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Na-Nm

Last checked or modified: Feb. 22, 1999

NAB: The Nucleic Acid Builder is a high-level language for manipulating macromolecules and their fragments. NAB uses a C-like syntax for variables, expressions, and control structures and has extensions for operating on molecules (e.g. new types and a large number of built-in functions for providing the necessary operations). It can be used for model building and coordinate manipulation of proteins and nucleic acids ranging in size from fairly small systems to the largest systems for which an atomic level of description makes computational sense. It provides an environment that eases many of the bookkeeping tasks involved in writing programs that manipulate 3-D structural models. The developers want it to serve to formalize the step by step process used to build complex model structures, and it can be used as a general purpose language for writing programs that deal with 3-D biomolecular structures.
The features of NAB include:

named objects such as points, atoms, residues, strands, and molecules which can be referenced and manipulated;

a high-level set of routines for specifying rigid body transformations of molecules or parts thereof;

an interface to distance geometry methods which allows relationships that can be defined in terms of internal distance constraints to be realized in 3-D models;

a form of regular expressions called ``atom regular expressions'' which provide a uniform and convenient method for working on parts of molecules;

the incorporation of many of the general features of awk including regular expression pattern matching; and

built-in procedures for linking NAB routines to external routines written in C or Fortran.

A source code distribution of NAB is available. It is written in C and can be compiled on generic UNIX platforms. It is documented in an extensive manual available in PostScript format.
[ftp://ftp.scripps.edu/pub/macke/]
[ftp://ftp.osc.edu/pub/chemistry/software/SOURCES/C/NAB/]
Nachos: Instructional software for teaching a course of operating systems. The distribution includes simple baseline code for a working operating system, a simulator for a generic personal computer or workstation, sample assignments, and a C++ primer. Nachos is itself written in an easy to learn subset of C++. The assignments cover all areas of modern operating systems including threads and concurrency, multiprogramming, system calls, virtual memory, software-loaded TLBs, file systems, network protocols, remote procedure calls (RPC) and distributed systems.
A source code distribution of Nachos is available. It is written in C++ and has been successfully desired on several platforms including Linux Intel. Documentation includes an overview paper and quite a bit scattered amongst several web pages accessible via the home site.
[http://http.cs.berkeley.edu/~tea/nachos/]
NAGS Spam Filter: The Netizens Against Gratuitous Spamming Spam Filter is a Perl script which can be used by those with a shell account on a UNIX system which has Perl installed. It uses a .forward file to first pass all incoming mail through the filter and then decide whether the mail should be passed along to the mailbox, rejected to the sender and/or postmaster of the originating site, or ignored. It should work with traditional UNIX mail software as well as with POP mail clients.
[http://www.nags.org/index.html]
nam: A Tcl/Tk-based animation tool for viewing network simulation traces and real world packet traces. Nam supports topology layout, packet level animation, and various data inspection tools. A source code distribution is available.
[http://www.isi.edu/nsnam/nam/nam.html]
Namazu: A full text retrieval search system intended for easy use. It can work as both a CGI script for web applications and for personal use in directories. The search engine consists of an indexer and a search client. It supports AND, OR and NOT searches, with search results printed in order of score with an abstract (and the score calculated by term frequency or by weight of HTML elements). A source code distribution is available under the GPL version 2.
[http://openlab.ring.gr.jp/namazu/]
NAMD: The Numerical Analysis of Molecular Dynamics package is a parallel, object-oriented molecular dynamics program designed for the high performance simulations of large biomolecular systems. It is part of the MDScope system which links NAMD to VMD to allow researchers to both simulate and interactively view the results of their simulations.
The features of NAMD include:

efficient full electrostatics using the Distributed Parallel Multiple Tree Algorithm (DPMTA) (which is, additionally, integrated using a multiple timestep integration scheme which computes full interactions only periodically);

scalable parallelism using a spatial decomposition scheme coupled with a multithreaded, message-driven execution to achieve load balance and overlap of communication with computation;

an object-oriented, extensible source code design written in C++ and fully documented in a programmer's guide;

portability to different parallel machines and message-passing systems using the PVM software;

compatibility with the XPLOR ($) package; and

the implementation of standard molecular dynamics features such as energy minimization, velocity rescaling, spherical harmonic boundary conditions, harmonic atom restraints, and Langevin dynamics.

The NAMD package is available as source code written in C++. It can be compiled using g++ and its use requires the PVM package. Documentation is available in the form of user's and programmer's guides in PostScript format. See Nelson et al. (1996).
[http://www.ks.uiuc.edu/Research/namd/]
Nana: A library that provides improved support for assertion checking and logging in C and C++. The functionality can also be implemented using a debugger rather than as inline code with a large saving in code space. The interface to Nana includes:

I.h, for C-based invariant checking, i.e. a replacement for assert.h;

DI.h, for debugger-based invariant checking;

L.h, for providing logging functions;

L_buffer, for logging messages to a circular buffer in core;

L_times.h, for recording events and times with a lower time and space overhead than with L_buffer.h;

DL.h, for supporting printf-style logging;

GDB.h, for sending plain gdb commands to the debugger;

Q.h, provides support for the quantifiers of predicate logic;

Qstl.h, provides quantifiers for STL containers;

now.h, some simple time measurement routines;

cycles.h, for access to CPU cycle counting registers;

eiffel.h, for Eiffel-type assertions;

assert.h, a drop-in replacement for the original assert.h; and

calls.h, implements a simple list of functions which can be modified and executed at runtime.

A source code distribution is available.
[http://wattle.cs.ntu.edu.au/homepages/pjm/nana-home/]
NAO: Numerical Analysis Objects is a project to investigate ways to ease the use and creation of software for numerical simulations, specifically those that require the solution of differential equations. NAO consists of four parts containing various objects and subroutines. The first part is a set of definitions of the interface to categories of abstract base classes. These classes define:

geometric regions including regions of space, mapped and stretched regions, and general manifolds;

sets of functions with the same domain and range;

functions that create maps from one geometric region to another including discrete functions that are represented by a finite number of values;

sets of operators with the same domain and range;

mappings from one function space to another including finite dimensional operators;

algorithms, e.g. ODE integrators, iterative solvers, etc.; and

problems, i.e. an object representing a problem to be solved.

The second part of NAO is a set of implementations of the base classes. These are objects implementing the base class interfaces to represent some particular type of class of object and include:

interfaces to several Netlib packages;

a function class that interprets a string;

an operator class that creates finite difference stencils on staggered grids; and

a routine that creates nonlinear finite difference operators by parsing an expression.

The third part is a set of utilities that provide common operations on objects including:

routines for performing various conversions, e.g. a function to a manifold;

routines for printing information about objects;

routines for performing simple graphics output operations like drawing lines and polygons; and

routines for verifying that objects are correctly implemented for debugging purposes.

The fourth part of NAO consists of a set of interfaces that allow it to be used from different languages and environments including:

a raw C++ interface which, being the lowest level interface, is called by the other interfaces;

a smart pointer C++ interface created for the use of overloaded operators and other features intentially left out of the raw interface;

a C interface that represents the class library as a C subroutine library;

a Fortran interface that represents the library as a Fortran subroutine library; and

planned (1/99) interfaces to DataExplorer and Tcl/Tk.

Various system level features are also offered by NAO including:

run-time type checking for safe down-casting;

memory management via reference counting;

tracking of created objects;

persistence via disk files; and

a double dispatching mechanism for binary operations.

A source code distribution of this C++ library is available upon filling out on online request form. This can be compiled with G++. Extensive documentation in HTML format is also available. The distribution contains a huge number of examples.
[http://www.research.ibm.com/nao/]
NAPACK: A collection of Fortran subroutines for performing tasks in numerical linear algebra and optimization. The functionality includes:

solving linear systems;

estimating the condition number or the norm of a matrix;

computing determinants;

multiplying a matrix by a vector;

inverting a matrix;

solving least squares problems;

performing unconstrained optimization;

computing eigenvalues and eigenvectors;

performing singular value or QR decomposition;

special routines for general, band, symmetric, indefinite, tridiagonal, upper Hessenberg and circulant matrices.

A source code distribution of NAPACK is available.
[http://www.netlib.org/napack/index.html]
NAS: The Network Audio System was developed for playing, recording, and manipulating audio data over a network. It uses the client/server model to separate applications from the specific drivers that control audio input devices. The distribution contains sample server implementations for several platforms (including VOXware/OSS for Linux), an application programming interface library, and a variety of sample applications. The features of NAS include:

device-independent audio over the network via TCP;

handling several audio file and data formats;

storing sounds in a server for rapid replay;

extensive capabilities for mixing, separating, and manipulation of audio data; and

simultaneous use of audio devices by multiple applications.

The NAS package contains several useful utility applications including:

auconvert, which converts from one sound or data format to another;

auctl, which is used to control audio server parameters when connecting new devices or setting user preferences;

audemo, a NAS record and play demo which allows a user to play pre-recorded files, record new ones, and manipulate NAS buckets;

audial, which generates touch tones suitable for dialing a North American telephone;

auedit, which provides a GUI for performing various editing tasks on a file including cutting, copying, pasting, and mixing;

auinfo, which shows information about an NAS server;

aupanel, which provides a GUI interface for adjusting the attributes of the devices provided by the NAS service;

auphone, which allows two-way real time voice communication between two servers via telephone;

auplay, which plays a sound file to a NAS server;

aurecord, which can record a sound file from a NAS server;

auscope, an audio protocol filter that can be used to view the network packets sent between an application and a server;

autool, an audio play/record tool compatible with the Sun audiotool program;

auwave, which demonstrates the use of waveform elements; and

checkmail, which plays a sound file when a user receives mail.

A source code distribution of NAS is available as is a Linux ELF binary. The package is documented in a set of manuals and technical reports in PostScript format.
[http://radscan.com/nas.html]
[http://sunsite.unc.edu/pub/Linux/apps/sound/servers/]
Nascent: A compiler used by the Sparser research group at the Oregon Graduate Institute to support experiments in advanced compiler optimizations for imperative languages for high performance computer systems ranging from high-end pipelined and superscalar processors to massively parallel supercomputer systems. The areas studied include languages and optimizations for parallel computers, dependence analysis and advanced loop transformations, back-end optimizations for superscalar RISC chips, and interprocedural analysis and optimizations. Nascent was the infrastructure in which all the experiments were performed.
The source code for the Nascent compiler is available. It is written in C++ and has been tested on g++ versions 2.5.8 and 2.6.2. Its used is documented in a user's manual included in the distribution in LaTeX format.
[http://www.cse.ogi.edu/Sparse/nascent.html]
NASD: The Network Attached Secure Disks storage system architecture is part of a project to design, implement, and evaluate scalable, distributed and parallel storage architectures, interfaces, and protocols to comprehensively reduce access latency. The goal is to develop a method to make commodity storage components the building blocks of high-bandwidth, low-latency, secure scalable storage systems. The features that identify a NASD system include:

direct client-drive data transfer in a networked environment using an object-based interface,

asynchronous oversight by the high-level filesystem,

cryptographic support for the integrity of requests,

storage self-management opportunities derived from a more abstract and independent role for storage systems, and

the ability to extend the feature set to demanding client applications without requiring modification of the file manager software.

The NASD architecture features disk management functions embedded into the device to offer a variable-length object storage interface while file managers enable repeat client accesses to specific storage objects by granting a caching capability. Data layout management is shifted to the disk so all data and most control travels across the network only once, eliminating the need for a store-and-forward computer. Partitions are variably-sized object groupings rather than physical disk regions. This enables the management of total partition space in a manner similar to virtual volumes on virtual disks.
The Extreme NASD Linux software package contains several components including:

the NASD drive, a software prototype for a NASD hardware device that is runnable on standard workstations;

NASD security;

the EDRFS file system including a file manager and client;

a prototype of an aggregate storage manager called Cheops;

configuration and management tools for the NASD drive and EDRFS file system;

the drive and filesystem executable as either user processes or loadable kernel modules; and

a choice of either TCP-based RPC or DCE RPC for communication.

[http://www.pdl.cs.cmu.edu/extreme/]
NASM: An 80x86 assembler designed for portability and modularity which supports a wide range of object file formats including Linux a.out and ELF, COFF, Microsoft 16-bit OBJ and Win32. It can also output plain binary files. The syntax is designed to be simple and easy to understand, i.e. similar to Intel's but less complex. It supports Pentium, P6, and MMX opcodes and includes a disassembler. NASM also has a macroprocessor which can handle macros both of the multi-line MASM type and the single-line C type. It supports multi-level file inclusions.
[http://www.web-sites.co.uk/nasm/]
[http://sunsite.unc.edu/pub/Linux/devel/lang/assemblers/]
[http://www.cryogen.com/Nasm/]
NaSt2D: A 2-D solver for the incompressible, transient Navier-Stokes equations including the temperature equation and free boundary problems. This uses finite differences for discretization on a structured, equidistant, staggered grid, central and upwind discretization of the convective pats, and an explicit time-stepping scheme. The free boundary problems are treated with the MAC technique. Several problems are implemented in this package including:

driven cavity flow;

flow over a backward-facing step;

flow past an inclined plate;

flow past a circular obstacle;

flow through a T-junction;

breaking dam flow, i.e. a free boundary value problem (FBVP);

the splash of a liquid drop (FBVP);

injection molding (FBVP);

flow over a backward facing step with a free surface;

buoyancy flow with heated side walls;

buoyancy flow with obstacles; and

buoyancy flow with heated upper and lower walls (i.e. Rayleigh-Bernard flow).

A source code distribution of this C package is available.
[ftp://ftp.lrz-muenchen.de/pub/science/fluiddynamics/cfd/NaSt2D/]
NAT: Network Address Translation is an Internet technology that enables load balancing for parallel processing, several types of access security, fault-tolerance and high-availability, and the simplification of basic network administration. The capabilities of NAT include:

Internet traffic load balancing via a router taking a TCP/IP connection request and redistributing it to one of many other web servers at different IP addresses;

Intranet compute-server load balancing, e.g. via rewriting incoming IP packet headers and forwarding database read requests to the least busy database in a cluster;

firewall security via masquerading wherein the IP headers of internal packages leaving a LAN are rewritten to make it appear that they are all coming from the firewall machine; and

interactive Web site security via Port Forwarding wherein a firewall can rewrite IP packets entering via a specific port number to forward them to the internal server providing the requested service.

NAT is defined in RFC 1631.
[http://linas.org/linux/load.html]
Nautilus: A program for engaging in encrypted voice telephone conversations via modem or TCP/IP. This provides usable speech quality at bandwidths as low as 4800 bps, making it usable with cellular modems. This packages uses a computer's audio hardware to digitize and play back speech using one of several different built-in speech compression algorithms. The compressed speech is also encrypted using a choice of three different encryption functions. The encryption key is generated by default using the Diffie-Hellman key exchange algorithm, although it can also be generated from a shared secret passphrase exchanged ahead of time. The available key ciphers are Triple DES, IDEA and Blowfish, with the latter used by default.
A source code distribution of Nautilus is available. This has been used on Sparcstations as well as DOS and Linux platforms. The Linux version uses the /dev/dsp interface to control the sound board, allowing it to use any sound card for which a driver is available.
[http://www.lila.com/nautilus/]
nauty: The ``no automorphisms, yes?'' package consists of a set of procedures for determining the automorphism group of a vertex-colored graph. It provides this information in the form of a set of generators, the size of the group, and the orbits of the group. It can also produce a canonically labelled isomorph of the graph to assist in isomorphism testing. Included in the package are: dreadnaut, a simple interactive interface; and makeg and makebg, for generating graphs and bipartite graphs.
A source code distribution of nauty is available. It is written in a portable subset of C and can be freely used for research purposes. A user's manual is included in PostScript format.
[http://cs.anu.edu.au:80/people/bdm/nauty/]
Nb: Nota Bene is a GUI for annotating the discourse structure of spoken dialogue, monologue and text. The GUI is extensible in that different annotation instructions and different theories about discourse interpretation and generation can easily be incorporated. Both instructions and the annotated text are clearly displayed, and typing is reduced to a minimum. The features include:

adding keyboard shortcuts for text tagging;

a utility that can convert any Nb-annotated files into standard SGML files;

tag editing via a simple mouse click; and

a search function that finds and highlights specified strings.

This is written using Tcl/Tk and requires at least version 7.4 and 4.0, respectively.
[http://www.sls.lcs.mit.edu/sls/publications/1998/]
nbench: A Linux/UNIX port of release 2 of BYTE magazine's BYTEmark benchmark program. It consists of a series of 10 native mode or algorithm level tests of a system's CPU, FPU and memory system. The tests include a numeric sort, a string sort, bit manipulation, floating point emulation, calculating Fourier coefficients, an assignment algorithm, Huffman compression, IDEA encryption, a neural net and LU decomposition. A source code distribution is available.
[http://www.tux.org/~mayer/linux/bmark.html]
NBI: The Normal-Boundary Intersection method is a technique for solving nonlinear multicriteria optimization problems. This is an implementation of NBI in the form of a Matlab toolbox. See Das and Dennis Jr. (1998).
[http://www.caam.rice.edu/~indra/NBIhomepage.html]
nb++: A C++ class library that provides an object-oriented interface to some basic OS features (e.g. multithreading, sockets and regular expressions) as well as help with reference counting and event dispatching. The available classes include:

EventMulticaster, a template class that maintains a registry of event listeners;

Exception, a base class for exceptions;

Handle, a reference counting, reentrant smart pointer template;

InetAddress, represents an Internet address;

List, a reference-counted wrapper for an STL list;

Lock, an object that acquires an exclusive lock from the mutex passed to it in its constructor;

Mutex, a fast mutex for synchronizing non-recursive methods;

ReadLock, an object acquiring a read lock from the RWLocker passed to it in its constructor;

WriteLock, an object acquiring a write lock from the RWLocker passed to it in its constructor;

RWLocker, a write lock and multiple read locks for synchronizing non-recursive methods;

Regex, represents a POSIX extended regular expression;

Runnable, an interface for objects that can be run in their own thread by a Thread object;

Socket, represents a client-side socket;

Thread, represents a POSIX thread;

UnixAddress, represents a UNIX domain address; and

Vector, a reference-counted wrapper for an STL vector.

A source code distribution is available under the LGPL. This used to be called ucppkit.
[http://nbpp.sourceforge.net/]
NCALC: A program for computing Manning's n value for flow in open channels. NCALC computes this roughness coefficient from known discharge, water surface profiles, and channel cross-sectional properties. The program can compute an n value for single or multiple cross-sections.
A source code distribution of NCALC for UNIX platforms is available. The primary documentation is contained within Jarrett and Jr. (1985). This is part of the USGS Water Resources Applications Software collection.
[http://water.usgs.gov/software/ncalc.html]
[http://www.geogr.uni-jena.de/software/ncalc.html]
NCBI Tools: The National Center for Biotechnology Information Tools consists of a core library for building portable software and a library and collection of routines for handling and building applications for ASN.1 data. The various parts of the Tools include:

CoreLib, a collection of multi-platform functions for memory allocation, file I/O, error and general messages, and time and date notification;

Vibrant, a multi-platform user interface development library;

Entrez, an application for browsing various molecular modeling databases;

cn3d, a 3-D molecular structure viewer; and

Sequin, an application for entering data into various molecular modeling databases.

A source code distribution of the NCBI Tools is available. It is designed to be used on generic UNIX/X11 platforms as well as on Mac and Windows platforms. It is extensively documented in a series of manuals written, unfortunately, in Microshaft Word format.
[ftp://ncbi.nlm.nih.gov/toolbox/ncbi_tools/]
NcFTP: A program that implements the File Transfer Protocol (FTP). It features several options not available in standard FTP packages such a a bookmarks file, a bookmark editor, configurable preferences, special downloading features, and more.
[http://www.ncftpd.com/ncftp/]
NcFTPd: An optimized FTP server that runs more quickly and efficiently than the standard ftpd or wu-ftpd servers. It also has some additional security features. This is free for non-commercial uses after registration.
[http://www.ncftpd.com/ncftpd/]
ncpfs: A NetWare client filesystem for Linux which works with NetWare versions 3.X and later. This enables mounting volumes from a NetWare server under Linux, printing to NetWare print queues, and spooling NetWare print queues to the Linux printing system. This does not support access to the NDS, though.
The utilities in the ncpfs package include:

ipx_configure, queries or configures IPX behavior with respect to automatic IPX interface detection;

ipx_interface, adds, deletes or displays an IPX interface;

ipx_internal_net, adds or deletes the IPX internal network;

ipx_route, adds or deletes an IPX route;

ncopy, copies files to locations on a NetWare file server;

ncpmount, mounts all volumes of a specified NetWare fileserver;

ncpunmount, unmounts a NetWare filesystem;

nprint, a NetWare print client for printing files on the queue of a NetWare server;

nsend, for sending messages to users;

nwauth, for logging into a NetWare server;

nwbocreate, for creating a NetWare Bindery Object;

nwbols, for listing NetWare Bindery Objects;

nwboprops, for listing properties of a NetWare Bindery Object;

nwborm, for removing a NetWare Bindery Object;

nwbpadd, for setting the value of a NetWare Bindery Property;

nwbpcreate, for creating a NetWare Bindery Property;

nwbprm, for removing a NetWare Bindery Property;

nwbpset, for creating a Bindery Property of setting its value;

nwbpvalues, for printing a Bindery Property's contents;

nwfsinfo, for printing information about the file server;

nwfstime, for displaying or setting a NetWare server's date and time;

nwgrant, for granting trustee rights to a directory;

nwmsg, for delivering NetWare user broadcast messages;

nwpasswd, for changing a user's password;

nwrevoke, for revoking a trustee right;

nwright, for showing effective rights for a file or directory;

nwsfind, for finding a NetWare server;

nwtrustee, for listing an object's trustee directory assignments;

nwuserlist, for listing users logged into a NetWare server;

nwvolinfo, for displaying information about NetWare volumes;

pqlist, for listing available NetWare print queues;

pqrm, for removing a job from a NetWare print queue;

pqstat, for listing jobs in a NetWare print queue;

pserver, connects to print queues on NetWare servers and feeds incoming print jobs to the Linux printing system; and

slist, lists all NetWare servers available in a network.

A source code distribution is available. The May 1997 issue of the Linux Journal has on article on using ncpfs.
[http://sunsite.unc.edu/pub/Linux/system/filesystems/ncpfs/]
[http://ftp.gwdg.de/pub/linux/misc/ncpfs/]
[http://samba.SerNet.DE/linux-lan/]
ncurses: A freeware emulation of UNIX System V Release 4.0 curses which uses the terminfo format, supports pads and color, multiple highlights, forms characters, function-key mapping, and has all the other SYSV-curses enhancements over BSD curses. The GNU ncurses contains an emulation of the termcap library routines and is now (9/97) recommended over the use of that library.
The features of Ncurses include:

implementations and documentation of all 257 of the SVr4 calls;

full support for SVr4 curses features (e.g. keyboard mapping, color, forms-drawing with ACS characters, automatic recognition of keypad and function keys, etc.);

emulation of the SVr4 panels library;

emulation of the SVr4 menus library which supports a uniform yet flexible interface for menu programming;

emulation of the SVr4 form library; and

utility options that allow the filtering of terminfo entries for use with less capable curses/terminfo versions.

Ncurses extensions to SVr4 include:

an implementation that is 8-bit clean and base-level conformant with the X/OPEN curses specification;

support for mouse event reporting under xterm; and

a function to resize windows and preserve their data; super hardware scrolling support.

The ncurses distribution was developed under Linux and should port easily to other platforms. It includes the source code and an introductory programming manual in HTML format. See Goodheart (1991) and Strang (1986).
[http://www.gnu.org/software/ncurses/ncurses.html]
[http://dickey.his.com/ncurses/ncurses.html]

PyNcurses

An Ncurses binding for Python created with the help of SWIG.
[http://pyncurses.sourceforge.net/]
Ncview: See under NetCDF.
NDimViewer: A visualization system for the numerical approximation of dynamical systems and the representation of the calculated data using several novel techniques. It is specialized for high dimensional systems with a dimension count up to 25, depending on the technique. The techniques implemented are:

extruded parallel coordinates (EPC), a technique for investigating characteristics of the trajectory (e.g. correlations and clustering) wherein flow is simulated by moving a parallel coordinate system along the third spatial axis after each plotting of a sampled point of a trajectory;

linking with wings (LWW), a similar technique to 2-D streamline plots wherein 2 of N variables are mapped into a 2-D subspace with the third dimension used to represent the other N-2 variables via extending the base trajectory with wings; and

three-dimensional parallel coordinates (TPC), for displaying a high-dimensional point with parallel coordinates by mapping each single variable onto 1-D lines, i.e. the coordinate axes, which are placed in parallel with the points on the coordinate axes connected by lines to create a polyline.

NDimViewer is implemented in Java 1.2 and uses the extension classes of Java3D 1.1.
[http://www.cg.tuwien.ac.at/research/vis-dyn-syst/NDimViewer/]
NDMP: The Network Data Management Protocol is an open standard protocol for enterprise wide backup of heterogeneous network-attached storage. A draft specification and a Software Development Kit (SDK) are available, with the latter intended to promote the adoption of NDMP and to facilitate implementations of the protocol.
[http://www.ndmp.org/]
nDVI: See under Netscape.
NEC: The Numerical Electromagnetics Code is a program for analyzing the electromagnetic response of an arbitrary structure consisting of wires and surfaces in free space or over a ground plane. The analysis method involves the numerical solution of integral equations for induced currents, with there being separate equations for smooth surfaces and wires. The input may be an incident plane wave or a voltage source on a wire, and the output may include current and charge density, the electric or magnetic filed in the vicinity of the structure, and radiated fields. The model may include nonradiating networks and transmission lines connecting parts of the structure, perfect or imperfect conductors, and lumped element loading. This integral solution approach is best suited to structures whose physical dimensions are up to several wavelengths, with larger structures better handled via high frequency approximations such as geometric optics, physical optics, or the geometrical theory of diffraction.
Features of NEC include:

a numerical Green's function (NGF) option which allows new parts to be added to the model without having to repeat all calculations;

a Sommerfeld/Norton ground method;

the computation of maximum coupling between antennas;

wires can have tapered radius and segment lengths;

rectangular surfaces with multiple patches can be specified;

patches can be specified as triangles, rectangles, or quadrangles;

both near electric and magnetic fields may be computed; and

an optional extended thin-wire approximation.

The most recent publicly available version is NEC-2. A distribution is available as either Fortran or C source code. Binary versions are also available for Mac, MS-DOS, Sun SunOS, IBM RS6000, Linux Intel, and HP-UX platforms. A user's manual is available in PDF, ASCII, and HTML format.
[http://www.qsl.net/wb6tpu/swindex.html]
[http://www.emclab.umr.edu/aces/]
[http://members.home.net/nec2/]
NEdit: A GUI style plain-text editor for X/Motif systems. It combines full use of the mouse and window manager with keystroke efficiency and a full complement of editing commands. Features include an efficient, proven command set with complete functionality and designed for intensive use, a design that is 100the ground up with true multi-windowing, mouse-based editing, and cut-and-paste with other X Windows programs, easy to learn features and special features for programmers, and easy installation. The source code is available as well as several binaries at the given home site, including (starting with version 4.0.1) a binary for Linux platforms. If you want to compile it yourself you'll need Motif. A statically built NEdit binary is also available at the standard Linux software sites and their mirrors, although as of this writing (3/96) they're made from an earlier version than 4.0.1.
[http://www.nedit.org/]
NEFCLASS: A neuro-fuzzy classification program that uses neuro-fuzzy models for data analysis. It learns fuzzy rules and sets via supervised learning. The features include:

representation of a fuzzy classification system;

incremental learning of fuzzy classification rules;

learning fuzzy sets by simple heuristics; and

a learning algorithm that doesn't afflict the semantics of the underlying fuzzy classifier.

This is freely available for scientific and personal use.
[http://fuzzy.cs.Uni-Magdeburg.de/nefclass/]
NEFCON: A program for neuro-fuzzy control that can learn fuzzy rules and sets via reinforcement learning. The features include:

representation of a normal fuzzy controller;

learning fuzzy rules incrementally or decrementally;

learning fuzzy sets via simple heuristics;

a linguistic error measure expressed with fuzzy rules; and

a learning algorithm that doesn't afflict the semantics of the underlying fuzzy controller.

NEFCON is freely available for scientific and personal use, and is available in source and binary forms.
[http://fuzzy.cs.Uni-Magdeburg.de/nefcon/]
NELSIS: A flexible, lightweight CAD framework enabling tool integrators to build high-performance design engineering environments. NELSIS is not concerned with the contents of a design description but rather with administering information about design descriptions, e.g. their hierarchical structure, levels of abstraction, where to find them, etc. The design requirements for NELSIS include:

not restricting the functionality of design systems built on it;

not enforcing particular design methodologies on users;

provision of high level design management services such as support for hierarchy and equivalence relations between design descriptions, versioning, consistency and concurrency control and design flow management;

configurability of high level design management services;

provision for creating an arbitrary number of design databases in a distributed hardware environment that will allow multiple design tools to work concurrently with mutual interference; and

independence of specific application domains, i.e. usable for electronics, mechanics, software design, etc.

The architecture of the NELSIS CAD framework includes:

a base layer consisting of a Meta Data Manager (MDM) for handling information about design descriptions according to a specified data schema;

Design Management Services (DMS) built on top of the MDM for performing various tasks such as access control, hierarchy and version management, and design flow management;

Framework User Services (FUS) for providing an interface between the CAD Framework and the designer, e.g. to invoke tools or browse information stored by the framework;

a Design Management Interface providing an implementation independent layer between the tools and both the FUS and DMS, allowing such actions as opening and closing design databases and checking out/in design descriptions;

an arbitrary number of design databases; and

an arbitrary number of tools.

Binary distributions of the NELSIS CAD framework are available for several platforms including Linux Intel, and may be obtained upon completing and returning a license form. Documentation includes various users guides and technical reports as well as an extensive set of man pages.
[http://www.ddtc.dimes.tudelft.nl/nelsis/]
NEMO: An extensible stellar dynamics toolbox which contains various programs to create, integrate, analyze and visualize N-body and SPH-like systems. There are also various tools to operate on images, tables and orbits as well as on FITS file to export to or import from other astronomical data reduction packages. NEMO also contains well-defined procedures for extending its capabilities with user-developed programs.
NEMO is structured into various groups of programs including:

the N-body group containing various programs to create N-body systems (e.g. spherical, disk), methods to compute the gravitational field (e.g. softened Newtonian, hierarchical, Fourier expansion), and time integrators (e.g. leapfrog, Runge-Kutta) as well as utilities to manipulate and anaylyze the data;

the orbit group containing programs to calculate the paths of individual orbits in static potentials and analyze them;

the image group containing programs to display and manipulate 2-D rectangular pixel arrays; and the table group containing programs to manipulate and display ASCII files containing arrays of numbers.

NEMO has been ported to several UNIX platforms and there is a special Linux Astronomy group to handle the port to the Linux operating system. The documentation is contained in a user's and programmer's guide available in PostScript and HTML format.
[http://bima.astro.umd.edu/nemo/]
nenscript: A clone of the proprietary enscript program from Adobe Systems which converts ASCII text files into PostScript files and prints them to a printer or a file. Nenscript produces output which fully conforms to the Adobe Document Structuring Conventions (DSC), supports normal or fancier output, supports single or double column output, allows the insertion of titles and headers in any font, can print multiple copies of a document, and automatically wraps long lines. The chief features of enscript not supported by nenscript is the ability to use fonts other than Courier for text output.
A source code distribution of nenscript is available. It is written is C and is portable to almost any UNIX flavor. It is documented in a man page and some text files.
[http://www.im.lcs.mit.edu/~magnus/nenscript/]
[http://sunsite.unc.edu/pub/Linux/system/printing/]
neon: An HTTP and WebDAV client library written in C for UNIX systems. The features include:

high-level interface to HTTP and WebDAV methods;

low-level interface to HTTP request handling to allow the easy implementation of new methods;

HTTP 1.0 and 1.1 persistent connections;

RFC 2616 basic and digest authentication;

proxy support including basic/digest authentication;

generic WebDAV 207 XML response handling mechanism;

XML parsing via the expat or libxml parsers;

generation of messages from 207 error responses;

WebDAV resource manipulation, e.g. MOVE, COPY, DELETE, MKCOL; and

WebDAV metadata support, e.g. setting and removing properties, querying any set of properties.

[http://www.webdav.org/neon/]
NEOS: A network-enabled problem solving environment (PSE) for a wide class of applications in business, science and enginerding. The NEOS Server is designed as a generic application service provider (ASP) which, upon installation, creates:

a web site for the ASP;

CGI scripts to parse generic web submissions;

scripts to parse email and TCP/IP socket submissions;

a database for tracking submission information along with appropriate tools for working with it;

instructions for adding new services; and

administrative tools for building a collection of services.

The process by which the NEOS Server handles user requests is:

user submissions are sent to a central Server machine;

the Server parses the submission and writes the key pieces of information to separate files for each type of service provided;

the Server sends job request files to distributed solver stations and executes the software thereon;

the software processes the request and sends a solution back to the Server; and

the Server returns the result to the original requestor.

The NEOS Server system is designed to run on standard UNIX platforms with Perl 5 installed. NEOS Clients built using both Tcl/Tk and Java are available.
[http://www-neos.mcs.anl.gov/]
neotec: A set of thin-plate and thin-shell finite element programs that can be used to model the deformation of the lithosphere, formulate tectonic hypotheses, fit geodetic data, estimate long-term seismic hazards, study plate rheology, or for teaching purposes. The rheology uses in anelastic and the programs incorporate frictional plasticity and fault sliding and/or power-law dislocation creep and/or linear Newtonian viscosity depending on local conditions. The isostatic approximation is used for the vertical equilibrium component, and the vertical normal stress estimated as lithostatic.
The neotec programs differ from the related paleotec package in that they are designed for neotectonic studies. That is, while they compute velocity, anelastic strain rate, fault slip-rate, and stress-anomaly integrals, they do not deform their own grids or step through time. They permit discrete fault elements to be included in the grid with assigned dips as well as lower friction than the blocks (i.e. microplates) between them.
The programs included in the neotec package include:

FAULTS, a thin-plate, flat-Earth finite element program for anelastic crustal deformation whose purposes are to:

solve the momentum equation (stress-equilibrium equation) under the quasistatic (creeping-flow) approximation for thin faulted plates of crust deforming anelastically on a flat Earth;

calculate long-term average velocities, average fault-slip rates, average anelastic strain rates, and average deviatoric stresses; and

provide either colored or black and white maps of the input data and computed results.

PLATES, a thin-plate, flate-Earth finite element program for anelastic plate deformation whose purposes are to:

solve the momentum equation under the quasistatic approximation for thin faulted plates of lithosphere (crust plus mantle lithossphere) deforming anelastically on a flat Earth;

calculate long-term average velocities, fault slip rates, and anelastic strain rates, and average stresses; and

provide graphical versions of model inputs and outputs.

SHELLS, a finite element program using thin-shell elements to economically represent large sections of the lithosphere featuring:

fault elements to simulate plate boundaries or other fault systems;

a rheology consisting of nonlinear frictional-sliding at low temperatures and dislocation-creep at high temperatures; and

separate crust and mantle-lithosphere layers.

Most of the neotec programs are written in Fortran 77 or 90, although some of the graphics programs are written in the sort of weird languages you might find on DOS/Windoze platforms since they're developed on such things. There may also be the odd call or two to IMSL routines here and there for solving various equation systems. Documentation can be found online as well as in a series of papers by the author. See Bird (1998a), Bird (1999) and Kong and Bird (1995).
[ftp://element.ess.ucla.edu/neotec/]
NeoWebScript: A server-side scripting environment based on Safe Tcl. This allows users to write NeoWebScript programs that perform sophisticated data procesing on on-the-fly HTML generation without risking or compromising the system by opening arbitrary files or running arbitrary programs on the server. This is available as a module for the Apache webserver. NeoWebScript is available in two forms. The first form includes all of the necesary Tcl and ancillary code needed for it to run, and the second is a mini-release containing only the specific source code for NeoWebScript for those who already have the appropriate Tcl programs installed.
[http://www.NeoSoft.com/neowebscript/]
NESL: A strongly-typed, applicative, data-parallel language which integrates concepts from parallel algorithms, functional languages, and implementation techniques. The main emphasis in the design of NESL was to make parallel programming easy and portable as well as to allow algorithms to be expressed more concisely than in most other parallel languages. The important new ideas behind NESL include nested data parallelism which offers the benefits of data parallelism and concise code while still being well suited for the development of irregular algorithms such as algorithms on trees, graphs, or sparse matrices. Another significant idea involves a language-based performance model which offers a formal way to calculate the work and depth of a program (i.e. measures of performance analysis). NESL is loosely based on the ML functional language.
NESL is a data-parallel language, i.e. it supports parallelism with operations over the data. The parallel constructs are:

parallel sequences or 1-D arrays;

a parallel apply-to-each command for applying any expression to each element of a sequence in parallel; and

a set of parallel operations on sequences, e.g. summing the elements thereof.

A significant feature is support for nested parallelism which allows any of these constructs to be nested to any number of levels. This feature is important for implementing algorithms with irregular nested loops and for divide-and-conquer algorithms.
The NESL distribution includes the source code and documentation in PostScript format. The installation of NESL requires GCL, CMUCL, or a commercial Common Lisp system as well as UNIX/X11 platforms. It currently (4/97) runs on UNIX workstations, the IBP SP-2, the CM5, the Cray C90 and J90, the MasPar MP2, the Intel Paragon, and on SMP machines such as the SGI Power Challenge or the DEC AlphaServer. A portable MPI backend is also being developed. In addition to the basic distribution a library of parallel algorithms written in NESL can be obtained. See Blelloch et al. (1994).
[http://www.cs.cmu.edu/~scandal/nesl.html]
Nessus: A project to provide a free, open-sourced and easy-to-use security auditing tool. The features include:

a plug-in architecture with each security test written as an external plug-in;

a Nessus Attack Scripting Language (NASL) designed for writing security tests;

an up-to-date security vulnerability database;

a client-server architecture;

simulataneously testing an unlimited number of hosts;

smart service recognition that recognizes services even when they're not running on standard ports;

multiple service testing;

cooperation among tests, e.g. if an FTP server doesn't offer anonymous logins then anonymous-related security checks won't be performed;

exportable reports detailing how to fix security problems; and

multilingual support.

[http://www.nessus.org/]
NEStra: An NES emulator for Linux.
[http://nestra.linuxgames.com/]
NET_SCCS: The Networked Source Code Control System is a project to provide a platform-independent layer on top of SCCS, the standard UNIX source code control system. The will create a single, centralized, efficient, and simple SCCS for use on all supported platforms. NET_SCCS will used TCP/IP and HTTP for communications and SCCS to store the source code. It will consist of two parts: back-end processes running under UNIX and front-end processes initially implemented as command-line utilities and eventually in some GUI form. This project is currently (5/98) in the early stages of development.
[http://www.voicenet.com/~mortis/projects/net_sccs/]
netatalk: A kernel-level implementation of the AppleTalk Protocol Suite (APS) that includes support for routing AppleTalk, serving UNIX and AFS filesystems over AFP (Appleshare), and serving UNIX printers and accessing Appletalk printers over PAP. Several printing and debugging utilities are also included. Netatalk includes support for EtherTalk Phase I and II, DDP, RTMP, NBP, ZIP, AEP, ATP, PAP, ASP and AFP.
DDP is in the kernel. A program called atalkd implements RTMP, NBP, ZIP and AEP and is the AppleTalk equivalent of the UNIX routed and ifconfig. A client-stub library is also available for NBP, and ATP and ASP are also implemented as libraries. The program papd allows Macs to spool to lpd or a pipe, and pap allows UNIX machines to print to AppleTalk connected printers. The program psf is a PostScript printer filter for lpd designed to use pap, and psorder is a PostScript reverser called by psf to reverse pages printed to face-up stacking printers. A Mac interface to the UNIX file system if provided by the program afpd.
The netatalk package is available as C source code which can be compiled on most generic UNIX platforms. All of the programs are documented via man pages. Linux-specific installation and use information is provided at the Linux netatalk site. See also CAP, MacGate, hfs_fs, hfsutils, and Linux Services for Mac and Windows Users. The January 1998 issue of the Linux Journal contains an article about netatalk.
[http://netatalk.sourceforge.net/]
Netaudio: A package which provides a standard way of sending and receiving a stream of audio between two machines using an IP connection. Netaudio allows the sending, receiving, and rebroadcasting of data with a single program, with a choice for which program to use for the audio compression. This can be used, e.g. to set up Netscape to receive a real-time audio feed.
The source code for netaudio is available and has been tested on Linux, NetBSD and FreeBSD platforms. The author recommends the use of GSM for audio compression. The program is documented in a man page.
[http://www.bitgate.com/netaudio/]
Netboot: A package for booting an X86-based computer over an IP network with accessing either a hard disk or a floppy. This can be used for a printer spooler, a terminal server, an X11 terminal, and various other specialized applications. This is used to create a boot ROM which gets plugged into a socket on the network card. A source code distribution is available.
[http://www.han.de/~gero/netboot.html]
NetBSD: A Linux competitor as a freely-available UNIX clone operating system. It's not polite to completely ignore the competition.
[http://www.netbsd.org/]
netcat: A utility for reading and writing data across network connections using the TCP or UDP protocols. It is designed to be a reliable back-end tool that can be used or driven by other programs and scripts. It can also be used as a network debugging and exploration tool since it can create almost any kind of connection and has many built-in capabilities. The features include:

outbound or inbout TCP or UDP connections to or from any ports;

full DNS forward/reverse checking with appropriate warnings;

using any local source port;

using any locally-configureed network source address;

built-in port scanning capabilities (with a randomizer);

built-in loose source-routing;

a slow-send mode, i.e. one line every N seconds;

hex dumps of transmitted and received data;

allowing another program to service established connections; and

a Telnet-options responder.

[http://www.l0pht.com/~weld/netcat/]
[ftp://coast.cs.purdue.edu/pub/tools/unix/netcat/]
NetCDF: The network Common Data Form is an interface for scientific data access and a library that provides an implementation of the interface. It also defines a machine-independent format for representing data. Data stored in the netCDF format is self-describing, network transparent, direct-access, appendable, and sharable. There is a netCDF interface to HDF available. An online NetCDF User's Guide can be browsed for further details. Several ancillary packages are described below. Graphics and/or analysis packages that can read and/or write NetCDF data include CRDtools, DDI, DODS, Envision, EPIC, GMT, GrADS, Gri, HDF, LinkWinds, and Zebra. See Rew and Davis (1990) and Brown et al. (1993).
[http://www.unidata.ucar.edu/packages/netcdf/]

cdf2asc

A program that dumps data in a NetCDF file to an ASCII file. It is written in C and documented in a man page.
[http://www-c4.ucsd.edu/~cids/software/visual.html]

cdf2c

A program that creates C code to read a given NetCDF file. It is written in C and documented in a man page.
[http://www-c4.ucsd.edu/~cids/software/visual.html]

cdf2fortran

A program that creates Fortran code to read a given NetCDF file. It is written in Fortran and documented in a man page.
[http://www-c4.ucsd.edu/~cids/software/visual.html]

FAN

The File Array Notation is an array-oriented language for identifying data items in files for the purpose of extraction or modification. The only data format currently supported is NetCDF. The package also includes four utility programs:

nc2text, which prints variable and attribute values from NetCDF files;

ncmeta, which prints metadata from NetCDF files;

ncrob, which reads data from one or more NetCDF variables, performs some process on it, and then either prints it or writes it to NetCDF variables; and

text2nc, which reads ASCII text data and writes it to a NetCDF variable or attribute.

The FAN language is used with these utilities to select individual data points or ranges of points from fields being processed or browsed. An Introduction to FAN is available online, and a manual is available in PostScript format.
[http://www.unidata.ucar.edu/packages/netcdf/contrib.html]

HOPS

The Hyperslab OPerator Suite is a bilingual, multi-platform software package for processing data in NetCDF files conforming to the the NCAR CCM or Ocean Model format. It is implemented in the languages of both the commercially available IDL and the freely available Yorick. HOPS is a suite of operators that act on data units called hyperslabs, and has an object-oriented design in which the operators treat the numeric data and the associated meta-data as a single object.
[http://www.cgd.ucar.edu/gds/svn/hyperslab.html]

NCIP

The NetCDF Interface Routines are set of Fortran routines designed to minimize the work required to read and write NetCDF files. The user's contact with NetCDF is reduced to a limited number of Fortran outines for which only an argument list must be supplied, i.e. low level NetCDF API calls are not required. A source code distribution is available for which compilation is currently (7/99) a slightly complicated process.
[ftp://ftp.gfdl.gov/pub/jps/netcdf/utils/]

NCO

The NetCDF Operators is a suite of programs which take a NetCDF program, perform some operation on it, and produce another NetCDF program as output. The operators are primarily designed to aid in the manipulation and analysis of scientific data. The available NCO programs include:

ncatted, for editing attributes in NetCDF files;

ncdiff, subtracts one file from another and creates a third;

ncea, performs gridpoint averages of variables across an ensemble of input files;

ncecat, concatenates an arbitrary number of input files into a single output file;

ncflint, linearly combines an arbitrary number of input files;

ncks, extracts a subset of data from an input file and prints it as ASCII text;

ncra, averages record variables across an arbitrary number of input files;

ncrcat, concatenates record variables across an arbitrary number of input files;

ncrename, renames dimensions, variables and attributes in a NetCDF file;

ncwa, averages variables in a single file over arbitrary dimensions.

A source code distribution is available which has been successfully compiled on several platforms including Linux. A user's manual is available in the usual formats.
[http://www.cgd.ucar.edu/cms/nco/]

Ncview

A visual browser for NetCDF format filesw. This allows a quick, easy, push-button look at NetCDF files. Capabilities include viewing simple movies of the data, viewing along various dimensions, taking a look at the actual data values, changing color maps, inverting the data, etc.
Ncview can be compiled on UNIX platforms under X11R4 or higher. It requires the Xaw library for compilation. Several binaries are available at the site, although not yet one for Linux Intel platforms. Not to worry, since I've compiled it on my box and make available a Ncview Linux Binary Package which contains just the Ncview binary and the modified makefile I used to create it. You still need to get the source package for some other needed files, though.
[http://meteora.ucsd.edu/~pierce/ncview_home_page.html]

NetCDF for Java

An ongoing project to create a Java interface to NetCDF. An alpha release is available as of 6/96.
[http://www.unidata.ucar.edu/packages/netcdf/java/]

NetCDFPerl

A Perl extension for accessing NetCDF datasets.
[http://www.unidata.ucar.edu/packages/netcdf-perl]

PythonNetCDF

A Python language interface to the NetCDF package.
[http://snow.cit.cornell.edu/noon/ncmodule.html]
[http://starship.python.net/crew/hinsen/netcdf.html]
NetComponents: A Java package that enables easy access to most commonly used Internet protocols including FTP, NNTP, SMTP, POP3, Telnet, TFTP, finger, whois, and others. It also has BSD remote command support, e.g. for rexec, rcmd/rshell and rlogin. The goal of this package is to not only make the global functionality of a protocol accessible, but to also provide access to the fundamental protocols so the programmer can construct his own custom implementations. But if a programmer doesn't want to deal with low-level details, comprehensive protocol client implementations are included.
A source code implementation of NetComponents is freely available under the terms of a non-exclusive, non-transferable limited license whose details are available at the site. Special instructions are included for making this work with the Linux JDK ports. The API is documented in HTML format.
[http://www.oroinc.com/]
[http://psaweb.pisa.otm.it/archweb/develop/software/java/misc/]
NetForge: An HTTP server written in Java. It is object-oriented, has a small server kernel, has an interface for custom responders (i.e. you can write your own objects and bind them to the server at runtime), and has runtime adminstration via the Web. It implements CGI 1.1 and has a servlet interface for running HTTP servlets. This was developed using JDK 1.0.2 under Linux.
[http://www.novocode.com/]
NetForum: A Web based group communication and collaboration system whose features include:

organization of forums into topics and messages;

an intuitive toolbar for acess to the features;

creation and management of forums via a Web interface;

editing and deletion of topics and messages with administrative tools;

customization of individual forum features;

online documentation for users and owners;

a wide range of toolbar buttons whose presence and position on the toolbar can be customized;

use of HTML in messages (with the capability of limiting this to non-annoying tags, i.e. no blinking HTML);

sending email to designated forum contacts when messages are left in a forum;

notification of group members via email; and

linking to a forum from another site.

This is written in Perl and should work on any UNIX-based platform with Perl 4.0.18 and with an httpd server that allows subdirectories within a cgi directory.
[http://www.medsch.wisc.edu/netforum/home.html]
NetKit: A collection of basic network tools that have been fixed and ported from BSD code. This collection contains:

biff, which informs the system whether you want to be notified when mail arrives;

comsat;

finger, which displays information about system users;

fingerd, the finger daemon;

ftp, a file transfer program;

inetd, a super-server daemon which listens for connections on several Internet sockets;

ping, which sends ICMP ECHO_REQUEST packets to network hosts;

rcp, a remote file copying program;

rlogin, a remote login program;

rlogind, the rlogin daemon;

routed, a daemon that manages the network routing tables;

rusersd, a daemon that returns information about users currently logged into a system;

rwalld;

bootparamd;

rpcgen, an RPC protocol compiler;

rpcinfo, which reports information from an RPC server;

rsh, a remote shell;

rshd, the rsh daemon;

rusers, which produces a list of users on all machines on a local network;

rwall, which sends a message to users logged on a host;

rwho, which finds out who is logged in on local machines;

rwhod, the rwhod daemon;

talk, which copies lines from one terminal to another;

talkd, the talk daemon;

telnet, a program to communicate with another host via the TELNET protocol;

telnetd, the telnet daemon;

tftp, a trivial file transfer program;

tftpd, the tftpd daemon;

timed, the time server daemon;

timedc, which is used to control timed;

write, which sends a message to another user;

writed, the write deamon; and

routed.

A source code distribution of NetKit-0.09 is available. This version is supposed to be the last with everything packaged together, with the plan being to make all of the individual components available individually. The utilities are all written in C and can be compiled and installed via the supplied makefile. Each utility is documented in a separate man page.
[http://sunsite.unc.edu/pub/Linux/system/network/misc/]
[ftp://ftp.uk.linux.org/pub/linux/Networking/]
Netlab: A Matlab toolbox designed to provide the tools needed to simulate well-founded neural network algorithms for use in teaching, research and applications development. The available Netlab algorithms include:

a Gaussian mixture model with EM training algorithm;

linear and logistic regression with IRLS training algorithm;

multi-layer perceptron with linear, logistic and softmax outputs and appropriate error functions;

radial basis function (RBF) networks with both Gaussian and non-local basis functions;

optimizers including quasi-Newton methods, conjugate gradients and scaled conjugate gradients;

multi-layer perceptron with Gaussian mixture outputs (mixture density networks);

Gaussian prior distributions over parameters for the MLP including multiple hyper-parameters;

a Gaussian approximation framework for Bayesian inference;

Automatic Relevance Determination for input selection;

Markov chain Monte-Carlo including simple Metropolis and hybrid Monte-Carlo;

Hinton diagrams for network weights;

K-nearest neighbour classifier; and

K-means clustering.

See Bishop (1998).
[http://www.ncrg.aston.ac.uk/netlab/]
Netlib: Huge mathematical and scientific software repository. This is searchable by keyword and subject. Many of the items in Netlib are listed and described here.
[http://www.netlib.org/]
NETPATH: An interactive Fortran 77 program designed to interpret net geochemical mass balance reactions between initial and final waters along a hydrologic flow path. NETPATH uses chemical and isotope data for waters from a hydrochemical systems, and can take into account dissolution, precipitation, ion exchange, oxidation/reduction, degradation of organic compounds, incongruent reaction, gas exchange, mixing, evaporation, dilution, isotope fractionation, and isotope exchange. Geochemical mass balance models are examined between selected evolutionary waters for every possible combination of the plausible phases that can account for the composition of a selected set of chemical and isotopic constraints in the system. The package also includes a database program for storing and editing the chemical and isotope data.
A source code distribution of NETPATH for UNIX platforms is available. Related programs in the USGS Water Resources Application Software series are BALNINPT and PHREEQC. The primary documentation is contained within Plummer et al. (1994).
[http://water.usgs.gov/software/netpath.html]
Netpbm: The Pbmplus package plus some additional conversion and manipulation utilities. The additional PBM programs include those which: add BDF font support, display on an AT&T 4425 ASCII terminal, convert to DEC LN03+, convert to PostScript, convert to and from a packed format font (PK), flip isolated pixels, and enlarge a PBM image with edge smoothing. New PGM programs include those that convert ASCII images, PBM files, Biorad confocal microscope images, and SPOT satellite images to PGM; generate a convolution kernel, and create a PGM file with random pixels.
The numerous new PPM programs include those which:

convert to and from Windows bitmap (BMP) format;

extract all colors from a PPM file;

convert to Mitsubishi S340-10;

convert from XV thumbnails;

convert to and from YUV triplets;

create a red/blue stereo image;

change image saturation and value on an HSV map;

change all pixels of one color to another;

dim a PPM file to total blackness;

brighten a picture to complete whiteout;

blend together two portable pixmaps;

normalize the contrast;

perform eight plane quantization;

shift lines of a portable pixmap left or right; and

convert to an HP PaintJet XL PCL file.

The new PNM programs include those which: convert to and from SGI image format and Solitaire image recorder format; a replacement for giftoppm which examines the input image and produces a PBM, PGM or PPM output file; converts PostScript to PNM (using Ghostscript; converts PostScript to PNM, implement an anti-aliasing filter, composite two PNM files together, and add borders to anymap files.
This package is available and will compile in a manner similar to Pbmplus. All of the new programs are documentation in additional man pages.
[http://sourceforge.net/projects/netpbm/]
[ftp://ftp.cc.gatech.edu/pub/linux/apps/graphics/convert/]
[ftp://ftp.cs.ubc.ca/ftp/archive/netpbm/]
[http://www.arc.umn.edu/GVL/Software/netpbm.html]
NetPipes: A package of utilities for manipulating BSD TCP/IP stream sockets. This makes sockets usable in shell scripts and can also simplify client/server code by allow the tedious programming tasks related to sockets to be skipped. The utilities in the package are:

faucet, serves as a fixture for a network pipe by behaving as the server end of a server-client connection;

hose, behaves as the client end of a server-client connection;

encapsulate, multiplexes several channels over a single socket with sampling of remote process exist status along with providing conversation termination without closing the socket;

sockdown, shuts down a socket by performing the shutdown system call;

getpeername, obtains information about either end of a socket's connection;

timelimit, spawns a subprocess and, if the child process doesn't finish within the given time limit, either kills it, exits, or leaves the child in the background; and

ssl-auth, provides SSL capability for simple programs and shell scripts.

A source code distribution is available.
[http://web.purplefrog.com/~thoth/netpipes/netpipes.html]
NetPlug: An extensible multi-connection, multi-protocol, network client program written in Tcl/Tk. The distribution currently (4/97) includes a complete IRC client plug-in, a Go game client, a memory plug-in to record favorite host/port combinations, an asynchronous event-driven file/pipe plugin, and a TCP/IP gateway and multiplexing plugin.
The source code for NetPlug is available and written in Tcl/Tk. It is recommended that Tcl 7.6 and Tk 4.2 or later be used on UNIX boxes. Documentation is sketchy thus far.
[http://www.demailly.com/~dl/netplug.html]
NeTraMet: The Network Traffic Meter is a meter for network traffic flows that implements RFC 1272 establishing procedures for real-time traffic flow measurement. NeTraMet consists of three components:

meters, i.e. small hosts attached to a network segment that monitor traffic on that segment;

meter readers that retrieve information from meters; and

managers that instruct meters as to which flows they should measure and meter readers as to which meters they should collection from and at what intervals.

The programs comprising the NeTraMet system are:

netramet, the basic metering program;

nemac, the combined manager and collector for the NeTraMet meter;

netflowmet, a meter that takes input from a Cisco router via Cisco NetFlow;

srl, an optimizing compiler for the Simple Ruleset Language (SRL);

fd_filter, which reads a flow data file and processes it as requested in a format file, e.g. computing flow rates, changing file formats, filtering flows or statistical records;

fd_extract, reads a flow data file and produces a data matrix file;

nifty, a network traffic flow analyzer that monitors network segments to which NeTraMet meters are attached and displays information about the traffic flow on that segment; and

nm_rc, a remote console program for NeTraMet for listing the busiest flows observed by a meter.

Source and binary distributions of NeTraMet are available, with one of the latter being for Linux Intel platforms. The documentation includes several manuals in PDF format along with a set of man pages.
[http://www.auckland.ac.nz/net/NeTraMet/]
[ftp://coast.cs.purdue.edu/pub/tools/unix/NeTraMet/]
NetRexx: A human-oriented language designed to make writing and using Java classes quicker and easier than in Java. NetRexx blends the syntax of Rexx with the robustness and portability of the Java environment, which results in a language tuned for both scripting and application development. The reference implementation of NetRexx is a compiler which first translates the NetRexx source code into Java source code. A Java compiler is then used to generate the Java bytecodes (i.e. class files) for execution. NetRexx can use any Java class and vice-versa. The compiler is written in NetRexx and should run on any platform that supports the Java toolkit and compiler, i.e. the JDK.
The NetRexx distribution includes the class files which should work on all Java platforms, the compiler which works on platforms for which the JDK is available, and documentation in both HTML and ASCII format. Separate documentation is also available in PostScript format. See Cowlishaw (1997).
[http://www.ibm.com/Technology/NetRexx/]
NetSaint: A program for monitoring hosts and services on a network which can email or page someone when problems arise are or resolved. This runs in daemon mode, intermittently running checks on various specified services. The actual checks are performed by separate plugin programs that return the status of various services to the daemon, which processes them appropriately. The features include:

monitoring of a wide array of network services;

an extensible plugin interface for user-developed service checks;

a wide variety of standard plugins for TCP ports, SMTP, POP3, FTP, NNTP, HTTP, ping, DNS, disk space, current users, processes, processor load, HP printers, MRTG traffic and generic. Novell servers, Oracle database servers and PostgreSQL databases;

defining event handlers to be run during service or host events; and

Web output, e.g. current status, notifications, problem history, etc.

A source code distribution is available under the GPL.
[http://netsaint.linuxbox.com/]
Netscape: A Web browser. The latest "killer app" from the folks who originally developed the Mosaic browser and went on to a net worth of billions in the market. The Linux version of the Netscape browser is freely available under certain conditions that are detailed at the site. It is also unsupported, but it seems to work pretty well for me.
[http://www.netscape.com/]

Fortify

A program that provides unconditional, full-strength, 128-bit cryptography to users of Netscape Navigator (v3 and v4) and Communicator (v4). While Netscape has been able to perform SSL encryption since v2 and the cipher functions have no inherent key length limitations, the export grade browser only generates and uses 40-bit secret keys. Fortify allows Netscape to generate and use 128-bit secret keys whenever possible. It does this by installing itself directly into the browser at a small number of places, i.e. neither SSL proxy servers/relays, supplementary libraries, or other support programs are needed or involved. Nor are special certificates required in the server or browser.
Fortify is run against a vanilla copy of Netscape to create an executable as strong as the U.S. domestic version. This will enable connections with full strength SSL servers to use 128-bit encryption from end-to-end in a manner completely transparent to the user. In Netscape 4.x versions it also upgrades the maximum RSA key size and the S/MIME email ciphers. Source and binary distributions are available. It should be noted that Fortify is only needed for export versions of Netscape. U.S. domestic versions already have the capabilities it can add.
[http://www.fortify.net/]

nDVI

A TeX VI viewer plugin for Netscape.
[http://www.nikhef.nl/~t16/public/ndvi/ndvi_doc.html]

netscape-wrapper

A sh script for invoking Netscape on a UNIX box. The functionality and features include:

copying initial default files;

implementing a Postscript bug workaround;

performing a security check;

setting up the environment;

an options subset for news and mail features;

defaulting to opening a new window before opening Netscape to avoid lock file problems.

[http://ssadler.phy.bnl.gov/~adler/netscape.wrapper/]

Plugger

A multimedia plugin for UNIX Netscape that handles Quicktime, MPEG, MP2, AVI, SGI-movie, Tiff, DL, IFF-anim, MIDI, Soundtracker, AU, Wav and Commodore 64 audio files. Version 2.2 or greater also allows MPEG audio and video to be played streaming. Plugger uses external programs to show and/or play the different formats, e.g. Xanim, TiMidity, Maplay, Tracker, and ImageMagick.
[http://www.hubbe.net/~hubbe/plugger.html]

Tcl Plugin

A Netscape plugin which allows the use of applets written in Tcl/Tk.
[http://www.scriptics.com/plugin/]
NetScript: A programming language and environment for building networked systems. NetScript programs are organized as mobile agents dispatched to remote systems and executed under local or remote control. This was created to simplify the development of networked systems and to enable their remote programming. A NetScript network consists of a collection of nodes (e.g. PCs, switches and routers) which each run one or more engines, i.e. a software abstraction of a programmable packet-processing device. Engines consist of dataflow components that process packet-streams that flow through them, with dataflow programs called boxes dispatched to remote engines and dynamically composed with other resident boxes. Composite packet-processing protocols are constructed by connecting together the typed ports of boxes. Typical boxes perform packet header analysis, packet demultiplexing and other protocol functions, and packets flow through successive boxes to perform various protocol functions. This architecture provides for, e.g. an IP router implementation to be dynamically extended with firewall functions simply by connecting more boxes to the dataflow.
The NetScript system consists of two components:

NetScript, a textual dataflow language for composition; and

NetScript Toolkit, a set of Java classes to which the language compiles.

The language itself consists of a dataflow composition language, a presentation language for defining the format of network packets, and a classification language for building packet classifiers. The current (12/98) distribution runs under Linux 2.0 or greater and also requires JDK 1.1.6 or greater. This also runs under the Kaffe virtual machine. Documentation consists of a tutorial and several technical papers.
[http://www.cs.columbia.edu/dcc/netscript/]
NetShell: A UNIX shell-like interface for handling Web information similar to how regular shells handle local information. NetShell works by viewing the Web as another I/O stream, i.e. it accepts I/O to and from files or windows and also provides an easy way to redirect the I/O stream to and from the Web. It communicates directly with Web browsers, i.e. it allows any UNIX program to operate on information obtained from the Web through any browser. The resultant actions can go directly to the browswer, a special TTY window, or to local files. This allow, for example, pages to be folded to included the contents of all links from them, an encrypted page to be decrypted and shown in the browser, or a list of images from the current page to be collected to a file. NetShell has its own GUI in which commands can easily be composed and then executed with a single click. A source code distribution is available which requires Perl and Tk 4.0.
[http://www.cs.arizona.edu/netshell/netshell.html]
NetSolve: A client-server application designed to solve computational science problems over a network. Users may access NetSolve computational servers through C, Fortran, Matlab or Java interfaces. The NetSolve system consists of a set of loosely connected (i.e. on the same local or international network) homogeneous or heterogenous machines (i.e. machines using different data formats can be in the system simultaneously). The three major components are the clients, the agents, and the computational resources. This leads to a three step problem solving procedure wherein: (1) the client sends a request to the agent; (2) the agent chooses the best NetSolve resource for the task according to the size and nature of the problem to be solve; and (3) the problem is solved in the chosen server and the results sent back to the client.
The NetSolve Client and Server packages are separately available. The package source code is written in C and Java and requires compilers for the first if you plan to use the C, Fortran, or Matlab interfaces, and for the second if you plan to use Java. A user's guide is available in PostScript format. Several tests and examples are also included in the distribution. See Casanova and Dongarra (1996).
[http://www.cs.utk.edu/netsolve/]
netstat: See NetTools.
NetStreamer: Software for streaming audio over a 28.8K modem or ISDN at a sample rate of 8 or 16 kHz. NetStreamer has a radio-like frontend that allows you to tune in on programs offered by the NetStreamer Server, a kind of reflector that passes on audio that may be offered by several transmitters. The sound quality is 16 bit mono at 8 or 16 kHz with every sample ADPCM compressed to 3 bits for a bandwidth of 24 or 48 kbit/s. The software includes a Server, a Transmitter, a Receiver, an X11 NetStreamer Receiver, and a NetStreamer Encoder for .tape files.
Source code distributions of all NetStreamer components are available as are Linux Intel binaries. Documentation is contained in an ASCII README file.
[http://flits102-126.flits.rug.nl/~rolf/NetStreamer.html]
netwatch: A program for monitoring network connections. This is based on Statnet but has been substantially for Ethernet emphasis. It dynamically displays the Ethernet status of each connection's activity, and can monitor hundreds of site statistics simultaneously. The features include:

measuring router statistics;

configuration file settings for logging and color times;

automatic mailing of special string occurrence;

MAC Ethernet address watching;

HTTP server connection types;

last GET commond retrieval in HTTP;

FTP server type (attempt);

an IP spoofing monitor;

NETBUS and Back Orifice packet watch; and

security fix for symbolic link attack.

Source and binary distributions are available.
[http://www.slctech.org/~mackay/netwatch.html]
network audio: Software which aids and/or abets the transmission of sound over networks includes:

CyberRadio

Icecast

MIDAS

NAS

Netaudio

NetStreamer

RPlay
Network Entrez: An application providing functionality for browsing, via the Web, bibliographic, nucleotide sequence, genome, protein sequence and 3-D structure databases. The features of Network Entrez include:

a tabbed-folder sequence viewer allowing the quick selection of alternate report formats for a sequence entry;

an explicitly structured 3-D structure database based on crystallographic and NMR structure determinations;

Cn3D, a 3-D structure viewer for viewing and rotating entries from the 3-D database;

a genomes division which presents genome-level views of a large number of complete chromosomes that are tightly linked to DNA and protein sequence records;

a number of completely sequenced chromosomes from viruses and organelles that can be explored via various mouse actions;

virtual complete sequence representations of complete large chromosome sequences that are stored as a series of smaller overlapping records that can be explored via mouse actions; and

partially sequenced chromosomes mapped onto a common coordinate system and aligned by any markers they share.

A source code distribution is available as is a binary for Linux Intel platforms. Documentation is available in Microshaft Word format.
[http://www.ncbi.nlm.nih.gov/Entrez/Network/nentrez.overview.html]
network management: Available software for network management includes:

autostatus, a network and server monitoring program;

btng, a package of network management software;

Cheops, the swiss army knife of networking utilities;

CMU-SNMP, a library providing core functions for writing SNMP agents and managers;

HNMP, a package for monitoring and graphing traffic on large, routed IP networks;

inner-apps, a collection of useful networking programs;

MRTG, a tool to monitor and graph the traffic load on network links;

ntop, a tool for showing network usage like top shows CPU usage;

OSIMIS, an environment for the development of OSI-based applications;

radvd, an autoconfiguration daemon used by routers for implementing IPv6 functionality;

Scion, for collecting SNMP data and producing useful statistics;

Scotty, a Tcl/Tk-based package for developing network applications;

SNMP Sniff, a network sniffer for SNMP packets;

SNMPY, a Python interface to SNMP;

SNMX, an SNMP manager, extensible SNMP agent, scripting language and development environment;

traffic-vis, a network traffic monitoring package;

UCD-SNMP, a library of network management tools based on CMU-SNMP;

Webbin' CMIP, a plug-in for Web servers for viewing, searching and modifying OSI data; and

WILMA, a package for the management of LANs using SNMP and expert systems.
neural nets: Programs that implement some sort of neural net include:

CuPit, a programming language designed to express neural network learning algorithms;

DDLab, a graphical program for studying the dynamics of finite binary networks;

DISCERN, a large and modular neural network system for reading, paraphrasing, and answering questions about stereotypical stories;

Flexible Bayesian Modeling, a package supporting Bayesian regression and classification using neural networks;

GENESIS, a general purpose simulation platform for neural systems;

LEE, an artificial life model and simulator of complexity that evolves populations of neural networks adapting to environments;

NeuronC, a neural circuit interpreted simulation language;

NNFit, a neural network-based data fitting package;

NNSYSID, a set of Matlab tools for neural network-based identification of nonlinear dynamic systems;

PDP++, a C++ library for neural network simulation;

SCNN, a universal simulating system for analog processing neural networks;

SESAME, a system for prototyping and implementing various types of neural nets;

SNNAP, a simulator for neural networks and action potentials;

SNNS, a simulator for neural networks;

SPRANNLIB, a library containing functions for creating, training, and testing feed-forward neural networks;

Swarm, a package for multi-agent simulation of complex systems with neural net capabilities;

Uts, a set of C libraries for building complex or experimental neural networks;

xldlas, an interactive statistical program with data fitting techniques that use neural nets; and

XploRe, an interactive statistical computing environment with neural net capabilities.