signal routing class comprises:

• SPKitFeedBack, which outputs the summed signal of two inputs;
• SPKitMux, a signal multiplexer; and
• SPKitSum, which outputs the summed signal of one or more inputs.

A source code distribution of SPKit is available. It is written in bare-bones C++ (i.e. templates and exceptions aren't needed). It requires ANSI C standard libraries and uses ANSI C routines for sound file I/O.

[http://www.music.helsinki.fi/research/spkit/]

 

SPLP

A subroutine which solves linear optimization problems. The user inputs the number of constraints and the number of entries in the solution vector, the coefficients of the linear objective function, the coefficient matrix, input parameters defining the form of the bounds for the unknowns, and an array containing switches for modifying various parts of the routine. A source code distribution of SPLP is available. It is written in Fortran 77 and documented via comment statements contained within the source code file. This is part of CMLIB.

[http://sunsite.doc.ic.ac.uk/public/computing/general/statlib/cmlib/]

 

SPM

A Matlab toolkit implementing Statistical Parametric Mapping for users familiar with the underlying statistical, mathematical, and image processing concepts (i.e. you really need to understand to concepts to use the software). It is used to test hypotheses about neuro-imaging data fro SPECT/PET and fMRI sensors. The SPM approach can be (reasonably briefly) summarized as a procedure in which: images are spatially normalized into a standard space and smoothed; parametric statistical models are assumed at each voxel with hypotheses expressed in terms of the model parameters assessed at each voxel using univariate statistics; and comparisons of all of the voxel statistics are simultaneously assessed using the theory of continuous random fields.

The functionality of SPM includes:

• realignment of image sequences,
• automated non-linear spatial normalization using basis warps of discrete cosine transforms,
• image segmentation into grey/white/CSF tissue types,
• coregistration,
• spatial smoothing via convolution with Gaussian kernels,
• formation and assessment of statist images,
• manipulation of results (e.g. plotting, overlaying statistical results onto structural images, rendering on template surface volumes),
• eigenimage analysis,
• global adjustment and image averaging, and
• image calculations.

A source code distribution of the SPM Matlab toolkit is available. It consists mostly of Matlab M-files and functions although some external C programs are also compiled and linked to Matlab via C-mex files. This is known to work with Matlab 4.2c. A great deal of documentation is available including technical reports and a set of tutorial course notes on both the use of the package and the methods used in the package.

[http://www.fil.ion.bpmf.ac.uk/spm/]

 

spock

A high-end molecular graphics package for displaying protein and nucleic acid structures as well as a powerful search engine which allows users to search through a directory of PDB files for proteins with specific characteristics. Spock provides typical molecular visualization views (e.g. ribbons of several types, line and rod bonds, etc.) as well as molecular and accessible surfacing routines. It also provides interfaces to DSSP for reading secondary structure information and a quasi-WYSIWYG interface for Molscript for producing publication quality output. Spock was designed from the ground up to be powerful, flexible, easy to use, and to bring molecular modeling programs into the age of the internet. The features of spock include:

• use of OpenGL for maximum portability;
• dynamic memory allocation with no hard-coded upper limits on the size of structures or the resolution of surfaces;
• a choice of bond display modes including line, ball, ball-and-stick, and cylinder styles;
• a choice of backbone ribbon styles including tubular, rectangular, secondary structure, and a variable radius style;
• calculation and display of molecular and accessible surfaces;
• calculation and display of 2-D and 3-D isopotential contours;
• determination of hydrogen bonding patterns from structure with secondary structure determined from this data;
• saving and easily switching between multiple views of a structure;
• defining and independently manipulating subsets of atoms;
• simple modeling features including dynamic bond editing, rotation of torsion angles, and a simple mutation facility;
• history and macro mechanisms for creating shortcuts to complex scripts;
• use of environment variables for command customization;
• calculation and display of axes of helices and major moments of sheets;
• export of results to Molscript, Raster3D, VRML 1.0 and 2.0 formats;
• a built-in function calculator for applying functions to atomic or surface properties;
• support for several image formats including RGB, JPEG, PPM, GIF, TIFF, FBM, and PostScript;
• a selection mechanism for easily specifying groups of atoms or molecules; and
• an integrated help facility with context-sensitive help which uses an external WWW browser.

Versions of spock are available for SGI IRIX and Linux Intel platforms. A user's guide is available in HTML format in addition to the extensive online help.

[http://quorum.tamu.edu/jon/spock/]

 

SPONG

A simple system monitoring package written in Perl. SPONG features include client-based monitoring, monitoring of network services, grouping of hosts, host specific contact and downtime information, configurability on a client-by-client basis, results displayable on the Web, a problem history, messaging via email or pager when problems occur, and verbose information to help with problem diagnosis. This is not SNMP-based but rather communicates via simple TCP-based messages. The source code for SPONG is available and requires Perl 5.003 or greater for installation and use. Also required are a web server which can run CGI programs and a browser on which to display results. [http://strobe.weeg.uiowa.edu/~edhill/public/spong/]

 

SPRANNLIB

The Statistical Pattern Recognition and Artificial Neural Network LIBrary is a combination of the former SPRLIB and ANNLIB packages, the former of which supports the easy construction and simulation of classifiers and the latter of which contains functions for creating, training, and testing feed-forward neural networks. Both use the same set of support routines for memory management, I/O, and the like so they were combined into SPRANNLIB. The pattern recognition methods implemented in SPRLIB include: mean and covariance estimation, within and between scatter estimation, principal component analysis, random number generators, the Fisher linear discriminant function, a K-nearest neighbor classifier, a nearest neighbor classifier, clustering methods, Parzen classification, a quadratic discriminant function, a multiclass Mahalanobis classifier, and error estimation routines. The feedforward networks supported by ANNLIB are multilayer perceptrons, shared weight networks, and maximum likelihood networks. Kohonen networks are also supported. The available learning methods include backpropagation, conjugate gradient descent, Levenberg-Marquardt, and psuedo-Newton.

A source code implementation of SPRANNLIB is freely available for academic or research purposes upon filling out an online request form. It is written in C and includes make files for several platforms including Linux Intel. The package also uses some of the routines in Press et al. (1994) which have to be obtained separately. A user's guide and reference manual is available either in HTML or PostScript format.

[http://www.ph.tn.tudelft.nl/~sprlib/]

 

Spread

A toolkit and daemon that provide multicast and group communications support to applications across local and wide area networks. Spread is designed to make it easy to write groupware, networked multimedia, reliable server, and collaborative work applications. It consists of a library with which user applications are linked, a binary daemon that runs on each computer that is part of the processor group, and various utility and demo programs. It is currently (6/98) supported on several platforms including Linux Intel. [http://www.cnds.jhu.edu/projects/commedia/spread/]

 

SPRLIB

See SPRANNLIB.

 

SPRNG

The Scalable Parallel Random Number Generators package is a set of libraries for scalable and portable pseudorandom number generator which has been developed especially for use in parallel Monte Carlo simulations. SPRNG provides user-friendly interfaces for parallel Fortran, C and C++ programs which enables the easy use of sufficiently uncorrelated pseudorandom number streams on different processors with minimal inter-processor communication. Random numbers can also be generated from more than one stream on each processor. The pseudorandom number generators included in SPRNG are:

• two versions of linear congruential with prime addend,
• modified additive lagged Fibonacci,
• combined multiple recursive generator, and
• prime modulus linear congruential generators.

The MPI message passing software is supported with PVM support planned for future versions.

A source code distribution of SPRNG is available. It is written in C and can be compiled into the five libraries on several types of parallel and serial platforms including Linux Intel. It is used by linking these libraries to programs written in any of the abovementioned languages. The documentation includes quick start and references guides, a user's guide, a reference manual, and an introductory guide to parallel random number generators.

[http://www.ncsa.uiuc.edu/Apps/SPRNG/]

 

SP (Semidefinite Programming)

The Semidefinite Programming software is an implementation of Nesterov and Todd's primal-dual potential reduction method for semidefinite programming. The package includes the full source code (written in C), a Matlab interface to SP (although it can also be used directly), Matlab examples, and the documentation. The C source code includes calls to LAPACK. The documentation is a user's manual in PostScript format. See also CSDP, INCT, LMITOOL, MAXDET, SDPA, SDPpack, and SDPSOL.

[http://www-ISL.Stanford.EDU/people/boyd/SP.html]

 

SP (SGML Parser)

A free, object-oriented toolkit for SGML Parsing and entity management. SP includes nsgmls, an SGML parser compatible with and a replacement for sgmls. Other features include access to all information about SGML documents (e.g. access to DTD and declaration, access to markup, etc.); support for almost all optional SGML features (e.g. SHORTTAG, OMITTAG, RANK, SUBDOC, etc.); a sophisticated entity manager that supports ISO/IEC Format System Identifiers, SGML Open catalogs, and WWW; support for multi-byte character sets (e.g. Unicode and Japnenese character sets); written from scratch in C++ in object-oriented fashion; fast and portable. It is currently (8/96) of production quality, having been tested using several SGML test suites and included in several commercial products. The SP source code is available as well as binaries for Windows 95 and NT, MS-DOS, Sparc Solaris, Linux and DEC Alpha systems. The documentation is separately available in HTML format.

[http://www.jclark.com/sp.html]

 

Sparse

A set of C subroutines for solving large sparse real or complex systems. Besides being able to solve large linear systems it solves transposed systems, finds determinants, and estimates errors due to ill-conditioning in the system of equations and instability in the computations. It is generally as fast or faster than other sparse matrix packages when solving many matrices of similar structure. Sparse has several features beyond the basic creation, factoring and solving of systems of equations. These include the ability to handle both real and complex systems of equations, the ability to quickly solve the transposed system, the dynamic allocation of memory for matrix elements, the ability to efficiently compute the condition number of the matrix, the ability to do much of the matrix initialization and to preorder modified node admittance matrices, the ability to exploit sparsity in the right-hand-side vector, the ability to scale matrices prior to factoring to reduce uncertainty in the solution, and much more.

The Sparse package includes the C source code, a user's guide in ASCII and Troff format, and a selection of test matrices.

[http://www.netlib.org/sparse/index.html]

 

SparseBLAS

The NIST Sparse BLAS library provides computational kernels for fundamental sparse matrix operations such as sparse matrix products and solution of triangular systems. This package supports various sparse formats such as compressed-row, compressed-column, and coordinate storage formats (together with block and variable-block versions of these). The source code for Sparse BLAS is written in ANSI C and the routines are callable from Fortran and C through the standard interface. The source code is available along with a user's guide and various other types of documentation in PostScript format.

[http://math.nist.gov/spblas/]

 

SparseLib++

A C++ class library for efficient sparse matrix computations across various computational platforms. The package consists of matrix classes encompassing several sparse storage formats and provides basic functionality for managing sparse matrices. Various preconditioners commonly used in iterative solvers for linear systems of equations are included. The focus is on support for iterative methods (e.g. IML++), but the objects in this package can be used in their own right. SparseLib++ matrices can be built out of nearly any C++ matrix/vector classes and is shipped with the MV++ classes. A PostScript manual is available. [http://math.nist.gov/sparselib++]

 

SparseQR

A C or C++ routine which computes the QR decomposition of a sparse matrix using row ordering. See Robey and Sulsky (1994). [http://www.arc.unm.edu/~trobey/]

 

SPARSKIT2

A basic toolkit for sparse matrix computations which takes the form of a general purpose Fortran library. It includes several useful tools for developing and implementing sparse matrix techniques, particularly for iterative solvers. Examples of the tools available include programs for converting data structures, printing simple statistics on a matrix, and plotting a matrix profile. It contains just about any algorithm you might need for performing a sparse matrix operation as well as several iterative accelerators and efficient preconditioners. The distribution also includes a repository of sparse matrices. SPARSKIT can handle conversions among most commonly used sparse matrix storage formats including the dense, LINPACK banded, compressed sparse row, compressed sparse column, coordinate, Ellpack/ITPACK generalized diagonal, diagonal, block sparse row, modified compressed sparse row, symmetric skyline, nonsymmetric skyline, linked list, jagged diagonal, symmetric sparse skyline, unsymmetric sparse skyline, and variable block row formats. Non-algebraic operations available include extraction of rectangular submatrices, filtering and sorting matrix elements, in-place transpositions, copying, extracting diagonals and upper and lower matrix portions, column and row permutations, extracting bandwidth information, and more. A module called BLASSM (Basic Linear Algebra Subroutines for Sparse Matrices) contains subroutines for computing various matrix products and sums. A MATVEC module contains routines for matrix by vector products and various sparse triangular solution methods. A matrix generation module contains routines for generating various symmetric and nonsymmetric matrices as might result from finite difference or finite element algorithms. An iterative solution module contains various subroutines including conjugate gradient, biconjugate gradient, generalized minimum residual (GMRES), several GMRES preconditioners, etc.

A source code distribution of SPARSKIT is available. It is written in Fortran 77 and takes the form of a library of efficient and well-tested subroutines. It is documented in a user's manual available in PostScript format as well as in some technical reports.

[http://www.cs.umn.edu/Research/arpa/SPARSKIT/sparskit.html]

 

Speak Freely

An application that allows you to engage in bidirectional conversations over the network. Speak Freely uses both GSM compression and sample interpolation to reduce the data bandwidth sufficiently to allow conversations over the Web. Conversations can also be encrypted using either DES or IDEA. The individual programs that comprise the package are:

• sfmike, for sending sound to remote hosts;
• sfspeaker, to receive sound from remote hosts;
• sflwl, a client program which requests information from a server running the Look Who's Listening server;
• sflwld, the Look Who's listening server which maintains a list of users running Speak Freely who have identified themselves;
• sfecho, a server program that receives sound from a remote host, buffers it, and then retransmits it to the sending host; and
• sfvod, which monitors connections to a given port.

A source code distribution of Speak Freely is available. The supplied makefile includes instructions on how to compile on several UNIX platforms including Linux Intel. The utilities are documented in separate man pages.

[http://www.fourmilab.ch/speakfree/unix/sfunix.html]

 

SPECDRE

A Starlink Project package for SPECtroscopy Data REduction. A typical SPECDRE data set is contained within a hyper-cube where each row or hyper-column is a spectrum. Any line or continuum fits calculated are stored along with the data in this format, as well as are bad values or errors. Variance information can also be included and is used in the processing steps, e.g. for statistical weights, if present. A SPECDRE extension to the basic NDF data format is used which is recognized by all SPECDRE applications and uncritically propagaged by other packages. The tasks performed by the SPECDRE applications include: using the data and errors of hyper-cubes to write to or read from printable/editable tables; plotting of spectra and data with full control of various aspects such as font, color, line styles, error bars, etc. as well as overlay on previous plots according to their world coordinates if possible; hyper-cube manipulations such as extraction of averaged hyper-planes, assembly of hyper-cubes from hyper-planes, and filling in hyper-cubes from several other hyper-cubes; resampling capabilities including resampling all spectra in a hyper-cube or resampling and averaging into one spectrum any number of input spectra; spectral fits using polynomials, blended Gauss, or triangle profiles with fit results stored along with data; and more.

A binary distribution of SPECDRE is available for DEC OSF/1, Linux Intel, and Sun Solaris platforms. The package is documented in a 78 page user's manual available in PostScript format.

[http://star-www.rl.ac.uk/store/storeapps.html]

 

SPECFUN

A collection of portable Fortran routines for calculating special functions. The routines include:

• ALGAMA, for calculating the log(gamma) function for positive real arguments;
• DAW, a program to evaluate Dawson's integral for real arguments;
• EI, for computing various exponential integrals;
• ERF, for computing the error function and its variants;
• GAMMA, for calculating the gamma function for a real argument;
• I0 and I1, for modified Bessel functions of the first kind and order zero;
• J0Y0 and J1Y1, for zero- and first-order Bessel functions of the first and second kind;
• K0 and K1, for modified Bessel functions of the second kind and orders zero and one;
• PSI, for evaluating the logarithmic derivative of the gamma function;
• REN, a random number generator;
• RIBESL, for Bessel functions of non-negative argument and order with or without exponential scaling;
• RJBESL, for Bessel functions of non-negative argument and order;
• RKBESL, for modified Bessel functions of the second kind of non-negative argument and order and with or without exponential scaling;
• RYBESL, for Bessel functions of non-negative argument and order;
• MACHAR, for determining the parameters of the floating-point arithmetic on a given machine.

A source code distribution of SPECFUN is available. All of the programs are written in Fortran and are available in single and double precision versions. Each program is documented in comment statements within the program.

[http://www.netlib.org/specfun/]

 

SpecIntLib

A Fortran 77 library containing the most common spectral transformations based upon FFTs. This package can be used for programming spectral methods when solving PDEs since it contains spectral interfaces that transform real or complex fields between spectral and physical spaces in various situations. It has a three level structure designed to isolate machine dependencies from the user as much as possible. The first or Code level requires only a few subroutine calls, e.g. a preparation subroutine and two routines to travel back and forth between the physical and spectral spaces. The second or Interface level deals with the spatial directions of the field. It calculates the increments and jumps of the indices and makes calls to the third or Basic level subroutines, which are the only machine dependent routines and thus the only ones that need to be modified between machines. The Basic level routines include: RFFTSB, a real fast Fourier transform; CFFTSB, a complex fast Fourier transform; RCOSSB, a real fast cosine transform; CCOSSB, a complex fast cosine transform; RSIMSB, a real fast sine transform; RSYMSB, a real fast symmetric Fourier transform; and CSYMSB, a complex fast symmetric Fourier transform.

A source code distribution of SpecIntLib is available. It is written in Fortran 77 and documented in a user's manual available in TeX format.

[ftp://ftp.cerfacs.fr/pub/Net-Sys/softs/fft/]

 

specPerl

A rewrite of SpecTcl for use with Perl. [http://keck.ucsf.edu/~kvale/specperl.html]

 

SpecTcl

A development environment for building applications with graphical user interfaces that run on multiple platforms. The SpecTcl packages lets you design GUIs interactively and graphically, uses a geometry manager precise enough to keep elements aligned across all platforms, enables the fast development of applications that can require many more lines of code in traditional procedural languages, provides flexibility at runtime to to, e.g. generate menus at runtime, allows the integration of Tcl/Tk scripts with scripts generated in SpecTcl, allows the quick alternation between design and execution for quick feedback on changes, produces executable files that use Tcl/Tk and don't require SpecTcl for use, and lets you develop and test simple applications separately and then combine them into subassemblies of a larger application. A source code distribution of SpecTcl is available. It is written in Tcl/Tk and requires recent versions of those to work. It is documented in a user's guide available in PostScript and PDF formats.

[ftp://ftp.sunlabs.com/pub/tcl/SpecTcl/]

 

spectral analysis

Packages for performing various types of spectral analyses include: ARfit, Cubic Spline Library, FFTPACK, Matlab Astronomy Library, SANTIS, SNP, SSA-MTM, STARPAC, and XQz.

 

SPEM

The S-coordinate Primitive Equations Model is a finite difference ocean circulation model written in Fortran 77. It has been used for a variety of regional and basin scale simulations. The features of SPEM include: an s-coordinate generalized topography following vertical coordinate designed to retain resolution in the upper ocean even over deep water so the mixed layer can be uniformly resolved independent of depth; staggered finite differences in the vertical; three available example simulations; floats and rotated mixing tensors; several C preprocessor flags to modify the model before compilation; options for using implicit time steps on the vertical viscosity and diffusion; options for computing the vertical diffusion and viscosity coefficients; an option for using NetCDF for input and output files; and much more.

The source code is available. It is written in Fortran 77 and can be compiled with several Fortran compilers, including g77. A user's guide is available in PostScript format. The NCAR Graphics library is required for using the built-in graphics capabilities of SPEM. A package called gridpak is also available for creating curvilinear orthogonal grids for use with SPEM.

[http://marine.rutgers.edu/po/spem.html]

 

Spherekit

An integrated toolkit for spatial interpolation and comparison of spatial interpolation algorithms developed at the NCGIA (National Center for Geographic Information and Analysis). The capabilities of the package include large-scale interpolation, smart interpolation, and error analysis. Spherekit can interpolate over continental and global scales since its computations are based on spherical distances and orientations, as opposed to conventional interpolations based on various planar projects of the Earth. It also permits the user to incorporate knowledge or information about the processes that produced the spatial fields in a process called smart interpolation. This is implemented via the interpolation of user-defined, derived variables. The performance of an interpolation method and its associated set of parameters is evaluated using cross-validation wherein the error at each observation point is defined as the difference between its actual value and its estimated value using the remaining n-1 points. The available interpolation methods are inverse distance weighting, triangulation, kriging, multiquadric, and thin plate spline.

Spherekit is UNIX based and includes a complete graphical interface. The source code is available and should compile on most generic UNIX platforms. It uses the GMT package for displaying interpolated fields.

[http://whizbang.geog.ucsb.edu/spherekit/]

 

SPHEREPAK

A library of 17 Fortran 77 routines for computing spherical harmonic analyses and syntheses. Harmonic analysis is used for problem solving in spherical coordinates in the same way that Fourier analysis is used in Cartesian coordinates. It simplifies the tasks interpolation and smoothing on the sphere, and significantly lessens the problems of solving partial differential equations (PDEs) on the sphere. The options include that the grid in the latitudinal direction can be either Gaussian or equally spaced, the number of grid points in either latitude or longitude are arbitrary, the analysis can be performed either on the entire sphere or only in the northern hemisphere, the associated Legendre functions can either be stored or recomputed as needed, multiple analyses or syntheses can be specified, and the spectral truncation is completely under user control. SPHEREPAK uses Gaussian integration to compute the analysis in the programs that use a Gaussian grid in the latitude direction, and uses multiple vectorized FFTs in the longitudinal direction. The programs in SPHEREPAK are:

• SHAEC, for computing an analysis on a equally spaced grid using computed functions;
• SHAECI, for initializing an array that may be used repeatedly by SHAEC;
• SHSEC, for computing a synthesis on an equally spaced grid using computed functions;
• SHSECI, for initializing an array that may be used repeatedly
• SHAES, for computing an analysis on a equally spaced grid using stored functions;
• SHAESI, for initializing an array that may be used repeatedly by SHAES;
• SHSES, for computing a synthesis on an equally spaced grid using stored functions;
• SHSESI, for initializing an array that may be used repeatedly by SHSES;
• SHAGC, for computing an analysis on a Gaussian grid using computed functions;
• SHSGC, for computing a synthesis on a Gaussian grid using computed functions;
• SHIGC, for initializing an array that may be used repeatedly by either SHAGC or SHSGC;
• SHAGS, for computing an analysis on a Gaussian grid using stored functions;
• SHSGS, for computing a synthesis on a Gaussian grid using stored functions;
• SHIGS, for initializing an array that may be used repeatedly by either SHAGS or SHSGS;
• DNLFK, which computes the Fourier coefficients in the trigonometric expansion of the associated Legendre functions;
• DNLFT, which computes the associated Legendre functions using the coefficients computed by DNLFK; and
• GAQD, which computes the Gaussian latitude and weights that are used in the Gaussian integration.

A source code distribution of SPHEREPAK is available. All the programs are written in Fortran 77. Several demonstation programs are also included. The documentation is mostly contained within the source code files.

[ftp://ftp.ucar.edu/dsl/lib/sphere/]

 

SPIM

A software simulator that runs assembly language programs for the MIPS R2000/R3000 processors which can read and immediately run files containing assembly language code. It can also read and run MIPS a.out files. SPIM implements almost the entire MIPS assembler-extended instruction set. Other features include a debugger, an X Window interface, a command line interface, a torture test to verify a port to a new machine, and an optional extension that performs a cycle-by-cycle MIPS simulation exposing the hardware pipeline. A source code distribution of SPIM is available. It is written in C and can be compiled and used on most UNIX flavors. A user's manual is available in either PostScript or HTML format.

[http://www.cs.wisc.edu/~larus/spim.html]

 

Spin

A package which supports the formal verification of distributed systems. Spin has been used to trace logical design errors in distributed systems design such as operating systems, data communications protocols, switching systems, concurrent algorithms, railway signaling protocols, etc. It checks the logical consistency of a specification and reports on deadlocks, unspecified receptions, flags incompleteness, race conditions, and unwarranted assumptions about the relative speeds of processes. A design is verified by building a formal model with the Spin input language PROMELA (Process Meta Language). PROMELA contains the primitives for specifying asynchronous (buffered) message passing via channels with arbitrary numbers of message parameters. It also allows for the specification of synchronous message passing systems and mixed systems using both. The language can model dynamically expanding and shrinking systems with new processes and message channels capable of being created and deleted on the fly. Correctness properties can be specified as standard system or process invariants using assertions or as general linear temporal logic requirements. Spin can be used in three basic modes: as a protocol simulator, allowing for rapid prototyping with random, guided, or interactive simulations; as an exhaustive state space analyzer, capable of rigorously proving the validity of user specified correctness requirements; or as a bit-state space analyzer that can validate even very large protocol systems with maximal coverage of the state space (a proof approximation technique).

A source code distribution of Spin is available. It is written in ANSI C and portable to most flavors of UNIX. It is documented in a user's manual, a man page, some research appears, and a book, with all but the latter available in the distribution. See Holzmann (1991).

[http://www.netlib.org/spin/]

 

Spinner

This HTTP server software has been renamed Roxen.

 

splib

The spectral transform library contains programs for a variety of spectral transform functions. It can handle both scalar and 2-D vector fields. Some splib functions are spectral interpolations between two grids, spectral truncations in place on a grid, and basic spectral transforms between grid and wave space. The programs in splib are written in Fortran 77 and are documented internally as well as in a large ASCII document which also contains several example programs. See also iplib.

[ftp://nic.fb4.noaa.gov/pub/nws/nmc/codes/interp/]

 

SPLIB

A library of iterative solvers with preconditioners for rapid prototyping of solvers for nonsymmetric linear systems of equations. SPLIB was primarily developed for comparing iterative methods and preconditioners in a uniformly coded implementation while facilitating interdisciplinary collaboration, although the solvers themselves are also of research interest. It is written in Fortran 77 and can be called as a subroutine from Fortran, C or C++. The number of arguments that have to be passed has been kept as small as possible, and common blocks are avoided except internally. The code is heavily instrumented to provide information such as convergence history, memory usage, and CPU time used. SPLIB implements 13 iterative solvers and 7 preconditioning methods, with the preconditioners including those that allow multiple levels of fill-in through positional and numerical strategies. All preconditioners are parameterized. The iterative methods available are BICG, CGNE, CGNR, CGS, CGSTAB, GMRES, QRMTF, BICGS, GMREST, JACOBI, GAUSS, SOR, and ORTHM. The preconditioners are ILU, MILU, ILUT, SSOR, TRID, ILU0, and ECIMGS.

A source code distribution of SPLIB is available. It is written in Fortran and reasonably portable to most compilers with a tweak or three. It is documented in a user's manual and reference guide available in PostScript format.

[ftp://ftp.cs.indiana.edu/pub/bramley/]

 

SPLIB

This is a set of Fortran routines for spectral methods, efficient tools for recovering accurate approximate solutions to differential equations in terms of high-degree trigonometric or algebraic polynomials. The polynomials bases used in this library include Jacobi, Legendre, Chebyshev, Laguerre and Hermite, and the integration formulas include Gauss, Gauss-Lobatto, and Gauss-Radau. A 180+ page PostScript format manual and reference guide resides in the same directory. [ftp://microian.ian.pv.cnr.it/pub/splib/]

 

spreadsheets

Freely available spreadsheets for Linux platforms are MacroCALC, SIAG, Teapot, VOTE, and xxl.

 

SPX

A system that provides public key based strong authentication for individual users and server principals in a distributed environment. Principals install their SPX credentials and then use SPX to generate authentication tokens to authenticate themselves to remote principals or to decide whether to accept a token received from a remote principal. SPX provides strong authentication with the network utilities flogin, fcp and fsh, all of which permit strongly authenticated remote access. [ftp://ftp.funet.fi/pub/unix/security/login/SPX/]

 

SQRL

A project to build a database full compliant with the ANSI SQL-92 standard. It will also be multi-threaded, written entirely in ANSI C, distributed, and fault tolerant. This is an ongoing project and as of 5/98 is still in the early stages. [http://www.sqrl.org/sqrl/]

 

Squeak

A rapid prototyping environment based on Smalltalk. This was originally creates by the folks at Apple but has been ported to various UNIX platforms by the wonderful folks at INRIA. The Squeak programming environment includes a Smalltalk-80 compiler, a run-time virtual machine, large class libraries, and an interactive development environment. It uses an integral Smalltalk-to-C translator which is used to generate the virtual machine, the source for which is actually written in Smalltalk and then translated and compiled. The features of the Squeak environment include:

• real-time sound and music synthesis written entirely in Smalltalk;
• extensions of BitBlt to handle color of any depth and anti-aliased image rotation and scaling;
• network access support allowing the simple construction of servers and other useful utilities;
• bit-identical running on many platforms;
• a compact object format that requires on a single word of overhead per object;
• a simple and efficient garbage collector for 32-bit direct pointers; and
• efficient bulk-mutation of objects.

Squeak distributions are available for several platforms and operating systems including Linux Intel. Documentation can be found in Smalltalk programming manuals. There are also several online tutorials on how to use the Squeak environment.

[http://www.create.ucsb.edu/squeak/]
[http://squeak.cs.uiuc.edu/ ]

 

Squid

A package which offers high-performance proxy caching for Web clients. Squid supports FTP, Gopher and HTTP requests, and the cache software is more than an order of magnitude faster then the CERN httpd and other popular Internet caches since it never needs to fork (except for FTP), is implemented with non-blocking I/O), keeps meta data and hot objects in virtual memory (VM), and caches DNS lookups. The caches can also be arranged hierarchically for an improvement in reponse times and a reduction in bandwidth usage. The features of Squid include:

• the use of private objects (i.e. objects associated with a single client as opposed to public objects which may be sent to multiple clients simultaneously);
• request resolution in a hierarchy which cuts down on the server load since neighbors and parents are only sent ICP queries for cacheable objects;
• the proper parsing of HTTP reply codes to determine which objects should be cached;
• support for an If-Modified-Since GET;
• access log improvements (e.g. only one log entry per client request with timestamp, elapsed, src-address, type/code, size, method, and URL fields);
• automatic reloading of cache metadata in the background;
• unlinking of swap files on restart and the -U option to remove invalid objects from the disk;
• a more flexible debugging scheme;
• a new access control scheme; changes to cache shutdown;
• using SIGHUP to reconfigure the cache; and
• assigning weights to cache neighbors.

Squid is distributed in source code form and is designed to install and operate on any modern UNIX system including Linux. The documentation, including a user's guide and a FAQ, is currently (4/97) available in ASCII text format.

[http://squid.nlanr.net/Squid/]

 

Relais

A cooperative Web cache which allows faster access to the Web, decreases network usage, and decreases server load. It can cooperate with a number of neighbor caches to group their contents and abilities. This is distributed as a patch to Squid and can be used on any platform on which the latter works. [http://www-sor.inria.fr/projects/relais/relais.html]  

Squirm

A fast and configurable redirector for Squid. The features include virtually no memory usage, re-reading its config files while running by sending a HUP signal, an interactive test mode for checking new configs, full regular expression matching and replacement, config files for patterns and IP addresses, and more. This can be used on any platform on which Squid has been installed. [http://www.senet.com.au/squirm/]

 

SR

Synchronizing Resources is a language for writing concurrent programs. The main language constructs are resources and operations, the former of which encapsulate processes and variables that are shared and the latter of which provide the primary mechanism for process interaction. SR provides a novel integration of the mechanisms for invoking and servicing operations, which means that local and remote procedure calls, rendezvous, message passing, dynamic process creation, multicast, and semaphores are supported, as well as global variables and operations. The implementation consists of a compiler that translates SR to C, a linker that serves as a front-end to ld, and associated other programs and library files. SR runs on one or more networked UNIX machines of the same architecture, with Linux being one of the supported platforms. The primary documentation for SR is contained within a book that must be purchased, although some technical reports about various aspects of SR are also available.

[http://www.cs.arizona.edu/sr/www/index.html]

 

SSA-MTM

The Singular Spectrum Analysis-Multiple Taper Method toolkit is a set of programs that perform detailed spectral analyses and decompositions on an input time series. It contains procedures for: decomposing time series into trends, quasiperiodic and period oscillations, other significant components, and noise; reconstructing the contributions of selected components of the time series; and estimating spectral properties of the time series or any of its components by modern spectral methods. Singular spectral analysis (SSA) is used for separating the various components of the time series. Spectral analysis can be performed via classic Blackman-Tukey correlogram estimation, the multi-taper method (MTM), and the maximum-entropy method (MEM). The numerical programs that comprise the toolkit are: ssa, which performs SSA decomposition of an input time series and reconstruction of selected components; mcssa, performs Monte Carlo tests of SSA against noise; spectrum, computes Blackman-Tukey correlogram and MEM estimates of power spectra; mtm, computes MTM estimates of spectral amplitudes; and carlo, which generates Monte Carlo realizations of white or red noise that resemble a given series. Each program can be used in stand-alone mode as standard UNIX-type commands, and all can be used via a GUI interface called spectra.

A source code distribution of SSA-MTM is available as is a binary distribution for Linux Intel platforms. It is written in Fortran 77 and C and can be compiled and used with the GNU compiler suite. The GUI is written using the Tcl/Tk toolkit. The results can be viewed graphically using either the ACEgr or Gnuplot packages. The package is documented in a user's guide and each program also has a man page.

[http://www.atmos.ucla.edu/tcd/ssa/]

 

ssh

A program that lets you log onto another computer over a network, to execute commands on a remote machine, and to move files from one machine to another. It provides strong authentication and secure communications over insecure channels. It is intended as a complete replacement for rlogin, rsh, rcp and rdist, and can replace telnet in many cases. It uses a packet-based binary protocol and listens on port 22 (which has been officially registered for ssh). The protocol exchanges random session keys using RSA with the rest of the session encrypted using 3DES or some other cipher. The key useed to encrypt the session key is never stored on disk but regenerated every hour with the old key deleted. The features of ssh include:

• strong authentication that closes several security holes (IP, routing, DNS spoofing, etc.) and provides new authentication methods, i.e. .rhosts together with RSA-based host authentication as well as pure RSA authentication;
• automatic and transparent encryption of all communications;
• X11 connection forwarding for secure X11 sessions;
• arbitrary TCP/IP ports that can be redirected over the encrypted channel in both directions;
• client RSA that authenticates the server machine at the beginning of every connection to prevent trojan horses and man-in-the-middle attacks;
• server RSA that authenticates the client machine before accepting .rhosts or /etc/hosts.equiv authentication;
• an authentication agent that can be used to hold the user's RSA authentication keys; and
• multiple convenience features that fix annoying problems with rlogin and rsh.

The source code is available and can be installed on most UNIX variants. Documentation is included in the distribution.

[http://www.cs.hut.fi/ssh/]

 

SSL

The Secure Sockets Layer is a security protocol developed by Netscape and implemented on top of a transport service such as that provided by TCP/IP. It actually consists of two protocols: a record protocol and a handshake protocol. The record protocol deals with fragmentation, compression, data authentication and encryption of messages provided by applications. It provides support for keyed MD5 and SHA for data authentication as well as RC4 and DES for data encryption. The keys used for these tasks are negotiated by the handshake protocol, which deals with the exchange of protocol version numbers and supported cryptographic algorithms as well as mutual authentication and key exchange.

Freely available implementations of the SSL protocols are the official Netscape implementation SSLRef and the third-party SSLeay package. Related software includes sslfd and SSLr.

 

SSLeay

A free implementation of Netscape's SSL, i.e. the software encryption protocol behind the various Netscape products. The encryption algorithms implemented by SSLeay are DES, RSA, RC4, and IDEA. [http://www.psy.uq.edu.au:8080/~ftp/Crypto/]
[http://drachma.varner.com/~mpearce/ssl.html ]
[http://vsys-www.informatik.uni-hamburg.de/others/sslfaq.html ]

 

sslfd

A wrapper library for the SSLeay package which implements the SSLv2 protocol. The sslfd library contains routines useful for adding SSL support to client and server programs, and has been used to add such support to telnet, rshd, and ftp programs. See the related SSLr package. [http://www.quick.com.au/ftp/pub/sjg/help/sslfd.html]

 

SSLr

A package which implements the standard BSD r* commands (e.g. rlogin, rsh, etc.) on top of the SSLeay library. The server program SSLrshd requires a client to supply a certificate to access any of the services. The available clients include SSLrsh, SSLrcp and SSLrdist. [http://www.quick.com.au/ftp/pub/sjg/help/SSLrsh.html]

 

SSLRef

A Netscape reference implementation of the SSL security protocols. [http://home.netscape.com/newsref/std/sslref.html]

 

SSORT

A set of Fortran 77 subroutines for the fast in-core sorting of real arrays (SSORT), integer arrays (ISORT), and character strings (CSORT). These are available as Fortran source code and are documented in comment statements within each source code file. This is part of CMLIB. [http://sunsite.doc.ic.ac.uk/public/computing/general/statlib/cmlib/]

 

SSSHMM

The Successive State Splitting with Hidden Markov Method is a program for optimizing hidden Markov networks using the same expectation maximization criteria as HMM learning. It features an HMM engine which controls HMM (i.e. Viterbi) learning, a network generator which generates a new network by splitting the chosen state, a network tester the evaluate the efficiency of the splitting and to determine which state to split and when to stop the algorithm, and a GUI monitor which shows the network shape as well as output and transition probabilities. A source code distribution of SSSHMM is available. It is written in C and requires the Motif library for the GUI component. A brief manual is ASCII format is available. This software is part of the ICOT project.

[http://www.icot.or.jp/AITEC/IFS/IFS-abst/097.html]

 

Ssystem

A solar system simulator that uses the OpenGL library. Ssystem includes the Sun, the planets, a few of the major satellites, and the background stars. Positions are not 100% accurate but within reasonable range of the actual posiitions on a given date. The camera can be freely moved and can be pointed at any planet or other position desired. Versions of Ssystem are available for Linux and Windows 95, with a source code version available for the former. The Linux version requires the Mesa 2.6 OpenGL clone.

[http://www1.las.es/~amil/ssystem/]

 

Stalin

The STAtic Language ImplementatioN is a compiler for Scheme. It is designed to be generate extremely efficient executable images for application delivery or production research runs. Stalin is a batch mode compiler which compiles a single Scheme source file into an executable image, although it does this indirectly via C. The executable has equivalent run-time semantics to loading the Scheme source file into an interpreter and then terminating its execution. The major limitation is that it is not possible to LOAD or EVAL new expressions or procedure definitions into a running program after compilation, although this is traded off for substantial global compile-time analysis of the source program. The strategies used for generating efficient code include: global static type analysis using a soft type system that supports recursive union types, a strategy that reduces and often eliminates run-time type checking and dispatching; low-level representation selection on a per-expression basis which allows the use of unboxed base machine data representations for all monomorphic types; global static life-time analysis for all allocated data which allows much temporary allocated storage to be reclaimed without garbage collection; and very efficient strategies for compiling closures.

A source code distribution of Stalin is available. It is written in Scheme and is currently (5/97) compiled with Scheme-to-C. It is documented in a long README file included in the distribution.

[http://www.neci.nj.nec.com/homepages/qobi/software.html]

 

Standard ML

One of the ML family of languages. One implementation is SML/NJ. [http://foxnet.cs.cmu.edu/sml.html]

 

Stanford GraphBase

A collection of programs which demonstrate the art of literate programming while offering state-of-the-art explanations of many important algorithms and data structures. They also define a workbench for combinatorial computing and offer a collection of standard sets of data which can be used for benchmark tests. The use of these programs requires the installation of CWEB. The collection is described and detailed in Knuth (1993) and is freely available at the given URL. Hundreds of additional programs which use the Stanford GraphBase will be made available as a supplement to Volume 4 of Knuth's The Art of Computer Programming series.

[ftp://labrea.stanford.edu/pub/sgb/]
[http://tug2.cs.umb.edu/ctan/tex-archive/support/graphbase/ ]

 

STAP

An interactive command line driven plotting program with the capability of performing simple statistical and data analysis procedures. It is based on the PGPLOT graphics library and the Numerical Recipes routines. [http://www.astro.wisc.edu/~han/stap/stap.html]

 

STAPLOT

A library of Matlab programs (m-files) designed to facilitate the analysis of oceanographic data during and after a cruise via a graphical user interface. The features include:

• station memory which allows them to be color-code by cruise, location, a property minimum and maximum, or by any other chosen attribute;
• the ability to add new user-defined properties at any time during a session (and save them from session to session);
• polar projections and 10-minute bathymetry/topography at 10 to 10000 meters available from within Matlab;
• the selection of stations by any property and property range;
• specification of a large number of user options which can be changed and saved for each cruise or data set;
• contouring of irregularly sampled data; and
• the automatic recalculation of distance between selected stations.

[ftp://grayling.umeoce.maine.edu/pub/staintro.html]

 

Starlink Project

A project established in 1980 to help astronomers use computers to analyze their observations. It consists of a network of computers used by UK astronomers, a collection of software to reduce and analyze astronomical data as well as to work on some types of theory, and a team of people offering hardware, software, and administrative support. The objectives of the project are to provide and coordinate interactive data reduction and analysis facilities for use as a research tool by UK astronomers, encourage software sharing and standardization to prevent unnecessary duplication of effort, and provide systems software support for astronomers. The main software product offered by the Project is the Starlink Software Collection (SSC) which consists of about 120 items divided into 40 packages, 40 utilities, and 40 subroutine libraries. Much of the software is available and can be obtained via the Web. It is divided into three general categories: applications and user interfaces, utilities, and libraries. Source code distributions are available for most packages as are binary versions for Linux Intel platforms.

The applications and user interface packages include:

• CCDPACK, for processing and reducing CCD-like data;
• CONVERT, for converting data files between Starlink Project format and other common data formats;
• CURSA, for manipulating astronomical catalogues and other tabular datasets;
• DAOPHOT, a stellar photometry package for dealing with crowded fields;
• DIPSO, a plotting package incorporating basic astronomical applications;
• ECHOMOP, for extracting spectra from 2-D data frames;
• ESP, for determining the photometric properties of galaxies and other extended objects;
• FIGARO, a general purpose reduction package for a wide range of images and spectra;
• GAIA, for displaying images;
• IRCAMPACK, for processing IRCAM data;
• IUEDR, which provides facilities for the reduction of IUE data;
• KAPPA, a general purpose package with over 180 programs for image processing, data visualization, and data manipulation;
• PERIOD, for searching for periodicities in data via time series analysis;
• PHOTOM, for measuring the sky corrected magnitudes and fluxes of astronomical objects within circular and elliptical apertures;
• PISA, for locating and parameterizing objects on an image frame;
• POLMAP, for the interactive data analysis of linear spectropolarimetric data;
• PONGO, for interactively plotting data;
• SAOimage, an astronomical image display program;
• SPECDRE, a package for spectroscopy data reduction; and
• TSP, for handling time series and polarimetric data.

Most of these applications can be used either from a UNIX shell or within the Starlink ICL (Interactive Command Language).

[http://star-www.rl.ac.uk/]

 

star

The fastest known implementation of a tar-like archiver. It can make backups at more than 12 MB/s if the disk and tape drive support it. The features of star include: a fifo that keeps the tape streaming, a pattern matcher to control the list of files to be processed, a sophisticated diff command, no limitations on filename lengths, automatic recognition of the type of archive so it can handle other archive types in their native mode, and automatic recognition and handlingof byte-swapped archives. A source code distribution of star is available. It is written in C and can be compiled on most UNIX platforms.

[http://www.fokus.gmd.de/nthp/employees/schilling/index.html]

 

Starlab

A package for simulating the evolution of dense stellar systems and analyzing the resulting output. It comprises a collection of loosely coupled programs which, in the traditional UNIX style, can be combined in arbitrarily complex ways to study the dynamics of star clusters and galactic nuclei. A novel feature of Starlab is a flexible external data representation scheme which guarantees that tools can be combined without loss of data or internal comments. The package consists of several modules containing:

• three- and four-body automated scattering packages constructed around a time-symmetrized Hermite integration scheme;
• a collection of initialization and analysis routines for use with general N-body systems;
• a general Kepler package for the manipulation of two-body orbits;
• N-body integrators incorporating both 2nd-order leapfrog and 4th-order Hermite integration algorithms; and
• a general N-body integrator called Kira which incorporates recursive coordinate transformations, allowing the uniform treatment of hierarchical systems of arbitrary complexity with the general N-body framework.

A source code distribution of Starlab is available. It can be compiled and installed on most generic UNIX systems. It is documented in a user's manual available in PostScript format.

[http://www.sns.ias.edu/~starlab/starlab.html]

 

STARPAC

The Standards Time Series And Regression PACkage (which was available in an earlier version called STATLIB) is a portable library of approximately 150 user-callable Fortran routines for statistical analysis originally developed at the NIST. It contains routines for normal random number generation, univariate sampling, one-way analysis of variance, correlation analysis, linear least squares, nonlinear least squares, digital filtering, complex demodulation, correlation analysis, spectrum analysis, and time series analysis. The Fortran 77 source code is available. The documentation is contained within a large ASCII document that prints out to well over 200 pages.

[http://www.scd.ucar.edu/softlib/STARPAC.html]

 

StarSplatter

A package for creating images and animations from astrophysical particle simulation data. StarSplatter renders collections of particles as Gaussian blobs or (more colorfully) splats. The position, color, opacity and size of each splat are controlled by the particle and bunch properties, with bunch properties being position, color, density, and scale length. The scale length provides a length scale for the exponential decay of bunches in the final image. A camera is used to define a viewpoint for looking at all of the particles, and a renderer is used to transform the camera and particle information into a final image. The features of the renderer include the anti-aliasing of points which produces good visual results even with very small particles. This is designed to work with the TIPSY package. A source code distribution of StarSplatter is available. It is written in C++ and |it Tcl and should compile and installed on most UNIX flavors with this software. Makefiles are provided for several platforms but not for Linux Intel, although one can be created fairly easily. A user's manual is provided in several formats.

[http://www.psc.edu/Packages/StarSplatter_Home/]

 

StarTeX

A typesetting system built on top of TeX. Starter TeX is designed to help students typeset reports, essays, and similar small documents quickly and easily, and as such hides many of the gory details behind an interface suited for those with little previous knowledge of document processing tools. It is also designed to be more robust, i.e. be more forgiving of various errors. [http://tug2.cs.umb.edu/ctan/tex-archive/macros/startex/]

 

statistics

Good places to search for statistical software are the Statistics and Statistical Graphics Resources site, the Guide to Statistical Computing Resources on the Internet , the Statistics on the Web site, and the Statistics Related Links at Duke University. Repositories for statistical software and other resources are Statlib, GASP (Globally Accessible Statistical Procedures), and the Geostatistics Web Site .  

Statlib

A repository for many megabytes of various types and sizes of statistical software, data, etc. [http://lib.stat.cmu.edu/]  

STATTAB

A package of Fortran routines that calculates cumulative functions, their inverses, and parameters of the following distributions: incomplete beta, binomial, negative binomial, chi-square, non-central chi-square, variance ratio-f, non-central f, incomplete gamma, normal, Poisson and t. Additionally, when normal or t cdfs are being computed, it calculates the associated two-sided p-value. The probability of exactly n events is calculated and printed with the cumulative distribution for the binomial and Poisson distributions. The distribution includes the source code and a 50+ page user's manual in ASCII format. [http://www.stat.cmu.edu/general/Utexas/]

 

STBasic

A structured BASIC interpreter which uses the program and data structures of Chipmunk Basic, an example program included in the p2c translator. It also uses the graphics routines from SGRP and the functionality of GFA-BASIC on Atari ST (i.e. basically GFA-BASIC ported to UNIX). The package includes the source and a binary distribution for Linux Intel programs. Installation from source requires the prior installation of p2c and SGRP, with both already included in the binary distribution.

[ftp://ftp.hrz.uni-kassel.de/pub5/linux/misc/stbasic09/]

 

Stella

A multi-platform Atari 2600 emulator for Linux, DOS, OS/2, Power Macs, UNIX/X, and Windows NT/95 platforms. There is a binary distribution for each platform which includes three 2600 ROM images (i.e. .BIN files): a test program, a game called Elk Attack, and a game called Okie Dokie. The ROM images from the Atari 2600 Action Packs by Activision can also be used with Stella. [http://www.classicgaming.com/stella/]

 

s3

The Stochastic Spatial Simulator is a package for the interactive exploration of particle systems on one and two dimensional grids with at most eight states at each site. It offers a number of built-in models which can be simulated from a variety of initial states. It is also designed for easy extensibility, i.e. new models can easily be added by writing C code which describes the simulation loop and then adding the name of that model to a parameter structure. The source code for s3 is available. It is written in C and can be compiled and used on generic UNIX/X11 platforms. An additional package containing user-contribed code is also available at the site. The documentation includes an installation manual and a tutorial.

[http://gumby.syr.edu/]

 

STIL

SGML Transformations In Lisp is a style sheet language with which you can build structure-controlled applications. It builds an abstract tree representation of an SGML document instance and allows you to express transformations using STIL functions. STIL is a superset of Common Lisp enriched by a set of constructs targeted for this task domain which can be used for manipulating the structure of an SGML document instance by accessing both the markup and the data. The source code for STIL is available. It is a CLOS application written in Common Lisp and requires both CLISP and sgmls for compilation and use. The package is documented in a 20+ page user's manual available in PostScript format. See also sdc.

[ftp://ftp.th-darmstadt.de/pub/text/sgml/stil/]

 

STk

A Scheme interpreter that can access the Tk graphical tools package. This can be seen as the Tk package where the Tcl language has been replaced by Scheme, and where a full object oriented system called STKlos (related to CLOS and Dylan) is also provided. The features of STk include:

• an interpreter that conforms to R4RS with some additions from R5RS such as multiple values and dynamic-wind;
• an extensive object-oriented system called STklos with multiple inheritance, generic functions, multi methods, and a Meta Object Protocol;
• extension of the interpreter via adding C modules;
• availability of all commands in Tk to the interpreter;
• callbacks in a GUI are Scheme closures;
• support for Tk 8.0;
• Tcl interpreter not used when using Tk widgets;
• a set of STklos classes have been defined to manipulate Tk commands as STklos objects; and
• building new widgets in Scheme by composition of existing widgets.

A source code distribution of STk is available. It has been successfully installed on several platforms including Linux Intel. Binaries are also available for Linux Intel platforms. Documentation includes a reference manual and a FAQ, both of which are available in several formats.

[http://kaolin.unice.fr/]

 

STL

The Standard Template Library is a C++ library that provides a set of easily composable C++ container classes and generic algorithms (i.e. template functions). The container classes include vectors, lists, deques, sets, multisets, maps, multimaps, stacks, queues, and priority queues, while the algorithms include many fundamental algorithms for the most common types of data manipulations, e.g. searching, sorting, merging, copying, and transforming. The ANSI/ISO C++ Standards Committee voted in July 1994 to adopt the STL as part of the standard C++ library. The GNU libg++ has included a patched version of the HP STL since version 2.6.2 although it reportedly didn't become truly usable until 2.7.0 and later versions. An SGI STL port by Boris Fomitchev is also reported to work with version 2.7.2. Several online tutorials with many examples are available via links at the given URLs. See Glass and Schuchert (1996), Ladd (1996), Musser and Saini (1996), and Nelson (1995).

[http://www.cs.rpi.edu/projects/STL/stl-new-sav/stl-new.html]
[http://www-leland.stanford.edu/~iburrell/cpp/stl.html ]
[http://math.nist.gov/tnt/stl.html ]
[http://www.cs.rpi.edu/~musser/stl.html ]

 

STLport

A project whose goal is to make the SGI STL implementation usable with most compilers while retaining full functionality. The main non-portability issue fixed is the default template class parameters for containers, although several other smaller problems are being smoothed over. Several extensions have also been added to ease the task of porting STL to the range of available C++ compilers. A source code distribution of STLport is available which has been successfully compiled and tested using a test suite on a wide range of compilers including GCC 2.7.2 and egcs. Documentation can be found on the site.

[http://www.metabyte.com/~fbp/stl/effort.html]

 

STonX

An Atari ST emulator for UNIX/X11 platforms. The features include: MC68000 CPU emulation, 4 or 14 Mb RAM, color or monochrome graphics modes, YM2149 sound chip emulation, IKBD, BIOS-level disk routines, a bootable UNIX filesystem interface, FDC emulation complete enough to run some games, emulation of serial and parallel ports, a VDI driver for Xlib, use of either an X Window or SVGAlib with Linux, and more. A source code distribution is available. [http://www.complang.tuwien.ac.at/nino/stonx.html]

 

Stony Brook Algorithm Repository

A comprehensive collection of algorithm implementations of eighty of the most fundamental problems in combinatorial algorithms. The problem taxonomy, implementations, and supporting material are drawn from Skiena (1997). The site provides implementations of useful algorithms via either links to sites that have them or local copies. The implementations for each type of problem are rated according to usefulness on a scale of 1 through 10, with usefulness defined as how likely it is that someone lookin for code will be happy with what they find. The author invite feedback on their ratings. The problems are classified by category (e.g. data structures, numerical problems, combinatorial problems, graphic problems in polynomial time, graph problems in exponential time, computational geometry, and set and string problems) and also by the computer language in which they are implemented.

[http://www.cs.sunysb.edu/~algorith/]

 

Stow

A GNU program for managing the installation of software packages. It enables packages to be kept separate while making them appear to be installed in the same place. Historically this has been a difficult task because of the need to administer, upgrade, install, and remove files in independent packages without confusing them with other files sharing the same filesystem space. The approach used in Stow is to install each package into its own tree and then use symbolic links to make it appear as though the files are installed in a common tree. This allows administration to be performed in the package's private tree with Stow being used to update the symbolic links. Stow was inspired by Depot but is much simpler, e.g. no database files are needed. A source code distribution of Stow is available. It is a Perl script which should run correctly under either version 4 or 5. A manual is available in the usual formats.

[http://www.gnu.org/software/stow/stow.html]

 

Strata

A stratigraphic modeling package designed for simulating the evolution of sedimentary ocean basins. The key assumption used by this model is that sediment transport behaves diffusively, with the sediment source proportional to water depth for carbonate simulations and a user-specified function for clastic simulations. It also has the capability of predicting the seismic response of a modeled basin since the density and sound velocity of all parts of the basin can be determined. The strata package consists of four programs:

• setbasin, for setting model parameters;
• simbasin, for running the model with the assigned parameters;
• plotbasin, for plotting results; and
• filmbasin, for creating animations of series of results.

The controlling variables set with the setbasin program are divided into several parameter groups including measures, ages, clastics, carbonates, sealevel, subsidence, compaction, and heat flow groups. The details of the parameters within each group include:

• measures - for setting total width, spatial divisions, total time, temporal divisions, and timelines for saving the simulation state at regular intervals;
• ages - for setting increments at which time slices should be saved or for saving individual slices;
• clastics - for defining the diffusion constant k for various materials as well as the pelagic sedimentation rate;
• carbonates - for setting parameters concerning calcium carbonate sedimentation including both epeiric and oceanic sedimentation algorithms and the rate constants for each;
• sealevel - for defining the eustatic curve in varying amounts of detail;
• subsidence - for setting the subsidence rate, type of profile (e.g. cratonic, foreland, or passive), isostatic compensation, flexural rigidity, and densities of the various materials;
• compaction - for determining whether compaction occurs and, if so, defining the decay constants, porosities, and whether erosion will affect it; and
• heat flow - for setting the heat flow constant in the steady state vertical thermal equation as well as the boundary temperatures and the thermal conductivities of the various materials.

A source code distribution of Strata is available under the GPL. It can be compiled and used on most generic UNIX/X11 platforms. It is documented in a user's guide as well as in several technical publications.

[http://hydro.geosc.psu.edu/Sed_html/strata_front_page.html]

 

Streamer

A radiative transfer model that can be used for computing either radiances (intensities) or irradiances (fluxes) for a wide variety of atmospheric and surface conditions. The features of Streamer include: computing fluxes using two or more either broad or narrow band streams; the use of DISORT for more than two streams; computation of radiances for any polar and azimuth angle using four or more streams; computation of upwelling and downwelling shortwave and longwave, net fluxes, cloud forcing, and heating rates; parameterization of 24 shortwave and 105 longwave absorption bands for various gases and overlapping gases and clouds; built-in atmospheric data including water and ice cloud optical properties, five aerosol optical models, four aerosol vertical profiles, and seven standard atmospheric profiles; computations performed on scenes consisting of a mixture of up to 10 cloud types occurring individually, up to 10 overlapping cloud sets of up to 10 clouds each, and clear sky (with all over some combination of up to three surface types); inclusion of spectral albedo data for open ocean, meltponds, bare ice, snow, green vegetation, and dry sand; and a user interface providing a looping structure for up to ten variables at a time.

A source code distribution of Streamer is available. It is written in Fortran for UNIX platforms. It is documented in a user's guide available in PostScript format.

[ftp://stratus.bu.edu/pub/streamer/]

 

STRIPE

A tool that converts a polygonal model into triangle strips to speed up rendering time. [http://www.cs.sunysb.edu/~evans/stripe.html]

 

Strn

Scan trn is a news reader based on trn. It contains all of the features of trn and adds several capabilities including: a newsgroup browser, virtual newsgroups, scoring/rating of articles, and easy configuration menus. [ftp://ftp.uu.net/.vol/10/news/readers/trn/strn/]

 

Studio

A sound editing tool which enables recording, playback, and simple cut and paste editing of sound files in diverse formats on a Linux PC with the OSS sound drivers. Studio is a Tcl/Tk application. [http://www.elec-eng.leeds.ac.uk/staff/een6njb/Software/Studio/screens.html]

 

STSDAS

A system for reducing and analyzing data from the Hubble Space Telescope. This runs in and requires the IRAF environment. [http://ra.stsci.edu/]

 

SU

Seismic Unix is a self-contained software environment for seismic research and data processing used by exploration geophysicists, earthquake seismologists, environmental engineers, software developers and others. It provides a standard environment for the testing of new processing algorithms. It is easy to use because it does not require learning a special language-its application uses only the standard facilities afforded by the UNIX operating system. Once UNIX shell-redirecting and pipes are mastered, there is no further artificial language to learn. The seismic commands and options can be used as readily as other UNIX commands. In particular, the user can write ordinary UNIX shell scripts to combine frequent command combinations into meta-commands (i.e., processing flows). These scripts can be thought of as ``job files.'' SU has a layered structure consisting of:

• cwp, a library of scientific routines (e.g. FFT routines) written in C as well as utility programs and shells;
• par, a library supporting the CWP programming style (e.g. self-documentation, error reporting, parameter passing, etc.); and
• su, seismic processing codes that use a standard SEG-Y trace structure.

There are also codes the buffer the graphics routines of PSPLOT, xplot, and Xtcwp, an internal X Window based graphics package. Some of the more common processing programs compute autocorrelations, gain, normal-moveout corrections, prediction error filtering, velocity analysis, and much more.

The source code to SU, written in ANSI C, is available and should compile successfully on almost any generic UNIX platform with a C compiler. The documentation is contained within a user's manual available in both HTML and PostScript formats. A version of this package called DSU that runs on a network of workstations is also available.

[http://timna.Mines.EDU/cwpcodes/]

 

SubArctic

A Java-based user interface construction toolkit. SubArctic is a complete, full-functioned, industrial strength toolkit designed to provide a solution to all user interface needs. It is based on 10 years of research and designed to offer advanced techniques that go beyond static interfaces and simple collections of widgets. As such is is highly extensible and supports a number of sophisticated effects not available in other toolkits. The features of SubArctic include: support for sophisticated drawing effects which can be applied to all interface elements; animation support based on a high-level path model with controlled timing; facilities for semantic snapping interactions; provision for standard and custom interactor (widget) styles that can be dynamically switched; support for semantic lens interactions; a full-functioned interactor library with the usual buttons, check boxes, and sliders along with more sophisticated techniques supporting dragging, snapping, lenses, and animation; techniques which support interactive interface debugging; a built-in, efficient, and easy to use constraint evaluator for support of flexible dynamic layouts; and a well-developed and carefully designed infrastructure for extensibility at all levels.

A distribution of SubArctic which contains both source and executables is available. The documentation includes a user's manual, a JavaDoc for the API, and a source code guide.

[http://www.cc.gatech.edu/gvu/ui/sub_arctic/]

 

SUDSODS

A set of Fortran 77 routines for the solution of overdetermined and underdetermined systems of linear algebraic equations. The SODS routine solves an overdetermined system of linear equations AX=B where A is M by N with M$\ge$N. If the rank of A equals N then X is the unique least squares solution vector, and if it is less than N then the least squares solution of minimal length can be provided. The SUDS routine solves an underdetermined system of linear equations AZ=B where A is M by N with M$\le$N. If the rank of A equals I then a vector X and a matrix U are determined such that X is the unique solution of smallest length. If the system of equations aren't compatible then only the least squares solution of minimal length is computed. A source code distribution of SUDSODS is available. The routines are written in Fortran 77 and documented via comment statements contained within each source code file. This is part of CMLIB.

[http://sunsite.doc.ic.ac.uk/public/computing/general/statlib/cmlib/]

 

SUGAL

A genetic algorithm package featuring a wide range of operators and datatypes. SUGAL was designed with particular emphasis on making it easy to extend and configure without having to modify the existing source code. [http://www.trajan-software.demon.co.uk/sugal.htm]

 

SUMMA

The Scalable Universal Matrix Multiplication Algorithm is a straightforward, highly efficient, and scalable implementation of common matrix multiplication operations. The algorithms are simpler than previously published methods, yield better performance, and require less work space. An implementation written in C for use with MPI is available in source code format. [http://www.cs.utexas.edu/users/rvdg/software.html]

 

Super Delaunay

A fully dynamic constrained Delaunay triangulation engine with which triangulations can be created point by point, e.g. individual points can be inserted or deleted at any time during the process and the triangulation will be dynamically changed. The features of SD include:

• inserting or deleting points from a triangulation by coordinates or reference number;
• creating or deleting constraints in a triangulation (from existing points or not);
• flipping triangles where the common edge becomes a constraint;
• saving the result in different formats including DXF, Inventor, 3DS, POV, ASCII and VRML;
• locating points in a triangulation, i.e. returning a triangle given coordinates; and
• defining specific areas with which to work.

SD is an ANSI C library providing the above functionality for 2-D triangulation. It is available in binary format for several platforms including Linux Intel by contacting the author at an address given at the site.

[http://www.dlc.fi/~dkpa/]

 

SuperLU

A set of subroutines to solve a sparse linear system. It implements Gaussian elimination with partial pivoting, and is currently the fastest algorithm available for a variety of problems. SuperLU is written in C and supplies a version of BLAS in C, but to maximize performance an optimimzed BLAS is recommended. A real version is currently available with a complex version in the works. The source code is available along with a users guide. [ftp://ftp.cs.berkeley.edu/pub/lapack/SuperLU/]
[http://HTTP.CS.Berkeley.EDU/~xiaoye/superlu.html ]

 

Surface Evolver

An interactive program for the study of surfaces shaped by surface tension and other energies and subject to various constraints. A surface is implemented as a simplicial complex, i.e. a union of triangles. An initial surface is defined in a data file and the Evolver evolves the surface toward minimal energy via a gradient descent method. The aim can be to find a minimal energy surface configuration or to model the process of evolution by mean curvature. The energy can be a combination of surface tension, gravitational energy, squared mean curvature, user-defined surface integrals, or knot energies. The Evolver can handle arbitrary topology, volume constraints, boundary constraints, boundary contact angles, prescribed mean curvature, crystalline integrands, gravity, and constraints expressed as surface integrals. Surfaces can be interactively modified to change their properties or to keep their evolution well-behaved. It was written for 1- or 2-D surfaces but can also do higher dimensions with some restrictions on available features. The Surface Evolver is available for UNIX, Windows 95 or NT, MS-DOS, NeXT, and Macintosh systems. On UNIX systems graphics are handled by means of an X Window System interface or by an interface to the Geomview package. The 150 page user's manual is available in both PostScript and HTML formats. Versions of the Evolver are also available which use either the MPI or PVM packages for distributed parallel processing. See Brakke (1992).

[http://www.geom.umn.edu/software/evolver/]

 

SurfIt

This has been renamed Plume.

 

SUSAN

The Smallest Univalue Segment Assimilating Nucleus is a program containing algorithms for image noise filtering, edge finding, and corner finding. In the SUSAN principle a circular mask with a center pixel called a nucleus is placed on images consisting of light and dark patterns. The brightness of each pixel within the mask is compared to that of the nucleus to define an area with a brightness similar to that of the nucleus, with this area known as the USAN. 2-D features and edges can then be detected from the size, centroid, and second moments of the USAN, with no image derivatives or noise reduction required as in most other algorithms. The USAN area is at a maximum when the nucleus lies in a flat region, falls to half of the maximum very near a straight edge, and falls even further when inside a corner. This gives rise to the SUSAN principle wherein an image processed to give as output inverted USAN area has edges and 2-D features strongly enhanced, with 2-D features enhanced more strongly than edges. The noise reduction algorithm is related to the SUSAN principle in that the USAN is used to choose the best local smoothing neighborhood. A source code distribution of SUSAN is available. It is a single self-contained C program which inputs and outputs PGM format images of any size, performing any of the three SUSAN algorithms. The use of the program is documented in comment statements within the code as well as in several technical reports available online.

[http://www.fmrib.ox.ac.uk/~steve/]

 

Sutra

A collection of visualization programs built on top of the Karma package. The programs include:

• xray and krot for the volume rendering of data cubes;
• kview and kubes to play movies of data cubes as well as inspect two cubes at the same time;
• kslice_3d for slicing a cube;
• ksnow and ktrek for rendering or flying through tabular data;
• cube2mpeg for compressing movies to MPEG format;
• khuei for superposing images;
• kpvslice for the interactive selection of position-velocity slices;
• krenzo for interactive renzograms; and
• koords for interactive coordinate placement.

Much of this package requires only the same basic system as does the Karma package, i.e. a generic UNIX/X11 platform, although special hardware may be required for a few programs. The package is documented in a user's manual available in PostScript format. It appears that this is slowly being absorbed into the Karma package.

[http://www.atnf.csiro.au/computing/software/visualisation/]

 

SUTRA

A finite element simulation model for saturated or unsaturated, variable density ground water flow with energy or chemically reactive single species solute transport. SUTRA can be used to areal and cross-sectional modeling of saturated ground water flow systems as well as for cross-sectional modeling of unsaturated zone flow. Solute transport can be used to model natural or man-induced chemical species transport including the processes of solute sorption and production and decay. Groundwater contaminant transport problems and aquifer restoration designs can also be analyzed. The solute transport capabilities can also be used for modeling variable density leachate movement and the cross-sectional modeling of saltwater intrusion in aquifers on near-well or regional scales with either dispersed or relatively sharp transition zones between freshwater and saltwater. The energy transport simulation capabilities can be used to model thermal regimes in aquifers, subsurface heat conduction, aquifer thermal energy storage systems, geothermal reservoirs, thermal pollution of aquifers, and natural hydrogeologic convection systems. The SUTRA model uses a 2-D hybrid finite element and integrated finite difference method to approximate the governing equations describing the processes simulated, i.e. fluid density-dependent saturated or unsaturated groundwater flow and transport of either solute or thermal energy in the groundwater.

A source code distribution of SUTRA for UNIX platforms is available. The primary documentation is contained within Voss (1984). This is part of the USGS Water Resources Applications Software collection.

[http://water.usgs.gov/software/sutra.html]
[http://www.geogr.uni-jena.de/software/sutra.html ]

 

SVDPACK

The Singular Value Decomposition PACKage consists of four numerical (iterative) methods for computing the singular value decomposition (SVD) of large sparse matrices using double precision ANSI Fortran 77. A compatible ANSI-C version (SVDPACKC) is also available. This software package implements Lanczos and subspace iteration-based methods for determining several of the largest singular triplets (singular values and corresponding left- and right-singular vectors) for large sparse matrices. The package has been ported to a variety of machines ranging from supercomputers to workstations: CRAY Y-MP, CRAY-2S, Alliant FX/80, SPARCstation 10, IBM RS/6000-550, DEC 5000-100, and HP 9000-750. The development of SVDPACK wa motivated by the need to compute large rank approximations to sparse term-document matrices from information retrieval applications. Future updates to SVDPACK(C), will include out-of-core updating strategies, which can be used, for example, to handle extremely large sparse matrices (on the order of a million rows or columns) associated with extremely large databases in query-based information retrieval applications. See Berry (1992). [http://www.netlib.org/svdpack/index.html]

 

SVGAGUI

A library for the creation of GUIs which will work with both SVGAlib and Xlib. The available objects include buttons (normal, light, pixmap, check, and radio), sliders (vertical, horizontal, nice horizontal and vertical, and nice value), image, browser, pulldown, text (normal and embossed), numbers (normal and digital), input (normal, float, and integer), and more. [http://rulhmpc38.leidenuniv.nl/private/multitrack/svgagui.html]

 

SVGALIB

A low-level graphics library for Linux platforms. SVGALIB was originally based on VGAlib 1.2, but has been greatly extended to support many more chipsets. It supports transparent virtual console switching, i.e. you can switch consoles to and from text and graphics mode consoles with just a keystroke. It includes code to hunt for a free virtual console on its own in case it is not being started from one, i.e. from over a network or within screen or xterm. When it is used by a program at runtime, the chipset is first detected and then the appropriate driver is used, thus enabling the graphics program to work on any card supported by SVGALIB if the mode it uses is supported by the chipset driver for that card. A source code distribution of SVGALIB is available which can be easily configured and compiled on Linux Intel systems. Documentation consists of some ASCII text files and an extensive set of man pages for the available library calls.

[http://www.sunsite.unc.edu/pub/Linux/libs/graphics/]

 

SVGATextMode

This uses extra features found in all SVGA video cards to enhance Linux text modes independently of what the BIOS can do. It is configured with an XF86Config-like file, and allows setting of pixel clock, H/V timings, font size, cursor size, etc. It enables using the video card AND the monitor to their full potential in textmode, as in the X Window system. [http://sunsite.unc.edu/pub/Linux/utils/console/]

 

SVMlight

A implementation of Support Vector Machines in C. SVMs are used in pattern recognition problems such as text classification. The features of SVMlight include a fast optimization algorithm, handling several thousands of support vectors, handling several tens of thousands of training examples, support for standard kernel functions as well as the capability of defining your own, and use of sparse vector representation. The source code is available as are binaries for Sun SunOS and Solaris and Linux Intel. Documentation is contained within a man page as well as in some technical reports.

[http://www-ai.informatik.uni-dortmund.de/FORSCHUNG/VERFAHREN/SVM_LIGHT/svm_light.eng.html]

 

Swarm

A software package for multi-agent simulation of complex systems intended to be a useful tool for researchers in a variety of disciplines, especially artificial life. The basic Swarm architecture, in which a large variety of agent-based models can be implemented, is the simulation of collections of concurrently interacting agents. The package provides object-oriented libraries of reusable components for building models and analyzing, displaying, and controlling experiments on those models. The Swarm libraries can be divided into three main categories: simulation, software support, and model specific libraries. The simulation libraries are further divided into: a swarmobject library which contains the core classes upon which agents in Swarm models are based; an activity library containing the heart of the simulation mechanism, i.e. the scheduling data structures and execution support; and the simtools library which is a miscellaneous collection of classes needed to build simulations, e.g. classes to control the execution of the entire simulation apparattus and classes for data analysis and display support. The software support libraries were written to support modeling but could also have applications beyond simulation, i.e. they encapsulate the basic engineering tasks needed to write effective software. The include general purpose tools for building object-oriented programs, a random number class, and a graphical interface library. The model specific libraries are those that are used for particular modeling domains, e.g. libraries for two-dimensional spaces, genetic algorithms, and neural networks.

The source code for the Swarm software is available as are binaries for some platforms (including Linux). It is written in GNU Objective C and the X Window system. It also requires the Tcl/Tk software. There is quite of bit of documentation available in PostScript and HTML format.

[http://www.santafe.edu/projects/swarm/]

 

SWB

See Scientist's Workbench.

 

SWIG

The Simplified Wrapper and Interface Generator is a tool for scientists and programmers to use to integrate common interface languages such as Tcl/Tk, Perl, Python and Guile with programs containing collections of functions written in C or C++. SWIG automates the process of writing highly specialized wrapper codes for each language and makes it easy to extend an interface language without having to worry about the nasty details. SWIG was developed to provide a system that would make it easy to put together interesting applications involving numerical simulation, data analysis, and visualization without having to worry about tedious systems programming or making substantial modifications to existing code. Applications of SWIG include simplified user interface programming, extremely rapid prototyping, improving debugging and testing, better performance (i.e. functions can be written in C instead of Tcl, Perl, etc.), and development of language independent applications. SWIG is used by first creating an interface file containing C style declarations of functions, variables and constants that you want to build into a user interface. Next a parser takes this file and converts it into an internal representation, which is passed to a code generation module which produces C code and a documentation module supporting ACII, LaTeX, and HTML. Each module is implemented as a collection of C++ classes which simplifies the process of supporting new languages and allows the user to expand the system.

The SWIG source code is available and can be compiled and installed on generic UNIX boxes with an ANSI C compiler, e.g. GCC. The documentation is contained within a 50+ page users guide available in PostScript and ASCII formats.

[http://www.cs.utah.edu/~beazley/SWIG/]

 

SWI-Prolog

A Prolog compiler in the Edinburgh Prolog family. The features of SWI-Prolog include: a comprehensive set of built-in predicates, a module system, a garbage collector, dynamic expansion of runtime stacks, an interactive development environment, an execution profiler, exception-based autoloading, a quick load format and fast compiler, a two way interface to C that is safe to the garbage collector, machine-independent saved states, and embedding in C applications. The speed of compiled code isn't great, but it does have fast database manipulation and efficient implementations for various meta-call procedures. The GUI development environment is supplied by connecting the XPCE package to SWI-Prolog. The source code for SWI-Prolog is available. It is written in ANSI C and can be easily compiled on Sun SunOS and Solaris and Linux Intel systems via the supplied configure file. An executable binary is available for Linux Intel platforms. The systems is documented in a reference manual available from within the program or as a separate document in either HTML or PostScript format.

[http://swi.psy.uva.nl/usr/jan/SWI-Prolog.html]

 

Swish

The Simple Web Indexing System for Humans is a tool that lets you create indexes of directories of files (including HTML files) and search them for key words or combinations thereof. The search process can be done via a command line interface or automated for use on a Web page using a program called WWWWais. Swish is simpler than some other indexing systems and is designed to work well with Web pages. It was written in vanilla C and should compile readily on UNIX boxes, e.g. it compiled using GCC on my Linux box on the first try. [http://sunsite.berkeley.edu/SWISH-E/]

 

SYISDA

Programs for finding all eigenvalues and eigenvectors of real symmetric diagonalizable matrices in parallel. These can be easily adapted to resolve only a part of the eigenvalue spectrum. SYISDA uses MPI for message passing, and as such should run on any machine support that message passing system, including Linux. [http://www.mcs.anl.gov/Projects/PRISM]

 

SYLU

Scott's Yet another Language Unification is a version of Xerox PARC's ILU written entirely in Python. It is on-the-wire compatible with ILU although all of the features are not yet (10/97) implemented. [http://coho.stanford.edu/~hassan/ILU/SYLU/]

 

SYMCON

A mixed symbolic numeric program package for the treatment of parameter dependent systems of equations. The program is a combination of symbolic and numerical computations with graphical output and menu interface. The numerical part is written in C, and the graphical part is supposed to run under either SUNVIEW or the OPENWINDOWS environment, the latter of which should be available for Linux platforms (although I haven't attempted this one yet). A source code distribution of SYMCON is available. It is written in C and is documented in a user's manual available in PostScript format. This is part of CodeLib.

[ftp://elib.zib-berlin.de/pub/elib/codelib/symcon/]

 

Symmetrica

A computer algebra package devoted to representation theory, invariant theory, and the combinatorics of finite symmetric groups and related classes of groups (e.g. the alternating groups, wreath products of symmetric or alternating groups, finite and infinite linear groups, and other classes of groups). It is meant to be a tool for those working on representation theory or on its application to mathematics, physics or chemistry. Symmetrica provides routines for handling several mathematical structures including: ordinary irreducible and Brauer characters as well as decomposition numbers of symmetric groups; ordinary irreducible characters of alternating groups; ordinary irreducible characters of wreath products of symmetric groups; ordinary and modular irreducible matrix representations of symmetric groups; ordinary irreducible polynomial representations of general linear groups; multivariate polynomials and, in particular, Schubert and zonal polynomials; Schur polynomials as well as several other series of symmetric polynomials; cycle indicator polynomials for combinatorial enumeration; and the ordinary group algebra of the symmetric groups.

The Symmetrica distribution includes the source code, written in standard C that should compile on most platforms with a C compiler, and a 180 page user's manual in TeX and PostScript format.

[http://www.mathe2.uni-bayreuth.de/axel/symneu_engl.html]

 

SYMMLQ

A program designed to solve systems of linear equations Ax = b where A is an n-by-n symmetric matrix and b is a given vector. The matrix A is not required to be positive definite but is intended to be large and sparse. Preconditioning is also offered as an option. The program is available as Fortran source code and is documented in comment statements in the code. [http://www.netlib.org/linalg/]

 

synpic

A ray tracing package. The ray tracer can handle a variety of quadric surfaces, a few planar objects, and circular tori. The tracer also supports reflection and refraction. A fully procedural description language has rich support for 3-D manipulation and offers vector arithmetic and colors and built-in types. The synpic system is written in ANSI C and can be installed on most generic UNIX platforms using a supplied configure script. The installation and use of synpic requires the uri library package. The ray tracer is documented in a man page.

[ftp://ftp.agso.gov.au/pub/Aegis/]

 

SYNTAX

A set of tools for the design and implementation of the front-end part of translators in the compilation field. The SYNTAX tools allow the generation of analyzers and the compilation of source texts with those analyzers. This has all the capabilities of lex and yacc plus some additional features including better error processing, i.e. an automatic (and tunable) error repair and recovery mechanism. The modules comprising SYNTAX are:

• BNF, a which takes a context-free grammar (CFG) and produces an internal form used by the other modules;
• CSYNT, which checks that the input CFG is LALR(1) compliant;
• LECL, a scanner generator which takes as input the lexical specification level in regular expression form;
• RECOR, which processes the lexical and syntactic error processing specifications; and
• TABLES-C, the collects the output of the other modules and generates a C program to be linked with the SYNTAX library.

Distributions are available for several systems including Linux Intel. A user's manual written in French is available in PostScript format.

[http://www-rocq.inria.fr/oscar/www/syntax/syntax-eng.htm]

 

system administration

Packages developed for administering one or more machines in other than a random way include:

• acct, a set of accounting utilities which provide information about system usage;
• ACUA, for administering user accounts and enforcing access restrictions;
• AgentD, a scheduling daemon which schedules system administration procedures at chosen intervals;
• Cfengine, a language for testing and configuring heterogeous UNIX-like systems;
• COAS, a project to improve the way users administer their Linux systems;
• DQS, which distributes computational resources across a network;
• GASH, a special shell for distributed NIS administration;
• ipfwadm, for administering the IP accounting and firewall services offered by the Linux kernel;
• KerbNet, an implementation of Kerberos that provides an administrative interface;
• Linuxconf, a fully integrated system administration tool for maintaining a working Linux system;
• SATAN, a security administrator tool;
• SNMP, under which several administration tools are listed;
• traceroute, for tracing the route that IPpackages take in getting to a destination system;
• Webmin, a Web-based interface for system administration; and
• XUser, an interface to the shadow password administration files.

 

System16

A emulator of the Sega System16 arcade machines. [http://electron.et.tudelft.nl/~jdegoede/system16.html]

 

szip

A freeware, portable, general-purpose, lossless compression program with high speed, compression, and memory demands. It uses a blocksort variant with a maximum blocksize of 4.1 MB, so compression is better for larger files. It uses a byte-oriented coder for output and a prediction model specifically developed for blocksort. A binary version of szip is available for Linux Intel platforms. [http://www.compressconsult.com/szip/]

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