2.8. Scientific and educational software.

Most applications mentioned in this section are easy to use educational. GNU/Linux is very preferable for scientific reseaches, some scientific applications are discussed, but there are many more special purpose researches scientific applications available for GNU/Linux but they are very complicated, far from being user friendly and targeted to scientific laboratories so they are not mentioned here, you could take a look at 'GNU/Linux AI & Alife HOWTO' by John Eikenberry for few examples of such applications. For a list of scientific Linux applications visit 'http://sal.kachinatech.com'

Section quotes:

• { (...) إِنَّمَا يَخْشَى اللَّهَ مِنْ عِبَادِهِ الْعُلَمَاءُ، إِنَّ اللَّهَ عَزِيزٌ غَفُورٌ} translation of it's meanings { (...). It's only those who have knowledge among His slaves that fear Allah (abstain from sins that He has forbidden). Verily, Allah is All-Mighty, Oft-Forgiving.}
      -- Chapter 35, Ayah 28 of Quran
• "Your mind understands what you have been taught; your heart, what is true."
      -- found on 'fortune-mod'
• "[the spirit of scientific cooperation] which used to be so strong that scientists would cooperate even when their countries were at war."
      -- Richard M. Stallman.
• "[the thirst for wonder] All children feel it. In a first grade classroom everybody feels it; in a twelfth grade classroom almost nobody feels it, or at least acknowledges it. Something happens between first and twelfth grade (...)"
      -- Carl Sagan, The Burden Of Skepticism, The Skeptical Inquirer, Vol. 12, Fall 87
• "[astrology] It sounds a lot like science, it sounds like astronomy. It's got technical terms. It's got jargon. (...) uses terms which come from science, come from metaphysics, come from a host of fields, but they really mean nothing."
      -- Astronomer Richard Berendzen, President, American University.

Section contents:

• 2.8.1. Educational software.
• 2.8.2. Calculators.
• 2.8.3. Numerical analysis and CAS software.
• 2.8.4. Visualization and plotting software.
• 2.8.5. Statistical analysis software.
• 2.8.6. Chemistry and Biology related software.
• 2.8.7. Cartographic and Astronomy related.
• 2.8.8. Electronics software.
• 2.8.9. CAD software.
• 2.8.10. Scientific publication software.

2.8.1. Educational software.

Keduca

Kalzium

• flashkard - a program used by the teacher to design questitons cards and then we run 'keduca' to open the saved cards so that the pupil use it, it removes correct answered cards and repeats others until the answer is drilled into his memory.
• ktouch - typing tutor.
• kvoctrain - learn English (and other languages) vocabulary.
• khangman - the classical hangman game, you have to guess a word before getting hanged.
• kmessedword - the well known messed word game, a way to learn new words.
• klettres - learn alphabet tutor for Danish,Dutch and French, it learn your kid how to read simple syllables.
• kpercentage - teach the pupil how to calculate percentages.
• kgeo - Interactive geometry program, so that the student sees how is the line length equals to ... etc.
• kmplot - mathematical function plotter.
• kstars - it's a desktop planetarium, if could display positions of starts, constellations, start clusters, nebulae, galaxies and plants as seen from any specified point on earth at any specified time and date, you may right click on any thing you see to get more information on it.
• kalzium - It shows the Periodic System of the Elements (PSE), it could display upto 118 elements discovered before year 2003 , and you could specify any year before, you may click on any one and get all known information about it, it offer exams and tell you the result.

On the other hand GNOME has similar applications but they are not part of official GNOME desktop so they are not included in many distributions (of course, Debian includes them), here is a small list of some GTK+ applications:

• GCompris - Educational games for small children through a very simple childish interface, it's inteded to teach them how to use a mouse, type on keyboard, do simple arithmetics through games, read analog clock, recognize letters after hearing their names and small games. It's part of The Fifth Toe of GNOME.
• mathwar - teaching arithmetics through flash cards.
• gperiodic - a GTK2+ Periodic System of the Elements (PSE) containing the 118 known chemical elements and some information about each.
• Dr. Genius (drgenius) - interactive geometry program that supports Guile based scripting, exporting to LaTeX and EPS formats. (examples included in '/usr/share/drgenius/examples')
• Dr. Geo (drgeo) - very similar to Dr. Genius.

Interactive geometry programs could be more complicated and used by a teacher to create modules, among them 'geomview' (visit www.geomview.org) show objects in Euclidean space, hyperbolic space or spherical space are moving and interact with user or be controled through external program. It supports lighting, shading and materials of objects through OpenGL.

Both KDE and GNOME provide a front end to access many public dictionary servers through the internet (many are maintained by The DICT Development Group), one installed on your LAN or your computer. Either you use 'kdict' from KDE or 'gnome-dictionary' (or 'gdict') which is part of 'gnome-utils' package, also you could add an applet by right click beside the clock (where you want to put the applet) then select Dictionary applet. In order to make them work you need to configure them to use a dictionary servers, if you don't have permanent internet connection you could install a dictionary server ('dictd' package) setting the front end to use the address 'localhost' (or 127.0.0.1) and at least one dictionary. Debian includes many different dictionaries of differerent languages, among them are the following English dictionaries:

• 'dict-gcide' - GNU Collaborative International Dictionary of English (decades ago dictionary, eg. 1913)
• 'dict-wn' - English language dictionaries, more updated supplementary dictionary (recommended along with gcide)
• 'dict-jargon' - Concept and terminology dictionary from The On-Line Hacker Jargon File.
• 'dict-foldoc' - computer terminology dictionary from the Free On Line Dictionary of Computing.
• 'dict-vera' - computer terminology acronyms

2.8.2. Calculators.

There are many calculators for GNU/Linux like 'kcalc' (part of KDE), many are scientific. Even scientific calculators like the (in)famous GTK2+ 'galculator' (http://galculator.sf.net) use limited precision float point calculations (upto 16 exact digits for mantissa and 3 digits for exponent) where numbers are represented as '0.3001x10³⁰' for example. There are many small digits dropped from the right end of the decimal point, they accumulates to make a large error. There are some scientific calculators that simulate HP-28/48 like the calc mode in XEmacs text editor or the ugly looking 'xcalc' (maybe it need an argument to passed to be so). If you want an arbitrary precision calculator, for example you may calculate 100 factorial (for studing number theory) or to calculate Pi approximated to 3000 digits!! The GNOME 'gcalctool' is one of them.

GNU BC is a command line-based arbitrary precision calculator, type 'bc' to get an interactive prompt, you may find '3 ^ 100 - 1' exactly, normal float point calculator it will be approximated (if it could) to some digits times 10 to the power something. 'bc' could approximate irrational values to enough precision like 'sqrt(2.0000000000)' for more precision type 'sqrt(2.00000000000000000000)' you may specify the number of digits with something like 'scale=20' you may use semicolon ';' to split commands in one line, for example 'scale=100; sqrt(2)'. Run it using 'bc -l' to load its library which provide the following functions: 's' for sine ,'c' for cosine, 'a' for arctan,'l' for natural logarithm, 'e' for raising e (Euler number) to a power and 'j(N,X)' the N-th Bessel function of X. For example to find Pi to 200 digits use 'scale=200; a(1)*4', see 'bc' manual page. GNU BC is a C-like arbitrary precision numeric language, it could be used as a scripting language.

GNU Desk Calculator 'dc' is a more complicated arbitrary precision calculator, it uses Reverse Polish Notation (RPN) that is like postfix syntax, where values (number and strings) are put first then the operators come, for example to 'print 10+20' we use '10 20 + p', this is a very fast compiled syntax it use no parentheses, it can be calculated directly, it read tokens one by one and when it read a value, it is pushed to a stack, but when it read an operator it pop its argument (2 in case of binary operations) from the stack and calculate them and push the result back to the stack, for example '(2+5)*3' is in 'dc' syntax '2 5 + 3 * p', 'dc' could do loops and complicated programs. The following small 'dc' program find the prime factorization of 1000 (just replace the first 1000 witht any number)

bash$ dc
 1000[p]s2[lip/dli%0=1dvsr]s12sid2%0=13sidvsr[dli%0=1lrli2+dsi!>.]ds.xd1<2

2.8.3. Numerical analysis and CAS software.

Numerical analysis software are intented to solve mathematical problems usually on matrices (like linear problems and differential equations) by an approximated numberical answers with reasonable error, while Computer Algebra Systems (CAS) are supposed to provide symbolic exact calculations, simplifications and solutions.

Tip

Algebra is an Arabic word which mean fixing, unbreacking and solving. It was first used in the currentely known meaning by the Muslim (non-Arab) mathematician Muhammad Alkhawarizmi (some times refered to as Algawarizmi) in his book 'Algabr wa Almuqabala' (Algebra and Equality) - the art of getting the unknowns from the knowns if there is a suitable formula connecting them. The words Algorithm and logarithm are named after him.

GNU Octave is a numerical analysis software that is mostly Matlab compatible. It's a high-level language (ie. used through a command line), primarily intended for numerical computations and it's included with most distributions. Beside its rich library a project called octave-forge (see http://octave.sf.net) contains over 500 contributed functions for GNU Octave in many topics like: audio, comm, control, geometry, ident, image, io, linear-algebra, optim, path, plot, set, signal, sparse, specfun, special-matrix, splines, statistics, strings, struct, symbolic and time. GNU Octave uses GNU Plot by default to draw functions but it could use others like 'kmatplot' or 'plplot' (see www.plplot.org).

GNU Linear Programming Kit ('glpk') is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It supports the GNU MathProg language (subset of AMPL) and the standard MPS and LP formats. 'lp-solve' is another application for same purpose that supports MPS input format.

Euler interface

Euler 3D plotting

Yorick is an interpreted programming language (very close to C) for scientific simulations or calculations involving large files of numbers and it could produce scientific graphics. It could be used interactively.

Yacas (Yet Another Computer Algebra System) is a very small (without documentaion, it's less than a single megabyte Debian package) and highly flexible computer algebra language (very close to Mathematica and C) in which you could write scripts (programs), also you could use it through command line (with OpenGL for graphic) or use a separated GUI for it called 'proteusworksheet' (light GUI using FLTK - Fast Light Tool Kit) found on a very small package (less 200KB) called 'yacas-proteus'. It features many ways of help, press TAB (once or twice) for auto-completation of what you have typed (like BASH), type 'Example();' (with big E, yes it's case sensetive) for a random example, type '??' for help index or a single '?' followed by a subject to get help about (eg. '?Sin'). You could declare symbols (variables or functions) with ':=' (eg. 'f(x):=x^2;'). Just type any formula and it will be evaluated exactely (eg. 'Sin(Pi/3);' becomes 'Sqrt(3)/2') even if it's a bit complicated (eg. 'Sin(ArcSin(a))+Tan(ArcTan(b));' gives 'a+b'), if the answer was not simple enough (eg. '(x+y)^3-(x-y)^3') you could use 'Simplify' and instead of typing it again you could use % which holds the last result, to make it look nicer use 'PrettyForm(%);'. Yacas could solve a formula for a variable with something like 'Solve(x^2+x == 0, x);' (which solves x²+x=0 for x). It could find limits (eg. 'Limit(x,0) Sin(x)/x;' which is the limit for sin(x)/x as x goes to zero), it could find first derivative using 'D(x) f(x);', and heigher derivatives (eg. 'D(x,3) f(x);' for the 3rd derivative of f with respect to x) and it could find integrals (eg. 'Integrate(x,a,b) f(x);' to find the integration of f(x) dx from a to b) and even definite integrals (eg. 'Integrate(x) Sin(x);').

There are may other CASs for GNU/Linux, like:

• Axiom - a general purpose CAS that that has been developing since 1973, it's useful for research and development of mathematical algorithms. Axiom programming languge defines a strongly typed, mathematically correct type hierarchy and has a built-in compiler. It was a commercial product but it has been released as free software (and included in Debian).
• GAP (Groups, Algorithms and Programming, visit www.gap-system.org) - a CAS (in a Pascal-like language) for computational discrete algebra with particular emphasis on computational group theory.
• Maxima - a CAS (in Common Lisp language) that is based on the original Macsyma developed at MIT in the 1970s, it works through its own command line interface (that depends on Tcl/Tk Wish for some why), a separated Tcl/Tk GUI called 'xmaxima' or a separated Emacs mode. Maxima is a full symbolic computation program capble of doing symbolic manipulation of polynomials, matrices, rational functions, integration, Todd-coxeter, graphing, bigfloats.
• PARI/GP ('pari-gp') - a CAS developed by efforts of volunteer from University Bordeaux I and University Paris XI, France.
• MuPAD (see 'www.mupad.de') - another GUI CAS application that has a syntax like Mable.
• gTybalt
• JACAL

2.8.4. Visualization and plotting software.

GNU Plot - a tool to plot mathematical functions (type 'gnuplot' in the command line), it gives an interactive prompt, you may type 'help', to plot the sine function type 'plot sin(x)', to specify the interval of x use something like 'plot [x=-10:10] sin(x)', you can plot more than one function use comma ',' in between them for example 'plot sin(x),x', GNU plot could be used to plot 3D function on the form 'z=f(x,y)', type 'splot f(x,y)' where f is a function of x and y, for example type 'splot 1/exp(x+y)'.

'kmplot' comes as part of KDE edutainment package, but there is a much more advanced gnuplot-like QT plotter called 'kmatplot' offering many 2D and 3D plotting types. It's is easier to use for unexperienced users than GNU Plot, it has a nice clickable GUI or could be used within Octave through functions like 'kplot' and 'kmesh'. There are many less famous mathematical graphing software like 'plotmtv' (2D and 3D), GNU 'plotutils' (2D) and 'geg' (a GUI GTK+ for simple 2D plotting).

KFract is a program to draw Chaos/Fractals plots, GIMP can do that as an art form through a filter. There some software to visualize even more complicated data into scenes like 'mayavi' (with nice GTK+ GUI) which could produce: PostScript files, PPM/BMP/TIFF/JPEG/PNG images, Open Inventor, VRML or RenderMan RIB files. OpenDX (IBM Visualization Data Explorer) is another one (the package is called 'dx'). If you think those are not complicated enough for you, try GRI (visit http://gri.sf.net) which is a language for scientific graphics and illustration programming that is much like TeX.

2.8.5. Statistical analysis software.

For simple statistical software try spreadsheet applications like Gnumeric (refere to '2.3. Office software.' section, for gnumeric screenshot). The most famous properietary statistical software is SPSS (Statistical Package of the Social Sciences), a free software replacement exists it's called PSPP (it's still under development, but it's functional), PSPP a very powerful tool for statistical analysis of sampled data.

The best free statistical software is GNU R, it's a clone of the award-winning S system, which was developed at Bell Laboratories. GNU R supports many file formats like Minitab, S, SAS, SPSS and Stata. It provides a wide variety of statistical and graphical techniques like linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering and much more. It could be used through an Emacs mode called 'ess', Tcl/Tk interface or through a GNOME GUI interface ('r-gnome') among other ways.

2.8.6. Chemistry and Biology related software.

We have mentioned some educational Chemistry software like viewers of PSE Periodic table (eg. 'kalzium' and 'gperiodic') and maybe the 'molecule' GL screen savers, in this subection we will jump into deep scientific software that are to be used by researchers. Chemical structure editors are programs to draw compounds (like vector graphic design tools) by putting atoms and join them with bonds then save the result in a file. Chemtool is an example of such software, it's a nice 2D GTK+ application, the structures could be exported to a few specific types Brookhaven Protein Databank (PDB) and Molecular Design Limited's Mol file format ,some general formats for vector graphics like SVG,XFig and PiCTeX drawings ,bitmap types or printer-friendly Postscript format. If the software does not support the chemical data file format you use, there are tools to convert and manipulate them, 'openbabel' as an example of such programs could handle Tripos' Alchemy, ChemDraw, CML, GAMESS, Gaussian, HyperChem, MDL Isis and Molfile, MOPAC, MPQC, PDB, SMILES and Minnesota Supercomputer Center's (MSC) XMol XYZ . 'readseq' is a similar program that reads and writes nucleic/protein (in Biology) sequences in various autodetected formats. There are many other software that render those files into a 3D image or animations that could be used for teaching or generation of publication-quality images. 'rasmol' (visit 'http://klaatu.oit.umass.edu/microbio/rasmol/') accept many file types like PDB, Alchemy, Sybyl Mol2 formats, (MDL) Mol and XYZ formats, it could work in simple molecules or very complex proteins, nucleic acids. Some applications focus on a single file format like 'garlic' which visualize biomolecules and membrane proteins in PDB format (version 2.1.), while 'xmakemol-gl' which accepts XYZ formats. 'xbs' could generate 3D ball-and-sticks models and movies of molecules. There are some applications could be used editing and visualizations like 'viewmol' which could generate a MPEG video file. I don't know much about ChemDraw but 'xdrawchem' it's free replacement with a nice QT interface.

Some software could give you the properties of a chemical molecule (given its structure) like The Massively Parallel Quantum Chemistry ('mpqc') program which uses ab-initio methods. All those programs are useful for Biology too, but for specialized program we have the Basic Local Alignment Search Tool ('blast2') from NCBI which has a large database of nucleotide or protein sequences, a program called 'blastall' could search it for a given sequence and summarize matches.

2.8.7. Cartographic and Astronomy related.

Beside Kstars we have many other educational star map viewers software like 'starplot' (with GTK+ GUI) and 'spacechart' (start map viewer and navigator). Some other educational Astronomy software allow the user to make a trip in our solar system in a real time 3D so that he could visit planets and major moons like OpenUniverse (OU for short, visit www.openuniverse.org and 'ssystem'.

Kworldclock (part of KDE) offers time in all of the major cities of the world on a map of earth that is light and dark depending on time. SunClock (from http://frmas.free.fr/li_1.htm) display a fancy clock showing time and geographical data in a similar manner. 'gworldclock' is a GNOME application for the same task. 'kmoon' (part of KDE) and 'glunarclock' (additional to GNOME) Lunar clock that displays the current phase of the Moon, also Emacs could do that through calender mode. XPlanet (visit http://xplanet.sf.net) Renderes a view of Earth into the X root window (the backround) in various projection systems, it could draw all of the major planets and most satellites.

There are a satellite location program called Seesat5 it uses the NORAD sgp4 algorithm to compute the location of a satellite, it provide many filters so that only those satellites that might actually be viewed are presented in the report. GpsDrive navigation system displays (or speeks if "festival" is installed) your position provided from your NMEA capable GPS receiver on a zoomable map, the map file is autoselected depending of the position and preferred scale.

XTide (visit www.flaterco.com/xtide/) provides current predictions of tides (using a significantly accurate algorithm by the National Ocean Service in the U.S.) in a wide variety of formats; Graphs, text listings, and calendars can be generated, or a tide clock can be provided on your desktop.

Geographic Resources Analysis Support System (GRASS) is a Geographic Information System (GIS) used for data management, image processing, graphics production, spatial modeling, and visualization of many types of data. Originally written by the U.S. Army Construction Engineering Research Laboratories (USA-CERL) and it's used by academic, commercial and governmental depatments including NASA, NOAA, USDA, the National Park Service, the U.S. Census Bureau, and USGS.

Drawmap program lets you draw customized maps including shaded relief maps and topographic maps (with or without roads, streams, place names, and so on) it taken input as raw USGS data files, the Digital Elevation Model (DEM), Digital Line Graph (DLG), Geographic Names Information System (GNIS) formats, SDTS, NAD-83, WGS-84, and GTOPO30 data.

Maps are drawn using a projection function, a program called 'proj' (visit www.remotesensing.org/proj) provide over 100 projections that could perform forward and inverse transformation of cartographic data to or from Cartesian data. The Generic Mapping Tools (GMT, in other context it means Greenwich Mean Time) is collection of about 60 UNIX tools that allow users to manipulate (x,y) and (x,y,z) data sets (filtering, gridding, projecting, ...etc.) to produce an EPS printable file, it support more than 25 map projections, and comes with supportive data such as coastlines, rivers, and political boundaries.

2.8.8. Electronics software.

There are many software for designing electrical circuites digital and analoge, some are for just drawn them some provide simulation to test them:

• Electric - a sophisticated electrical CAD system that can handle many forms of circuit design, including custom IC layout (ASICs), schematic drawing, hardware description language specifications, and electro-mechanical hybrid layout.
• gEDA - The GNU EDA (http://geda.seul.org/) an Electronics design software (many examples included in 'geda-examples' package).
• GnuCAP - The GNU Circuit Analysis Package, a console circuit simulator (interactive or a server for GUIs) capable of performing nonlinear dc and transient analysis, Fourier analysis, and ac analysis linearized at an operating point.
• KLogic - digital circuit editor and simulator for KDE.
• 'pcb' - Printed Circuit Board Design program, a handy tool for the X Window System build to design printed circuit boards.
• 'xcircuit' - a generic drawing program tailored for making circuit diagrams (just draw).
• 'chipmunk-log' - a large circuit editing and simulation environment system. It has facilities for digital simulation (the original LOG), analog simulation (AnaLOG), network generation (LOGNTK), and plotting (LPLOT).
• TkGate (http://www-2.cs.cmu.edu/~hansen/tkgate/) - Event driven digital circuit editor and simulator (Tcl/Tk GUI). It supports a wide range of primitive circuit elements as well as user-defined modules for hierarchical design. The distribution comes with a number of tutorial and example circuits (including a simple CPU) which can be loaded through the "Help" menu.
• GAEL - The Gnome Assisted Electronics (http://gael.sourceforge.net
• NG-SPICE http://ngspice.sourceforge.net

• gtkwave - a viewer for Value Change Dump files which are usually created by digital circuit simulators.
• gwave - a viewer for the output of spice-like simulators and other viewing of analog data.
• gerbv - Gerber file viewer for Printed Circuit Board (PCB) design which is used for communicating designs to manufacturers.

2.8.9. CAD software.

There are some Computer Aided Design (CAD),Computer Aided Manufacturing (CAM) and Computer Aided Engineering (CAE) software available for GNU/Linux, like QCAD (a light QT CAD system for constructing 2D drawings and save them in AutoCAD DXF format), dcad, varkon, tomcad, thancad, http://lignumcad.sourceforge.net, giram, jcad (java), freeEngineer, opencascade and pythoncad (but CAD here means Computer Aided Dispatch/Drafting). I'm not an engineer, this subsection is just a draft.

2.8.10. Scientific publication software.

There are some applicatons for creating scientific figures, diarams and charts like Dia which could be used to design a flowchart, a computer network or even an digital circuit. Kivio and KChart, which are part KOffice suite, could be used for similar task. Vector graphics applications could be used, they are discussed in section '2.5. Graphic design software.'. The old X application XFig (visit 'www.xfig.org' or 'www-epb.lbl.gov/xfig/') was very common for viewing XFig files and drawing them, a package called xfig-libs contains several clip art libraries for it.

The same way GNU/Linux is widely used for researches at many universities and labratories, it's also used to generate publications for them, in an automated manner, quoted from Diploma package description: "Debian GNU/Linux is widely used at universities to do research and to write papers with LaTeX", it contains examples of how could measurement data be processed and convert results into nice figures. Most scientific publication software are following WYSIWYM style not WYSIWYG, where you describe what do you mean not how do like it to appear and the software choose the right appearence according to the output media (among other things). The main generic WYSIWYM system is DocBook XML language but it's not designed for scientific applications, mean while LaTaX (visit www.LaTeX-Project.org) macro language is designed for such task, its compiler could be found on teTeX package, documents in such format are called TeX files (.tex). They could be written manually on any text editor or with aid from some Emacs mode like YaTeX (www.yatex.org) that make it very handy to write TeX code yourself. Kile (part of KDE) is a GUI enviroment for TeX. There are some GUI applications where you could write TeX files as simple as working with word processors in Office applications but with much power, they are called document processors as LyX (visit www.LyX.org). Another application of TeX is TeXPower which is a bundle of style and class files for creating dynamic online presentations with LaTeX. The online GNU manuals are formated as Info pages which are generated from Texinfo (.texi) files, Textinfo is designed to produce both high quality printable documents (Postscript or PDF) or online help files (Info or HTML)