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There is a program, originally developed at IBM, that does exactly this. In its present form, after IBM open-sourced the code, it's called OpenDX. However, it is used in a very specific environment. The treatment of data into graphical images. It's less than trivial to understand how it works, and the code is pretty outdated (e.g. no parallelization). However, it's good at what it does and I used it in several scientific publications.

BTW, I suppose you'd like to have a look at Data Mining examples gallery first.

Check out OpenDX, its visualization capabilities are way beyond Graphviz's and it provides a GUI. It's an open source version of IBM's famous Visualization Data Explorer (initially released in 1991), which IBM converted into an open source project a couple of years ago.

Quoting the site: "OpenDX is a uniquely powerful, full-featured software package for the visualization of scientific, engineering and analytical data: Its open system design is built on familiar standard interface environments. And its sophisticated data model provides users with great flexibility in creating visualizations."

For a short glimpse at its capabilities, visit the gallery here.

Check out OpenDX, its visualization capabilities are way beyond Graphviz's and it provides a GUI. It's an open source version of IBM's famous Visualization Data Explorer (initially released in 1991), which IBM converted into an open source project a couple of years ago.

Quoting the site: "OpenDX is a uniquely powerful, full-featured software package for the visualization of scientific, engineering and analytical data: Its open system design is built on familiar standard interface environments. And its sophisticated data model provides users with great flexibility in creating visualizations."

For a short glimpse at its capabilities, visit the gallery here.

It has its own website here too:

OpenDX

Here's a community that looks to be more recently active (that is, it has been dormant for a shorter period) than the original IBM site, having taken the last IBM build and worked on it - http://www.opendx.org/news.html.

Disclaimer: I looked at OpenDX for a project, but never went anywhere with it.

take a look at OpenDX http://www.opendx.org/

OpenDX is good. is also popular, leading to some nice packages like MayaVi2. ChomboVis is no longer under development but may also prove useful. GGobi is another very nice toolkit. For a more mathematical visualization, there's also always Octave.

If they're abandoning it, it's a pity as AmiPro/WordPro/WhateverItIsThisMonthPro was a nice alternative wordprocessor a few years back. I had been told unofficially by an IBMer once that they had an internal port to Unix started, but vehement managment opposition to it ever seeing the light of day. I'd kind of hoped they'd treat it like DataExplorer, and let it fly free. (They would be encouraged to keep Notes down on the farm, preferably muzzled and in a cage.

A really powerful and flexible (generalized) viz tool is OpenDx http://www.opendx.org/ which started as a commercial IBM venture and is now an open source project. It uses visual programming (EG plugging modules together) to generate the visualizations so you don't need to write your on OpenGL or something. Even with just three "modules" plugged together (and all default settings) you'll start to see your data in 2-space or 3-space.

Molecular Physicists/Computational Chemists have made available through a variety of open licenses, including GPL, highly complex, well-developed, robust simulation codes. We're undoubtedly a smaller niche than MechE's, but we have a good couple dozen solid production codes to choose from (if you mix the quantum people and the classical MD people), for between Free (beer/speech) to Freeish (moderate license fee, or restrictions on code redistribution).

Maybe the problem is cultural: people who can write such software, write it for money. There isn't enough money in electronic structure packages, so at least half of them remain free. The money that's charged is frequently to cover duplication costs, and to chase off dilettants.

Maybe the bigger problem is the parent poster is expecting a level of user-obsequiousness from his software. Most of my community's free codes are somewhere between User-Indifferent to User-Surly, but you get used to the ones that are relevant to your own work rather quickly.

However, I would list Octave http://www.octave.org/ and OpenDX http://www.opendx.org/ as good starting places for tools. That will get you a good programming environment, and an absolutely killer visualization framework.

OpenDX ( http://www.opendx.org/ ) is very powerful, and unlike VTK, it has free documentation.

VTK simply encourages you to buy their books - the books are in no way necessary to use VTK. They have quite comprehensive documentation which can be found online, downloaded as a tarball, or as compressed html, or if you like, generated from the source download via Doxygen.

If you want a less technical introduction, or a lon detailed explanation of how the 3D moelling technology works then the User's Guide or VTK Textbook may come in handy, but to claim they are charging to documentation is to say that Perl charges for documentation via the O'Reilly books. It is entirely optional, and a wealth of detailed tecnical documentation is already available for free.

I have used both OpenDX and VTK. It didn't take me long to see the clear benefits of VTK. Knowledge of any of C++, Java, Python, or Tcl will see you producing stuff in VTK very quickly and the variety and power of the libraries are far in advance of what OpenDX offers.

Jedidiah.

OpenDX ( http://www.opendx.org/ ) is very powerful, and unlike VTK, it has free documentation.

Not really a toolkit, but if you need a more heavy weight data visualization tool, check out OpenDX.

i personally prefer opendx for my scientific data, it's somewhat complex but can make great navegable visualizations.

"[We, the Science Musuem of Minnesota,] are frustrated by a lack of consolidated resources and discussion about open-source, scientific visualization development tools"

• OpenDX - powerful data visualisation software
  • Open source but downloading requires you to register and to acknowledge their patents. This software became open-source in 1999
  • as first discussed here on Slashdot (why does Slashdot still use the same old Slashcode which even after 7 years of development still destroys the nesting of all its archived articles after 2 weeks???)
  
  
• Vis5d - has a unique interface for explicit 5d data visualisation
  • Open source but development has ceased.
  
  
• Webwinds - 3d data visualisation software
  • Open source, Java.
  
  
• LinkWinds - 3d data visualisation software
  • Open source but restricted download and development has ceased.
  
  
• OpenQVIS - 3d realtime volume visualisation on commodity desktop computers
  • Open source.

Sorry, but I fail to see what Blender and the GIMP have to do with real scientific visualization. Blender is for 3D modelling, and the GIMP is for image processing.

If you're looking for complete, open source scientific visualization and data analysis packages, try VisIt, which supports dozens of input formats and runs on Linux, Windows, and MacOSX. Pick it up at http://www.llnl.gov/visit, or get the latest binaries from FTP here.

I have less knowledge of ParaView, but it is also free: http://www.paraview.org.

Both of these are also developed in part by the national labs; they can run parallel to handle terabytes of data, so if you've got small dataset they should be smokin' fast, and if you've got your own cluster you should be able to visualize some huge data.

If you're looking for just a toolkit to build your own application, try OpenDX or VTK.

This the point where I remind people of OpenDX, which is the open sourced IBM Visualization Data Explorer. DX used to be an extremely expensive commercial product, but it's been open source for a couple of years now.

It's very good. If you're into scientific visualization it's worth examining.

• R, including several add-on packages (such as tseries, RODBC, coda, mcmcpack, gtkdevice, rgtk, rquantlib, qtl, dbi, rmysql), out-of-the box support for the powerful ESS modes for XEmacs as well as the Ggobi visualisation program;
• A complete teTeX, TeX, and LaTeX setup for scientific publishing, along with TeXmacs and LyX for wysiwyg editing;
• Perl and Python with loads of add-ons, plus ruby, tcl, Lua, and Scientific and Numeric Python;
• The Emacs and Vim editors, as well as Gnumeric, kate, Koffice, jed, joe, nedit and zile;
• Octave, with add-on packages octave-forge, octave-sp, octave-epstk, and matwrap;
• Computer-algebra systems Maxima, Pari/GP, GAP, GiNaC and YaCaS;
• the QuantLib quantitative finance library including its Python interface;
• GSL, the Gnu Scientific Library (GSL) including example binaries;
• The GNU compiler suite comprising gcc, g77, g++ compilers;
• the OpenDX, Plotmtv, and Mayavi data visualisation systems;
• it includes apcalc,aribas,autoclass,

Other tools which I have come across, but haven't really worked with: Axiom (symbolic computations, CAS); Scigraphica (graphing); opendx (data explorer + visualization).

I've actually never really used R (by the time I came across it, I was done with my physics labs), so I can't really compare any of the others to it. But it definitely looks like one of the tools that I should add to my suite.

I especially like OpenDX, which I use to visualize data that I collect in the lab: http://www.opendx.org/index2.php

The software has really matured over the years and is now available for a multitude of OSs

For fancier stuff there are fancier tools (including opendx ), but for simple stuff gnuplot works well, is reasonably priced and is hard to beat.

These people http://www.ibm.com/linux/ can help. Worldwide, 24 hours a day, 7 days a week. Look at http://www.openafs.org/ , http://www.opendx.org/ , http://www.research.ibm.com/resources/news/2003111 4_bluegene.shtml if you want to be convinced they know what they are talking about; both on the 'giving' and 'receiving' sides of the coin.

Check it out: www.opendx.org

Excellent (and surprisingly easy) for complex 3D stuff but a bit over the top for simple 2D plots.

It's Free Software, but I don't know if it works for MacOS though.

Where I work (an environmental science organisation) the emphasis is on getting the job done, whichever tool is approiate for the job, or whichever tool is familiar to the scientist gets used. (I'm not saying that this is necessarily the best policy, just what happens here.)

There are a range of programming competancies from people who take code written by someone else that they have always used and feed data through it black-box style, through to scientists who write their own F90 or C++ code with MPI and BLAS libraries for running on the HPC clusters.

We have OpenDX, Matlab, octave, IDL, Statistica, S, SPlus, R. Programming in F90, F77, C++, C, Perl, Python. The platforms include Windows*, Linux, FreeBSD, Solaris, Tru64. Some instrument makers use labview. You name it, someone here will be using it somewhere.

Quite often one person will develop using a particular package, then anyone s/he collaborates with will have to use the same package to read the files or run the programs.

I've been mucking about with python and Vtk.

And I use Linux all the time.

In fact, all our web-based energy visualisation products were developed and run on Linux, and the 3D energy visualisation work I do on this in my spare time:

screenshot

is also developed and run on Linux.

The devices we use to interface ethernet with meters are too lightweight to run linux, they simply provide a TCP-IP -> serial connection for the meter's RS-232/422 interface and an ethernet port for connection to a LAN.

Many meters only support pulse-output, which does require a device such as this to count pulses, convert them to kWh or other relevant measurement, buffer these readings for some period and provide a interface for this data to be extracted, which is what this device is.

It is nice to see multiple inputs for temperature etc, as energy consumption data alone often does not provide enough of a picture to make decisions that can really cut your energy peaks or identify areas of inefficiency.

http://www.opendx.org/, a now open source product from IBM. Does wonderful 3-D stuff. Source code available, and binaries available for AIX, FreeBSD (might compile on OS-X), HPUX, Irix, Linux, Linux PPC, Solaris, and Microsoft OS.

Be sure to check out the highlights: http://www.opendx.org/highlights.php

Using this software won't be point, click, drag, like using Visio, but I'm sure you could easily compose the modules that would parse data, and create what you need. Look at the samples and highlights on the web page before you decide.

http://www.opendx.org/, a now open source product from IBM. Does wonderful 3-D stuff. Source code available, and binaries available for AIX, FreeBSD (might compile on OS-X), HPUX, Irix, Linux, Linux PPC, Solaris, and Microsoft OS.

Be sure to check out the highlights: http://www.opendx.org/highlights.php

Using this software won't be point, click, drag, like using Visio, but I'm sure you could easily compose the modules that would parse data, and create what you need. Look at the samples and highlights on the web page before you decide.

I have been using a scientific visualization package called OpenDX. It is a complicated, but very powerful tool, and well worth the effort to learn if you have piles of data to look at. The documentation is good, and the mailing list has been newbie friendly. I used PV-WAVE in grad school, and spent a long time afterwards looking for an open source alternative - this is it. The only real downside is that it is a Motif app.

It used to be IBM's Visualization Data Explorer; they made it an open source project a couple of years ago (wow - go IBM). Available on a variety of Unix/Linux platforms and Windows (if you run an X server). We have it on two Linux machines and two W2k machines (latter using Cygwin/XFree86-4.1.0); 3D hardware acceleration is supported on the Linux machines - and presumably on windows too if we shelled out the $$$ for a commercial X server.

Take a look at some of the pictures on this page to see some examples of the kind of images I'm talking about. Or, if you have some spare time, download IBM's open source viz program, OpenDX, and play with it (warning: time consuming business, this isn't your typical end user app.)

One of the benefits of a volumetric display is being able to move your head or body and actually see the object from a different angle. Humans are intuitively programmed to be able to understand the 3D objects that we interact with in real life, and cues like what happens when you move your head are important. Dealing with a 2D representation of a 3D object, some of this is inevitably lost.

For a concrete example of this, run a game like Doom and position your character near a window. If you move your (real) head from side to side, the view outside the window doesn't change. This isn't realistic, and gives a misleading impression of the relationships between objects on the screen. When the objects are unfamiliar ones, like the innards of a virus, this makes a difference to one's intuitive grasp of the object's structure.

gnuplot is insanely powerful and flexible, because it's scriptable and supports a ton of output formats. I don't know if it can do the shaded area between two curves bit, though. It also has some limited support for 3D plots, although if you're serious about 3D you should really look at IBM's OpenDX.

grace is also a good choice if you like GUI plotting tools, but I'm so used to gnuplot that grace seems awkward...

--Troy

OpenDX can do just about anything you want. It's an extremely powerful and flexible scientific visualization tool. And IBM has recently opened the source code (under the IBM Public Liscense). There is, however, a considerable learning curve. Check out the gallery.

OpenDX can do just about anything you want. It's an extremely powerful and flexible scientific visualization tool. And IBM has recently opened the source code (under the IBM Public Liscense). There is, however, a considerable learning curve. Check out the gallery.

The wonderful ferroconcrete world we live in has more lawyers than rats. There are patents underlying the most obvious software designs (yes, a simple lawsuit showing prior art will defeat three quarters of them, but I for one won't spend my life savings on them, and companies with pockets that are deep enough prefer not to invalidate competitors patents for fear of getting blasted themselves).

Patent issues aside, there's the legal debate about licenses. If we (the Open Source developers) cannot put our legal squabbles aside (my license is more free than yours -- no, mine is), how would anyone expect to put big business to put theirs aside? Beside ego, they've got shareholders to take into account.

I've been mighty impressed with IBM's venture into the Open Source arena. I think they've taken the boldest steps of all. It's not just half-baked Java stuff (with tremendous investments behind them) or stuff without direct revenue potential (like jfs, which they couldn't sell as long as competitors think their mouse trap is better). If you search for "IBM Visual Data Explorer" on www.ibm.com, you'll get a price list with a rather hefty price tag (and if you dig deeper, you'll find an impressive array of Fortune 500 companies and research institutes that paid those prices and got their moneys worth). If you look at opendx.org, you'll see the same software, free. The stuff is awesome!

Whatever their motivation, I rate IBM highly for its commitment to Open Source. It's a rather stunning move, given their revenue streams and the fact that they spearheaded the move from free to paid-for software eons ago.

There is not yet a publicly available CVS tree, and the mailing lists are explosively overactive (I have no idea how the guys working on this project for IBM get anything else done), but they have been extraordinarily helpful and receptive to suggestions. Lesstif is being closely examined and apparently improved as a side effect (since most Linux users do not purchase Motif, duh). Distributed DX and an RPM are in the works thanks to the efforts of the IBM crew, and I am trying to SWIG parts of DX so it can be scripted from the web with minimal effort. And for whatever it's worth, I have started working on DX2Octave again now that I have access to DX on my machines.

As far as the code goes, it's a little crufty, but anyone who tells me that (for example) the original Mozilla codebase was any cleaner is insane. And OpenDX worked out-of-the-box, the day it was released, on many platforms. Plus, IBM is licensing some of its own patents to outside developers by releasing DX in its working entirety. They went the extra mile than Netscape did not, which is why I bring up Mozilla vs. DX.

I am very pleased with IBM Research's involvement in their open-sourced projects, and IMHO they are a great example for other companies to follow.

DX homepage, with downloads and license info

OpenDX.org