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Subject: 3/3 Sc. Softw. Map/LinUX [54 Kb]
From: Aldo-Pier Solari <[log in to unmask]>
Reply-To:Academic forum on fisheries ecology and related topics <[log in to unmask]>
Date:Mon, 16 Dec 1996 19:55:51 GMT

text/plain (1011 lines)

                The LinUX Scientific Software Map
           For circulation in the scientific community
             High Quality Free Scientific Software
                           Part 3/3


GNUPLOT -- 3.5.   Gnuplot  is  a  command-line driven interactive
function plotting utility for UNIX,  MSDOS,  and  VMS  platforms.
The  software  is  copyrighted  but freely distributed (i.e., you
don't have to  pay  for  it).   It  was  originally intended as a
graphical program which would allow scientists  and  students  to
visualize mathematical functions and data.  Gnuplot supports many
different  types  of terminals, plotters, and printers (including
many color devices, and pseudo-devices  like LaTeX) and is easily
extensible to include new devices.  Slackware comes with  gnuplot
binary.        ftp      /pub/gnuplot,      WWW

PlotMTV --  1.4.1  --19/Dec/95.   PlotMTV  is  a multipurpose X11
plotting program and specializes in contour  plots,  but  it  can
also  handle  2D  and  3D  plots.   The plot-types supported are:
contour plots (rectangular grid, as  well as triangular mesh), 2D
line and scatter plots (x-vs-y), 3D surface ,  line  and  scatter
plots,  vector  plots,  probability plots, histograms, barcharts.
The program has an rough but functional Graphical User Interface,
through which it is possible  to  zoom  in, zoom out, pan, toggle
between 2D and 3D plots, and rotate 3D  plots.   Both  color  and
grayscale     postscript     output     are    supported.     ftp       /pub,       ftp
/contrib/applications,                                        WWW,

XGraph with animation.  XGraph  with  animation is a modification
of the popular XGraph plotting program.   It  is  an  interactive
plotting  program  for creating line plots and restricted surface
plots.  WWW

robot  --  0.48  --  30/Oct/93.   XView  based  scientific  graph
plotting program.  Includes  data manipulation, fitting, numerous
plot styles.  Graphs can  be  saved  as  PostScript  files.   ftp      /pub/astrod,      ftp

ACE/gr  --  (xmgr 4.00 alpha -- motif, xvgr 2.10pl1 -- xview).  A
general 2D XY plotting  package  with mouse-powered editing, pan,
zoom, output in PostScript, HPGL,  and  Framemaker  format.   ftp  /pub/users/pturner/acegr,  ftp
/pub/Linux/X11/xapps/math,                                    WWW

GLE  -- 3.3h -- 09/Mar/95 tool to create 2&3 Dim.  graph.  GLE is
a high quality graphics package  for scientists, combining a user
friendly interface with a full range of facilities for  producing
publication  quality  graphs,  diagrams, posters and slides.  GLE
provides LaTeXquality  fonts  together  with  a flexible graphics
module which allows the user to specify any feature  of  a  graph
(down  to  the line width of the subticks, for example).  Complex
pictures can be drawn  with  user  defined subroutines and simple
looping sturctures.  Current device drivers  support  DECWINDOWS,
REGIS,  TEK4010,  all  PC  graphics  cards,  VT100s, HP-Plotters,
PostScript Printers, EPSON  Printers  and LaserJet Printers.  ftp     /graphics/graphics/packages/gle,      ftp             /pub/Linux/apps/math,             WWW

Gri  --  2.050  --  08/Oct/95.  Gri is a programming language for
drawing science-style graphs.   It  is  not  mouse-driven, and it
does  not  draw  business-style   graphs   (e.g.    pie   charts,
three-dimensional graphs).  Gri has substantial power in advanced
applications.  It has been proven to be easy to learn; for simple
applications,  the  learning  curve  is  less than an hour.  Many
users regard Gri as the plotting equivalent of the LaTeX document
preparation       system.         ftp
/users/kelley/gri/,                                           WWW

DAVID (DAta VIsualization and Diagnostics) system is entirely  in
'C' and runs within the Unix operating system, under the X Window
System,  Version  11R5  and  can  be  printed through any printer
supporting PostScript.  Graphics  can  be  displayed on black and
white as well as color graphics monitors, and can handle graphics
on multiple windows as well  as  on  multiple  graphics  displays
simultaneously.     DAVID   facilitates   extraction,   tracking,
quantification and  mathematization  of  evolving and interacting
amorphous  objects,  from  e.g  time-dependent   multidimensional
simulations.   DAVID can also provide a highly interactive way to
compare different variables  with  two  variable distribution and
juxtaposition.  It can extract skeletal  representation  with  an
interactively  controlled  smoothing  algorithm even from a noisy
environment.  DAVID  can  interactively  analyze  skeletal lines,
graphs, display and label quasi-local slope  and  curvature.   An
interactive  threshold-adjusting  tool provides a way to discover
hidden coherent structures.  DAVID can also produce journal-ready
and visual aid  hardcopies.   Compilation  is required for Linux.

Mesh-TV is an interactive graphical analysis tool for visualizing
and analyzing data on 2D and 3D meshes.  It is a general  purpose
tool  in that it handles many different mesh types, provides many
different  ways   of   viewing   the   data,   and  is  virtually
hardware/vendor independent while still providing graphics at the
speed of the native graphics hardware.  Linux port is  available.
Binaries  for  other  workstation and documentation is here.  WWW

Xgraphic is a very easy to use graphic software to plot curves on
Unix                      workstations.                       WWW

xgobi  --  1/Nov/94.   XGobi  is  an  X  Window  application  for
interactively  exploring  data.   Current  functionality includes
brushing, identification, and the editing of connected lines,  as
well  as  rotation  and  the grand tour, with several interactive
projection pursuit indices.  Several  functions  can be linked so
that actions in one window are  promptly  reflected  in  another.

xfarbe  is  a contouring program for iso-lines with the following
characteristics:  *  high  quality  nonlinear  interpolation with
bicubics on a  rectangular  grid  *  area  filling  capability  *
X-Window and Postscript output * Customization with resource file
*  Interactive  labeling  of  contour  lines  *  Interactive data
probing for value and derivatives  * Placing of symbols according
to information read from a file  *  Exact  location  extrema  and
saddle  points  *  Computation  of profiles.  WWW http://www.fhi-

Xdang does  vector  plots,  contour  plots,  and  color maps.  It
slices and dices  3d  data  and  has  cartesian  and  cylindrical
coordinates.  WWW http://barkley.ME.Berkeley.EDU/~dan/

yplot  --  0.9 -- 10/Jun/96.  yplot is an interface to the PLplot
plotting library (see next  section)  written  as an extension of
Yorick.  This combination allows one to quickly and easily create
high-quality scientific plots from data, even in large structured
files.  yplot implements  2D  line  and  scatter  plots,  contour
plots,  3D surface, mesh and scatter and line plots.  The user is
given full  control  over  every  aspect  of  the plot, including
symbol types, line  types,  label  placement,  fonts,  etc.   ftp /pub/Linux/apps/math/


Vogl  -- 1.6.2g.  VOGL is a device portable graphics library that
tries to be Silicon  Graphics  Iris GL compatible.  Our intention
is that any VOGL program will  compile  unchanged  on  a  machine
running   SGI   GL.    Supported   devices  are:  postcript,  sun
workstation, apollo workstations, X11,  tektronix, hpgl, dxy, and
the ibm pc cards.  This library is callable  in  C  and  Fortran.

Ygl  emulates  SGI's GL routines under X11.  Included are most of
the two-dimensional graphics routines, the queue device routines,
some query  routines,  doublebuffering,  RGB  mode with arbitrary
visuals and ditering and most of the window  attribute  routines.
ftp       ftp.thp.Uni-Duisburg.DE       /pub/source/X11,      WWW
http://WWW.thp.Uni- Duisburg.DE/Ygl/ReadMe.html

libglto -- 16/Dec/94.  Libglto is  an  X Windows based version of
GL.  It allows programs that depend on GL to  be  run  on  any  X
Windows              based              machine.              WWW

Mesa -- 2.0 -- 10/Oct/96.  Mesa is a 3-D graphics library with an
API which is very similar  to  that of OpenGL($$).  To the extent
that Mesa utilizes the OpenGL command syntax  or  state  machine.
However,  the  author  makes  no  claim that Mesa is in any way a
compatible  replacement   for   OpenGL.   ftp
/pub/Mesa, WWW

Following are some packages that could work with Mesa:

GLUT -- 3.1.  OpenGL  Utility  Toolkit.   It  is  a  nice  OpenGL
toolkit  which  allows  one  to write OpenGL applications without
having to know anything about the window system and its interface
to OpenGL.   It  is  much  nicer  than  the  aux  and tk toolkits
initially  used  by  SGI.   It  works   with   Mesa   too.    WWW,    WWW

f90gl is a fortran interface for Mesa and GLUT, which can also be
used  with  OpenGL.   It  provides both fortran 77 and fortran 90
interfaces.  WWW

Togl   is   a    Tk    widget    for   OpenGL   rendering.    WWW

Dore  --  6.0.1  --   20/Feb/95.    (Dynamic   Object   Rendering
Environment).    Dore'  is  a  powerful  3D  graphics  subroutine
library.  It provides a  comprehensive  set of tools for creating
graphics applications.  It is also easy  to  use,  portable,  and
extendable.   This  version  has  interfaces/drivers to X11, PEX,
IrisGL, OpenGL, Postscript  and  more.   It  has been ported onto
most unix systems, including Linux and FreeBSD.  It has also been
ported    to    Windows    NT     3.5.      ftp
/graphics/graphics/packages/dore,       ftp

TAGL  -- 2.2 -- Mar/96 (Threedee Advanced Graphic Libraryis) is a
C++ library  for  3D  graphics,  gouraud  shading,  ZBuffering, a
subset of SGI-GL.  ftp /pub/Linux/libs/graphics/,
ftp   /pub/packages/development/graphics,   ftp
/pub/sci/virtual-reality/software/tagl/tagl21src.tgz,         ftp            /graphics/graphics/tagl,             WWW

Grxlib  --  1.03g  -- 28/Aug/95.  This is the GRX library that is
used under the DJGPP DOS Extender.  It has been converted to work
under the Linux OS  with  support  from the svgalib library.  ftp /pub/Linux/libs/graphics/

EZWGL.  The EZ Widget and Graphics Library (EZWGL) is a set of  C
functions  for  developing  graphical  user  interface  (GUI) and
writing graphics applications  under  the  X  window system.  The
goal of EZWGL is to provide a tool that simplifies the design  of
graphics  applications  under  the  X  window  system programming
environment.  The EZWGL programming  interface  is designed to be
simple, and yet  still  meet  the  needs  of  moderately  complex
graphics applications.  WWW

AGL  (Astronet  Graphic Library) is a graphic library designed to
be portable on different  systems,  with  both  a C and a FORTRAN
programming interface.  ftp /pub/agl/

gd is a graphics library.  It allows your code  to  quickly  draw
images  complete with lines, arcs, text, multiple colors, cut and
paste from other  images,  and  flood  fills,  and  write out the
result as a .GIF file.  WWW

cd is a graphics library.  It allows your code  to  quickly  draw
images complete with lines, arcs, rectangles, polygons, text, and
multiple  colors.   most geometric shapes can be filled or have a
hatch  pattern  as  well.   The   output  is  a  CGM  file.   WWW

lib3d -- 0.1.7 -- 28/Jul/96.  A fast z-buffer  rendering  library
with an api optimized for software implementation.  Provides flat
shading with ambient - directional lighting.  Currently makes 25k
poly/sec   in   a   dithered   8   bit   Xwindows   visual.   ftp /pub/Linux/X11/devel/


StarOffice -- 3.1 (second beta).   Star  Office 3.1 is a suite of
office productivity applications containing StarWriter 3.1  (word
processor),  StarCalc  3.1  (spreadsheet), StarDraw 3.1 (graphics
and presentation  package),  StarImage  3.1  (image manipulation)
StarChart 3.1 (bar-, pie- and  other  charts)  and  StarMath  3.1
(formula  design).  StarOffice 3.1 makes heavy use of common code
in shared libraries, therefore using relatively few resources for
the level of functionality.   The  final  version will be free of
charge for non- commercial use.  You will have to buy  a  license
for        commercial       use.        ftp
/pub/Linux/apps/staroffice,                                   WWW

LyX  (formally  Lyrix)  --   0.10.0   --  30/Jul/96.   LyX  is  a
word-processor for X11, using LaTeX (2e) to  format  the  output.
It   allows   easy   access  to  LaTeX  formatting  commands  and
almost-WYSIWYG display.   latex2e  is  necessary  to  compile the
documents and print.  Unlike xword, it is very much  usable  now,
and  is  undergoing rapid development.  Unlike WordPerfect, it is
small, fast, and free (GPL'd).   While the author still considers
it alpha, he think it's quite stable.  The biggest lapse  now  is
documentation,   which   will   be   forthcoming   shortly.   ftp         /pub/Linux/X11/xapps/editors,         WWW,                       WWW

Cicero is a  wordprocessor  running  under  X11R6 using Motif2.0.
Cicero deals with mulitple fonts at any size you like and  X  can
display.   It  comes  with  an  easy  to  use fontinstaller, that
installs Postscript Level 1 Fonts  in X, ghostscript, TeX (dvips)
and Cicero.  This is a must because without  these  unique  fonts
WYSIWYG          is          not          possible.           WWW

*Word (early development).  It is a wordprocessor being developed
via   the   Internet  by  a  lot  of  enthousiast  people.   Main
development is done on the Linux-platform, but it is designed for
portability.  It  will  support  X-windows,  under  a  variety of
window- managers,  and  text-mode,  through  a  curses-interface.
This     is     one     of     the     Linux    Projects.     WWW

SciTeXt -- alpha 3 --  11/Nov/96.  SciTeXt is a new wordprocessor
for UNIX - Systems.  It tries to combine  the  requirement  of  a
modern  office-packet.  The following list enumerates some of its
most important  features.   o  User-Interface  --- Objectoriented
handling, Full WYSIWYG with free choice of zoom, Supports  Type-1
PostScript  fonts,  Contextsensitive  toolbars  with bubble help,
Independent of  language  by  a  special  Translation-Table, Free
keyboard and menu shortcuts  with  a  configurable,  ActionEvent-
Table  Online  help with own Tcl/Tk helpbrowser, Userinstallation
with  Tcl/Tk-Script.    o   Wordprocessing   ---  Parapraph-  and
Documenttemplates, Auto-Correction, spellchecker,  Thesaurus;  no
data   yet   :-(,   Footnotes,   table   of   contents,  indices,
chapternumbering, glossary,  Itemize  and  enumeration.  o Layout
--- Free  frames  for  text,  graphic  etc.,  Formulars,  Tables,
charts,  mathmatical  plots.   o  Documentexchange  ---  Send and
receive SciTeXt documents via  E-Mail,  Drag & Drop, Many import-
and exportfilters for text und graphic, Faxing of  documents.   o
Miscellaneous  ---  Variable  choice  of  printer  with automatic
detection  of  usability  Usable  as  an  Integrated  Development
Environment          similar          to          WEB         WWW,                        WWW

TeX Shell -- not really a word  processor.   If  you  don't  mind
typing   TeX/LaTeX  commands  and  you  are  just  tired  of  the
editing-compiling-viewing cycle,  TeX  Shell  is  what you should
get.  It allows you to edit  your  document  and  then  click  to
compile,  click to view and click to print.  There are three such
programs available  as  far  as  I  know  of.   TS:  TeXShell for
X-Window (Tcl/Tk) ftp  /pub/Linux/apps/tex  look
for  tsYYMMDD.tgz X-Window Shell for TeX (OpenLook or Xaw/Xaw3d))

xtem:  a  graphical  user  interface  to  control  the  TeX/LaTeX
facilities.                                                   WWW

Linuxdoc-SGML -- 1.5.  Linuxdoc-SGML is a text-formatting package
based  on  SGML  (Standard  Generalized  Markup  Language), which
allows you to produce LaTeX, HTML, GNU info, LyX, RTF, and  plain
ASCII  (via  groff)  from  a  single  source; due to the flexible
nature of  SGML  many  other  target  formats  are possible.  WWW

Quikscript  is  a  portable  typesetting   system,   written   in
PostScript.   It  enables documents to be prepared on any type of
hardware, using visible layout marks to control the appearance of
the  output,  and  produce  output  on  a  PostScript  printer by
despatching  Qs  and  the  document  file  to  the  device.    No
processing  is  performed by the host hardware; all processing is
done within the printer.  WWW

Qist  (formerly  called  Vinea).    Qist   is  an  SGML  document
engineering utility for the X Window system.  It  is  written  in
Tcl/Tk,   and  features  a  nice  graphical  user  interface  for
manipulating SGML documents.  It  does not do anything remarkable
by itself.  It merely acts as a kind of a launch pad for  several
free  SGML  utilities (so it serves as a TeX Shell too), covering
the whole process  -  writing, validating, formatting, previewing
and printing the finished document.  Vinea also makes use of  the
bibliography  database  features  of  LaTeX  and GNU refer, which
makes   referencing    other    works    extremely   easy.    WWW

Doc from InterView Package -- available in Slackware.  Doc  is  a
WYSIWYG  document  editor.   In  addition to text, doc contains a
simple table editor, and it  can import graphics generated by the
drawing editor Idraw (also in Interviews) and  several  types  of
rasterized images.  The editor's functionality and terminology is
modeled  loosely  after  the LaTeX docu- ment preparation system.
In particular, doc  stores  its  documents  in  a  format that is
reminiscent of LaTeX; you can translate many LaTeX documents into
doc format with relatively little effort.

The Andrew User Interface System (AUIS)  --  63L4.   AUIS  is  an
integrated  set  of tools that allow you to create, use, and mail
multi-media documents  and  apps  containing  formatted  text and
embedded objects.  This package is aimed at the  WORD  PROCESSING
audience.    ftp   /pub/Linux/X11/andrew/,  ftp            /pub/AUIS/bin-dist/,            WWW

MathSpad Editor.  The editing tool MathSpad has been developed to
facilitate writing mathematically  oriented documents.  At first,
the main goal was to create an interface for  editing  structured
expressions combined with plain text.  The editor was built so as
not to restrict the user to any mathematical convention, notation
or  symbol  set, since the initial target group often created new
notations and symbols.   The  principle design element introduced
in order to realise this requirement was the notion of a  stencil
consisting  of a number of templates.  The flexibility built into
the original design has meant that  the system is also useful for
the creation of structured texts other than  mathematical  texts,
such  as  HTML  documents,  these  applications  not  having been
envisaged   when    work    on    the    project    began.    WWW

Xy-pic -- 3.2 -- 18/Oct/95.  Xy-pic is a package for  typesetting
a  variety  of  graphs  and diagrams with TeX.  Xy-pic works with
most formats  (including  LaTeX,  AMS-LaTeX,  AMS-TeX,  and plain
TeX), in particular Xy-pic is provided as  a  LaTeX2e  `supported
package'.   It  uses  the  principle  of  `logical composition of
visual components'.  It  is  structured  as several modules, each
defining a mnemonic plain text notation for a particular kind  of
graphical  object  or  structure.   Example  objects  are arrows,
curves, frames, and  colouring/rotation  on  drivers that support
it; these can be  organised  in  matrix,  directed  graph,  path,
polygon,   knot,   and   2-cell   structure.    ftp
/diku/users/kris/TeX/,  ftp  /pub/maths/TeX/,
WWW,       WWW

Lollipop is `TeX made  easy'.   Lollipop  is a macro package that
functions as a  toolbox  for  writing  TeX  macros.   It  was  my
intention to make macro writing so easy that implementing a fully
new  layout in TeX would become a matter of less than an hour for
an average document, and that  it  would  be a task that could be
accomplished by someone with only a very basic  training  in  TeX
programming.   Lollipop  is  not  compatible  with  plain TeX and
LaTeX, though.  Even though  LaTeX  is  used pretty much all over
the scientific world, developing styles in Lollipop  is  so  much
more easier than in LaTeX.  ftp /pub/eijkhout/tex/

Thot  is  a  structured  document  editor,  offering  a graphical
WYSIWYG  interface  under   X-Windows.    It   offers  the  usual
functionality of a word processor,  but  it  also  processes  the
document  structure.   It includes a large set of advanced tools,
such as a spell checker and  an index generator, and it allows to
export documents to common formats  like  HTML  and  LaTeX.   WWW

DocuGen  -- 2.0.  DocuGen is a collection of several programs, or
tools, that can be used  to  help  you more easily create complex
documents.  With the same source file,  the  DocuGen  tools  will
allow you to generate professional documents in HTML, ASCII Text,
and  Platform Independent Text.  This can save hours of time that
would otherwise be spent  retyping  and reformatting text you had
already written.  DocuGen seems to be mainly used by HTML authors
because of the extensive support for HTML.   Document  templates,
include   files,  auto  image  sizing,  detailed  date  and  time
functions and much more all ease  an HTML author's job of keeping
an entire Web site running smoothly with  their  own  specialized
"look-and-feel".  WWW

Didot  (early development).  The Didot Project is the creation of
a publishing software package.   We  plan  to  implement a lot of
common and uncommon features but at the  moment  we  are  in  the
early  phases  of  the  implementation.   The  component software
architecture  will  support  easy  creation  and  manipulation of
compound documents, so you can use Didot  as  a  word  processor.
WWW http://physkn00.phys-te.uni-

Lout  -- 3.08 -- Jun/96.  Lout document formatting system reads a
high-level description of a  document  similar  in style to LaTeX
and produces a PostScript file which can be printed on many laser
printers and graphic display devices.  Plain text output is  also
available.   ftp /jeff/lout, ftp

Dtop --  Beta  1.4  (The  official  release  will be commercial).
Chinese-English  desktop  publishing  package  (Behavior   Design
Corporation,  Taiwan).   It has full-featured high quality WYSWYG
DTP  functions,  including  text,  equations,  graphics,  tables,
images, copy-paste,  etc.   Note  that  the  documentation  is in
Chinese.                     ftp          
/pub/software/linux/X11R6/dtop1.4/README.DTP,  ftp

Here is a document that shows  how  to  combine  text,  pictures,
figures  and  images  in a LaTeX document.  ftp


Hv (For Hot Views)  is  a  library  for developing graphical user
interfaces for scientific and engineering  applications.   It  is
based on X, Xt and Motif and has been tested on most Unix flavors
including  Linux.   It also include Hvplot, a scientific plotting
package built using the  Hv  graphical user interface development
library.  WWW

XForms -- 0.81 --  5/Jul/96  (free  for  non-commercial  use  and
binary  only).   XForms is a graphical user interface toolkit and
builder based on Xlib for X Window Systems.  XForms is a portable
and efficient C  library  that  can  be  used  in  both C and C++
programs.  The library works in all visuals and all depths (1-24)
and comes with a rich set of objects such  as  buttons  (of  many
flavors, including color XPMs as labels) , browsers, sliders, and
menus  integrated into an elegant event/object callback execution
model that allows fast  and  easy construction of X-applications.
It also has OpenGL (on SGI) and Mesa support.  The Forms  Library
is  very  intuitive  and  simple  to  use.   It  is  by  far  the
easiest-to-learn and easiest-to-use system for X GUI development.
You  can  start writing XForms based programs within an hour once
you go though the first five  pages of the documentation and have
run and read a couple of the demos.  Actually, you don't have  to
write  any code, the bundled GUI builder will do it for you.  ftp  /pub/xforms,  ftp /pub/XFORMS,

PyXForms  is  a  binding  between   Python   and   XForms.    WWW

Qt  --  1.0 -- 01/Oct/96.  Qt is an object-oriented framework for
developing graphical  user  interface  applications.  It includes
around  100  classes,  both  GUI-specific  and  general   utility
classes,  as  well  as  support  for  component programming.  ftp      /pub/linux/qt,      ftp
/pub/Linux/devel/c++, WWW

wxWindows -- 1.66B  --  21/May/96.   wxWindows  is  a toolkit for
developing multi- platform, graphical applications from the  same
body of C++ code.  X11, motif, xview, open-look, ms-windows.  ftp    /pub/packages/wxwin,   ftp
/pub/Linux/X11/devel/wxWin,                                   WWW

Fresco  is   an   object-oriented   user   interface  system  for
development  of  window-based  applications.   It  is  a   design
evolution  of  the  InterViews  toolkit  that  was  developed  at
Stanford  University in the late `80s and early `90s.  The Fresco
architecture brings together objects  that traditionally have not
mixed.  User interface objects such as sliders, buttons, and text
editors - as well as the "layout" objects used to compose them  -
can  mix arbitrarily in Fresco with graphical objects (those that
perform  graphical  transformations).   Fresco  uses  a  standard
object model, CORBA ,  which  allows  for object distribution and
provides a  standardized,  high-level  notation  called  IDL  for
object  definition.   Fresco  also provides support for Tcl-based
scripting,   multi-threading,    resolution   independence,   and
internationalization.  Fresco is currently under  standardization
process       within       the       X      Consortium.       WWW,                   WWW for Linux specific info.

VXP -- 2.0 --  10/Feb/95.   VXP  is an integrated Motif graphical
user interface (GUI) builder.  Application developer can build  a
working  Motif GUI in minutes, simply by pointing and clicking on
predefined icons which represent Motif widgets, then dragging and
dropping them on  the  design  space.   VXP provides developer an
environment  to  design  a  Motif  GUI   for   your   application
interactively,  and  generates the C code required to produce the
GUI.   VXP  also  lets   developer   edit  non-GUI  code  of  the
application,  compile  the  application   and   test   it.    WWW

Amulet (Automatic Manufacture of Usable and Learnable Editors and
Toolkits) is a user interface development environment for C++ and
is  portable  across  X11  and Microsoft Windows NT.  A Macintosh
version will be available probably in late '95.  Amulet helps you
create graphical, interactive user  interfaces for your software.
More than just another free virtual toolkit, Amulet includes many
features  specifically  designed  to   make   the   creation   of
highly-interactive,    graphical,    direct   manipulation   user
interfaces significantly  easier,  including a prototype-instance
object model, constraints, high-level  input  handling  including
automatic    undo,    and   a   full   set   of   widgets.    WWW

SNAPIX --  3.1.9  --  29/Mar/96.   X11/Motif  user  interface and
application generator.  Snapix is based  on  a  complete,  typed,
structured,  event driven, object oriented language which offers:
* ease of use, wellknown C  syntax (no lengthy learning curve), *
short development cycle, *  very  scalable  and  maintainable,  *
small  memory  and  disk  footprint, fast execution speed, * high
reliability.  The package  includes:  *  an advanced, structured,
object oriented language, * a  graphics  editor  which  generates
Snapix source code, * an interpreter/compiler, * a runtime/driver
for  standalone  application  usage,  *  full documentation: ref.
manual,  installation  and  user  guides,  (poscript  files), and
online hypertext help.  personal use  (nonprofit,  noncommercial)
and education read package embedded COPYRIGHTS file before usage.
ftp /linux

Marx  is an interpreted script language based on a C-like syntax.
It provides a quick way  of creating Graphical User Interfaces in
X windows.  Besides GUI building, marx also  provides  simplified
schemes  for  UNIX  process  control, direct shell command/script
execution  and  inter-client   communication  via  sockets.   WWW

XF allows you to interactively build and modify a user  interface
based  upon  the Tcl/Tk package.  The output generated by XF is a
script that  can  be  executed  with  wish  or  any  other Tcl/Tk
interpreter.  WWW

SpecTcl -- 0.1a -- 8/Nov/95.  An alpha release of a Visual  Basic
style   GUI   builder   for   Tk/TCL   4.0/7.4   from  SUN.   ftp   /tcl/,   ftp

V is a portable  C++  GUI  Framework  intended  to develop a wide
variety  of  applications  on   different   graphical   interface
platforms.  It is very complete and suitable for a large majority
of  custom GUI applications.  Applications developed using V will
have the look  and  feel  of  the  native  platform,  yet will be
portable  across  platforms.   Most  standard  GUI  objects   are
supported  by  V, including windows with menus, status bars, tool
bars, and a drawing canvas;  modal  and modeless dialogs with the
most common controls (buttons, lists, labels, text  entry,  check
and  radio  buttons,  etc.);  and portable printing support.  WWW

MrEd is a graphical user interface (GUI) development environment.
MrEd's underlying language  is  Scheme,  extended  with an object
system  and  a  thread  package.    The   Scheme   implementation
(MzScheme) is fast and smoothly integrated with the environment's
graphical   primitives  (wxWindows).   These  primitives  include
text-editing tools that can be employed within an application for
editing    a    mixture    of    text    and    graphics.     WWW

VisualX (early beta).  Works/looks  similar to Microsoft's Visual
Basic; but based on tcl/Tk.  A user generates a user interface by
dragging widgets  from  a  toolbox.   Event  handlers  for  these
widgets  may  be  written  in  C, C++, Smalltalk, or tcl/tk.  WWW (not yet) contact Dr.  Peter Beery

XVisual -- 1.0.1.  Xvisual is a system to allow X-users to create
X applications using  a  visual development environment.  Xvisual
supports the Athena 3D widget set (it will support  the  standard
set  soon)  and  allows  visual  positioning  and  planning of an
application.  Xvisual also  allows  the  programmer  to write C++
code segments and compile these with the visual components  as  a
'project'.    ftp   /pub/xvisual,  WWW

XPIP.  The  X  Portable  Interface  Package  (XPIP)  is  a freely
distributed development tool which allows application programmers
to quickly construct  graphical  user  interfaces  (GUIs)  in  an
X-Windows  environment.  The interface takes the form of a series
of user- definable  widgets  -  buttons,  sliders, dials, etc.  -
which applications employ for varying parameters,  control  flow,
input/output, and other alterable processes.  Although not nearly
as  comprehensive  as  several  commercial and other freeware GUI
packages such as xtoolkit  and  Tcl/Tk.   XPIP provides a balance
between ease of use and sophistication which  make  it  appealing
for       the       more       casual       programmer.       WWW

lxb -- 0.4 --  11/May/96.   An X/Motif interactive graphical user
interface builder.  With it you can build a GUI made up of  Motif
widgets  instantiated  by clicking on icons, move and resize them
with the mouse,  edit  their  resources,  and  move  about in the
widget heirarchy via the arrow keys.   Once  the  GUI  is  built,
pressing  a  button  will  produce all required C source files to
build the GUI, and an X resource file and Makefile.  This version
of lxb is not completed.  Not all Motif widgets are included, nor
can       all        resources        be       edited.        WWW

Grafix -- 1.2 -- Nov/95 a C++-package for  assisting  programmers
to  write  programs  with  graphic  user interfaces for X-window,
mainly a class library  for directly instantiating window objects
and deriving new classes, many realistic example  programs.   ftp /pub/Linux/X11/devel

MGUI  --  1.6.1 -- 18/Sep/96.  MGUI library has a 100% compatible
API and  an  identical  look  &  feel  in  DOS,  Windows and Unix
X-Window environments.  A manager object automatically  positions
and  resizes  its  children,  making  layout construction simple.
MGUI Designer is a code  generator tool that helps programmers in
the construction and maintenance of the application windows.  ftp /pub/Linux/X11/devel/

FL is a GUI toolkit written in C++.   It  was  created  to  build
in-house  applications at Digital Domain for image processing and
3D graphics.  FL is designed  to  be somewhat compatable with the
popular Forms Library, but it is a  complete  rewrite  into  C++,
with  the  Forms  objects and function pointers replaced with C++
objects        and         virtual         functions.         WWW

User Interface Software Tools.   A  fairly  complete  list.   WWW


WEKA  --  2.1 .  A machine learning workbench, is a collection of
machine learning methods,  linking  them  together  with a common
data file format and an intuitive user- interface.   There  is  a
command line interface to the system which is provided to develop
scripts that analyse and process extremely large volumes of data,
with  the  user-interface  adding  a  simple guided procedure for
running experiments using different  machine learning methods and
data visualisation tools.  WWW

AERO -- 1.7.0 -- 31/Aug/96.  AERO (Animation Editor for Realistic
Object motion) is an  X-window  based  tool  for  simulation  and
visualization  of  rigid-body  systems.  AERO contains a 3D scene
editor for designing simple blocks  world scenes.  Objects may be
placed in space, linked to each other, and forces may be  exerted
onto  them.   AERO can be used for exploring the physical laws of
mechanics and also for  generating realistic computer animations.
AERO is available free of charge as public domain software.   ftp          /pub/AERO.           WWW

Genghis.   This  is  a  graphics simulation that was developed as
part of  author's  PhD  studies.   It  models  the  structure and
control  system  of  a  well  known  six   legged   robot.    ftp /pub/techreports/RDT/code/

COOOL  (CWP  Object-Oriented  Optimization  Library).  COOOL is a
package  of  tools  for  writing  optimization  code  and solving
optimization  problems.   Our  special  interest  is  in  solving
inverse problems, but the  library  should  be  useful  for  many
different  kinds of problems.  COOOL consists of a library of C++
classes which facilitate  all  aspect  of developing optimization
codes.  Further, it has a suite of general purpose  routines  for
solving   linear   and   nonlinear  optimization  problems.   WWW

NAMD is a  parallel,  object-oriented  molecular dynamics program
designed for high performance molecular dynamics  simulations  of
large  biomolecular  systems.   Linux  port is mentioned in their
installation             README             file.             WWW

MOPAC  is  a  general-purpose  semi-empirical  molecular  orbital
package for the study of chemical structures and reactions.   ftp /mopac7/LINUX/

UNCERT is a public domain uncertainty analysis and geostatistical
software  package.   It was developed for evaluating the inherent
uncertainty   in   describing   subsurface   geology,   hydraulic
properties,  and  the  migration  of  hazardous  contaminants  in
groundwater  flow  systems.   The  package  is  well  suited  for
evaluating  hazardous  waste  sites  and  evaluating  remediation
methods, but the package also  has many general modules which are
usable  by  researchers  from  a  wide   range   of   disciplines
(especially  statistical module that could be useful even if your
are       not       interested       in       geology).       WWW

tacg -- 1.5 -- Sep/96.  A command line tool for  the  restriction
enzyme analysis of DNA.  ftp /pub/tacg

fetch  (Free  Extraction  Tool  for Computational Humanoid) is an
easy swissprot protein  sequence  retrieval  utility.  It is text
based.  It is available in Perl and Linux binary format  compiled
by  Perl compiler.  It can extract any sequences you want as long
as they are in swissprot sequence database(primarily).  Swissprot
is distibuted as a  file  called  'seq.dat'  (around 100 mb, Oct.
1996).  fetch creates an index file (seq.idx) for the entries for
speed.  WWW

MOLMOL -- 2.2.0  --  May/96.   MOLMOL  is  a  molecular  graphics
program   for   displaying,   analyzing,   and  manipulating  the
three-dimensional structure  of  biological  macromolecules, with
special emphasis on  the  study  of  protein  or  DNA  structures
determined       by      NMR.       ftp
/pub/software/MOLMOL, ftp /pub/bruker/MOLMOL

RasMol -- 2.5.1  --  15/Jan/96.   RasMol  is a molecular graphics
program intended for the visualisation of proteins, nucleic acids
and small molecules.  The program is aimed at  display,  teaching
and    generation    of    publication   quality   images.    ftp /pub/rasmol

Raster3D is a set  of  tools  for  generating high quality raster
images of proteins or other molecules.  The core program  renders
spheres,  triangles,  and  cylinders  with specular highlighting,
Phong shading,  and  shadowing.   It  uses  an efficient software
Z-buffer algorithm which is independent of any graphics hardware.

gOpenMol  is  the  graphics  interface  to  the  OpenMol  set  of
programs.  gOpenMol can also be used for the analysis and display
of molecular dynamics trajectories and the display  of  molecular
orbitals,  electron  densities  and electrostatic potentials from
programs         like         the         GaussianXX.         WWW

Babel is a program designed to  interconvert  a  number  of  file
formats  currently  used  in  molecular modeling.  The program is
available  for  Unix  (including   Linux),  DOS  and  Macs.   WWW

PIMM  (Pi-SCF-Molecular  Mechanics   Program)   is   a   combined
SCF/molecular   mechanics   program  for  organic  molecules  and
complexes,     with      parameters      for     compounds     of
C,H,N,O,S,P,Si,F,Cl,Br and ions of Li, Na, K, Mg, Ca, Fe, Co, Ni,
Cu, Zn, Ce, In, Zr, Th.  It is written in Fortran 77  and  tested
on                           Linux.                           WWW

XtalView is  a  complete  package  for  solving  a macromolecular
crystal structure by isomorphous replacement, including  building
the  molecular  model.  It has a simple but comprehensive windows
based  interface.   Standard   file   formats   are  used,  which
facilitates communication between XtalView and programs  such  as
X-PLOR,  TNT,  and  MERLOT.   Free  for  non-commercial use.  WWW

CACTVS Tools.  A visualization  package for chemist.  Features: *
A full-featured 2D structure editor  (csed),  *  A  2D  structure
browser  (csbr),  *  An  Image viewer, which can also compute GIF
images from connectivity alone  (csimg), * A multi-spectra viewer
(NMR, IR, UV/VIS, MS), especially usefil for spectra found on the
WWW (csir), * An NMR viewer with rather restricted  capabilities,
*  An structure data access/download tool for Chemical MIME files
on the WWW  (cswa),  *  A  WWW  structure  database access client
(csws), * An XY  grapher  for  numeric  information  attached  to
structure  datasets,  *  A  client for a database of computed NMR
shieldings (cssharc), *  A  GUI-less  basic  client which can for
example be used for computation services  on  the  internet  (via
dedicated  ports or as CGI program) and for command-line function
testing (csts).  ftp /pub/cactvs/

GAMESS is a program  for  ab  initio quantum chemistry.  Briefly,
GAMESS can compute wavefunctions ranging  from  RHF,  ROHF,  UHF,
GVB,  and MCSCF, with CI and MP2 energy corrections available for
some of these.  Analytic  gradients  are  available for these SCF
functions, for automatic geometry optimization, transition  state
searches,  or reaction path following.  Computation of the energy
hessian permits prediction of vibrational frequencies.  A variety
of molecular properties,  ranging  from  simple dipole moments to
frequency dependent hyperpolarizabilities may be computed.   They
have    Linux    port    but    is    not    tested   yet.    WWW

PLATON is a versatile  crystallographic tool implementing a large
variety of standard geometrical calculations,  tests,  utilities,
graphics,    and    several    filters.     ftp

ORTEP-III.   The Oak Ridge Thermal Ellipsoid Plot (ORTEP) program
is a computer program,  written  in  Fortran, for drawing crystal
structure illustrations.  Ball-and-stick type illustrations of  a
quality suitable for publication are produced with either spheres
or    thermal-motion   probability   ellipsoids,   derived   from
anisotropic temperature factor  parameters,  on the atomic sites.
The program also produces  stereoscopic  pairs  of  illustrations
which  aid  in the visualization of complex arrangements of atoms
and   their    correlated    thermal    motion   patterns.    WWW,                         ftp   /pub/ortep/linux   (for   Linux

RAD       is       a        radiosity        program.         WWW

tierra  --  4.3.   This  is a program that simulates evolution of
creatures (virtual assembly code  programs)  to observe the power
of natural selection.  ftp /tierra

XSurface is an  X11  application  which  allows  the  interactive
design  and  viewing  of  three dimensional smooth surfaces using
multiple Bezier patches.  ftp /pub

Xephem -- 2.8.   An  interactive  astronomy  program for all UNIX
platforms, including Linux, plus VMS.   Requires  X  Windows  and
Motif.    Several   static   executables   are   available.   ftp contrib/xephem/

SESAME  --  4.10  --  24/Oct/94.   SESAME  stands  for  "Software
Environment for the  Simulatio  of  Adaptive  Modular Systems", a
strongly object  oriented  simulation  system  for  computational
architectures   involving   neural  networks.   ftp

SNNS (Stuttgart Neural Network Simulator) is a software simulator
for  neural  networks  on  Unix  workstations  developed  at  the
Institute for Parallel  and  Distributed High Performance Systems
(IPVR) at the University of Stuttgart.   The  goal  of  the  SNNS
project  is  to  create  an  efficient  and  flexible  simulation
environment  for research on and application of neural nets.  WWW

nn/xnn  is  a  system  for  designing,  studying  and  simulating
artificial neural networks.  WWW

PDP++ .  The PDP++ software is a neural-network simulation system
written in C++.  It  represents  the  next  generation of the PDP
software originally released with the  McClelland  and  Rumelhart
"Explorations  in  Parallel Distributed Processing Handbook", MIT
Press,                         1987.                          WWW

LightPipes is a portable set of UNIX-style tools written in C. It
can help you to build  models of optical devices when diffraction
is essential.  Toolbox consists of a set of filters.  Each filter
represent an optical element or a step in a free-space light beam
propagation.    There   are   apertures,    intensity    filters,
beam-splitters,  lenses  and  models of free space diffraction in
LightPipes.  WWW

PCCTS is the Purdue Compiler  Construction  Tool Set and is a set
of software tools designed  to  facilitate  the  construction  of
compilers  and  other translation systems.  PCCTS consists of two
tools, ANTLR  (Another  Tool  for  Language  Recognition) and DLG
(DFA-based Lexical analyzer Generator), assorted  support  files,
sample  Pascal  and  C  grammars,  and  full  source  code.   WWW

The  Linux Software Review (LSR).  A forum to discuss the various
software programs and packages that are available for Linux.  Its
main purpose is to save  you valuable time downloading, compiling
and testing programs that you are not going  to  use  after  all.
You  can  read  the  comments of others, add comments to programs
that are beeing discussed or add a new program or category to the
discussion.  WWW

Linux   software    for    scientists    by    S.    Baum.    WWW

Astronomical        Software        on        Linux.          WWW

Linux  and Chemistry.  Links to chemistry software on Linux.  WWW

Chemistry       Software        for        Linux/UNIX.        WWW

Biocomputing             and             Linux.               WWW

Programs   &   Scripts   For  Information  Retrieval  and  Corpus
Linguistics.  WWW

High       Energy       Physics        and       PC's.        WWW

Linux       in       High-Performance       Computing.        WWW

Linux        Fortran        Information        Page.          WWW

Linux       AI      &      Alife      mini-HOWTO      .       WWW


Scientific                         Web                        WWW

Scientific                     Resources                      WWW

Scientific      Data      Format      Information     FAQ     WWW

Mathematics           Information           Servers           WWW

Some             Mathematics             Resources            WWW

Eric's      Treasure      Trove      of      Mathematics      WWW

Mathematics            Virtual            Library             WWW

Sci-Math                          FAQ                         WWW

Statistics             and              Computing             WWW

Objective-Oriented          Numerics           Page           WWW

Parallel         Programming         with         C++         WWW

Amara's               Wavelet               Page              WWW

Optimization                     Software                     WWW

Catalog     of      Algorithms      for     Approximation     WWW

Computer       Graphics       and        Visualization        WWW

3D Engines List WWW

Software     for     Graphics     and     Data    Analysis    WWW

Graphics   viewers,    editors,    utilities    and    info   WWW

Computer Graphics WWW

Scientific           Visualization           Sites            WWW

Internet        Parallel        Computing       Archive       WWW

Artificial             Life              Software             WWW

SINCRIS  software  list  (Software  for  Crystallolgraphy).   WWW

Biological                      Software                      WWW

X-related programs:

ftp /contrib

GNU-related    programs:     ftp     /pub/gnu
end of Part 3[3]

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