Goodbye Fedora 9

June 27, 2009 at 5:36 pm (Linux News)

I upgraded to the Fedora Core 9 Alias Sulphur distribution, more than a year ago. The one I had at that time (werewolf), was so buggy that I told some one to download the FC9, within the first week of it’s release. Everything you see in this blog, and many other up to 200 programs which were not the standard distribution of the DVD were tested on Fedora 9.

Bye Bye Sulphur

Bye Bye Sulphur

So it’s like loosing an old faithful friend to me. I learned FOSS up to this level from Fedora 9, Although I was using FC8 and FC7 before, they somewhat did not give me the feeling to experiment. And talking about fedora, it’s the best distro to experiment… bit harder than ubuntu, I know.. but that’s what pure Linux is.

Other than trying to be new, there’s some major improvements in utility programs I expect from FC11. As almost a year has passed by now, the new versions of the programs and compleately fresh programs came this year, seemed too mush to be handled by old FC9.

  1. Qt 4.3 to 4.5 – This has caused me to stop installing about 20 programs. People these days need Qt for GUI as they need coke
  2. Mono 1.9 – 2.x – C# happy people tends to right code in newest way possible to them. So until now, I was unable to install mono 2.0 !
  3. Boost libraries – Try installing some stastics programs without old versions. It gives hell.
  4. Gnome 2.26 – Always easy to do things when you have new GUI !
  5. Xulrunner – FC9 came with a beta, and it did give hell.

Other reasons are bugs:

  • Sleeping problem – FC9 system couldn’t sleep, it shuts down !
  • The authentic driver for 945GZ failed. So I used an experimental one.
  • GDM had a bug, so I can’t logout and loggin with another user, using GUI.
  • So many more

Anyway, of those 200 programs, many of them were compiled from source. So the RPM does not know about them and if the FC11 has the .rpm for those, it will overwrite the files, and this could cause problems. And above programs were compiled for kernel year ago, so I expect many programs to fail at the new OS. So I have listed all the manually installed programs, current list of RPM’s , bins and includes. This is hoe I did it.

rpm -qa >> filename ‘saves all RPM to a file

ls /usr/bin >> filename ‘saves list of binaries

ls /usr/include >> filename ‘saves list of source files

In case neede to search for something,

cat filename | grep <search string>

Ok i’m going to start it now. I hope current won’t go off.

Special thanks for Isuru Udana for providing me the FC9 DVD.


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    Moonlight 3D – Linux can do 3D animation

    June 24, 2009 at 8:39 pm (1, Graphics) (, , , , )

    Some 2 weeks ago, I posted an article about Genious, an excellent Java program. When writing that blog I recalled another brilliant Java program I installed about an year ago. It’s a 3D animation program ! No one will think Java can do that.

    It’s a simple program written using Swing, mostly like 3D studio max to design and animate 3D objects. A grid is there as usual with space vectors x,y,z. 3D view and xy,yz,xz plane views are shown simultaneously. A timeline is visible when you hit create animation button. Additionally, python scripts can be used to program the animation.  You can select one of many basic shapes under create object pane, and modify it from the modify menu bar. So my first drawing looked like this. (I’m not good at graphics). Anyway, you can have some fun with this program, whatever you know.

    3D graphics I created - version 0.2.0 running on JRE 1.6

    3D graphics I created - version 0.2.0 running on JRE 1.6 (@ FC9)

    According to their homepage , these are the features of version 0.2.2

    • Modelling – Unique history-based approach ,Support for non-manifold meshes, including polygons with arbitrary vertex counts ,3D manipulators ,Object instancing ,Fully editable object history at any time
    • Materials, Lighting and Rendering-Fully integrated Sunflow, a renderer with support for modern lighting features like ambient occlusions, global illumination and caustics ,Omnidirectional, spherical and spot light sources ,HDR image output ,GLSL support including GLSL shader editor
    • Animation-Multiple animations of scenes ,Virtually all parameters in the construction history are animateable separately,Rendering of animations
    • Other-Flexible user interface that can be adapted to the user’s needs ,Flexible and extensible plugin based architecture ,Full Python scripting capability,Headless batch mode ,Integrated script editor
    The operator graph of moonlight 0.2.0

    The operator graph of moonlight 0.2.0

    You can download the binary files version 0.2.2 for Linux from this link (14MB). Just make sure you have latest Java Runtime installed to run the program. Untar the downloaded file and double-click on or at the terminal type,
    Moonlight Application Framework
    Is the package for programming moonlight components, specially it’s plugins. My knowledge is limited on this subject, anyway you can download the source code from here.

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    Open dialect – IDE for building flash 9 movies, AIR apps in Linux!

    June 16, 2009 at 5:59 pm (1, Other multimedia) (, , , , , , , , , )

    After I found out about gnash (blog article here) – the open source Shockwave flash player, I thought why FOSS people are not programming an application to build flash movies so we can have it running on Linux. I was wrong, they’ve already built one… and it’s one of the best! It’s core is based on open source Adobe Flex language. IDE is written using C# (.NET Framework) and ported to Linux by mono and GTK#. Look the below screenshots to see how nice it is..

    Open Dialect 0.6 running on mono 1.9 in FC9

    Open Dialect 0.6 running on mono 1.9 in FC9

    It’s easy to use as the flash, and this gives people the ability to build flash contents very fast which would be put on the internet. It’s flash-like because, it has all those programming components (buttons, sliders,text boxes, labels etc…) with the drawing components (circles,lines,squares,tables etc..); and it has the noticeable time line too. All of these can be dragged and dropped like in flash or VB. There are wizards for beginners like in MS Office, but If you need, you can switch to the flex code right away. This program is like power point because it allows transitions between “slides” like in PP.

    The most important 2 features of this program is:

    • It can export Flash 9 SWF’s

    • It can design & compile AIR (Adobe Integrated Runtime) applications

    Anyone knows how flash and AIR rocking the internet these days. This makes open-dialect a FOSS community priority, as it may be the only FOSS applications to handle both these types. Some people already say open dialect is the future of flash IDE’s.

    Building a AIR application using OD

    Building a AIR application using OD

    For more information, you can visit their home site at this link.


    It’s easy as ABC as pre-compiled binaries are already avialable. Download the version 0.6 from this link. Double click on the compressed .tar.gz file and drag and drop where you want them to be. Run the file opendialect. In the command line use the command ./opendialect (Please notice that your Linux distribution should be new enough for this).

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    Geneious – Let’s decode some DNA

    June 13, 2009 at 8:27 pm (Chemical engineering) (, , , , , , , , )

    This article is about a bio-informatics program which is capable of manipulating data gained on genetics. It’s important to notice that this program is not free… But the basic edition of this is free (and doesn’t time up) and runs on Linux.

    The big long tough end semester exam of my chemical engineering (includes biochemical engineering) degree is now over. So, I can blog again friends… I thought of giving a start from stuff currently on my head!I found this brilliant program some time ago Gene – eious , name implies it’s work…..truly this is a work of a genius! It was a quiet a bit of surprise to me as I didn’t think that bio-informatics has come this far.

    The code of virus HIV, good heavens!  (version 4.5.4 running on FC9)

    The code of virus HIV, good heavens! (version 4.5.4 running on FC9)

    Usually people need to take help from many programs like blast, pymol, swisspdb viewer to view and manipulate coding in DNA, proteins, nucleotides,virus and other stuff. Simply it has been a mess. Blast is a powerful pattern matching search engine for sequences of codes (genes), but it lacks the help of a good GUI to to show it’s results.

    And you have to manually search and download genetic codes without this kind of program ….. You may think it’s nothing …. I’m talking about a one of the biggest databases in the world… the human genome alone won’t fit on to a DVD ! Features of this doesn’t stop here.

    Graphics used in presentation of data in Geneious is excellent, one of the best Java GUI I had seen. It’s very user friendly.

    The shape of DNA in 3D -- you rotate or edit.

    The shape of DNA in 3D -- you rotate or edit.

    If you don’t understand a thing I say, let’s go and have some fun. When you open up the program there’s a sample documents folder on tab on the left. Click any of these to load the default files available. You can watch the code of the virus HIV, the code of a mice gene, and some human gene too… Isn’t it awesome? These tiny little scary things?

    Comparison of animals by sequence of code

    Comparison of animals by sequence of code

    The features of Geneious is too big to mention here… You can go to the about page on their website for a list of them. Or you can download the manual in PDF format here.

    Computer geeks may think what is the relationship bio-stuff with codings… decode DNA? (like in computer programs– but they are machines?) . I have mentioned why in a little note at the bottom of this article. Just scroll down.

    Installing Geneious:

    Simply visit their download page at this link.  If it’s linux, you’ll be downloading a .sh file. You can double click on this file after download to install. Or type,

    ./ as root in command-line

    It has a completely inter active installation process like in windows. So installing won’t be a problem. I’m using the version 4.5.3, and the current version is 4.6.4

    Sequence of coding of an enzyme (a complex protein)

    Sequence of coding of an enzyme (catalyst protein)

    The coding of nature (most of stuff is omitted to simplify world for computer geeks ).

    Every living thing on earth carries DNA on their cells, which is a encrypted database of all the stuff you need to build a copy of that living being. The whole thing is encrypted as bases Adenin(A), Guanine(G), Cytosine(C) & Thyomine(T). (Similarly in computers, they use 1,0). These are in a sequence like in binary file of a computer (–ATGAGGTAA– in DNA, –100110101– in computers). When decoding, 3 of these in sequence (similar to 8-bit byte) is taken and it gives 4*4*4=64 combinations. But as only 20 amino acids are there, according to the value an amino acid is formed in the other side choosing from that 20 acids possible. As I told you, the DNA is in sequence, so a sequence of amino acids are formed (like a binary 8-bit file). This is cold a protein. The encrypted sequence of code in DNA for building up this protein is called a gene. There are lacks of genes in a DNA (similar to file database in IT).

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