This research is funded by    
  Supplementary material for the paper
"GenClust : A Genetic Algorithm for Clustering of Gene Expression Data "
by V. Di Gesų, Raffaele Giancarlo, Giosuč Lo Bosco, Alessandra Raimondi and Davide Scaturro,
BMC Bioinformatics 6:289, 2005



Genclust Software :

In the link below you can download the source code, the binary code and the dataset files to test the software Genclust. Genclust uses the GNU General Public License by the Free Software Foundation and is free (as in freedom) software. In particular, it comes with NO WARRANTY  whatsoever and it is ditributed as is. On the bottom of the page you can also find reports on new experiments discussed in the second subsection of the experiment section of the manuscript.

 

Downloads of Genclust software :

  • Entire package including all of the files listed below (zip format or tar.gz format).

  • Microsoft Developer Studio workspace file of the Genclust source code for Microsoft Visual C++ 6 (Windows Platform) (zip format or tar.gz format).

  • Source Code of Genclust for gcc compiler (Linux/Unix), including the makefile for automatic compilation (zip format or tar.gz format) (compilation tested on : Linux fedora core 3 kernel 2.6.12 gcc version 3.4.4, Linux Debian 3.1 kernel 2.6.12 gcc version 3.3.5, Linux Gentoo kernel 2.6.12 gcc version 3.3.6, Linux Slackware 10.2 kernel 2.6.13 gcc version 3.3.6, Mac Os X 10.4 Darwin 8.0 PPC gcc version 4.0.0).

  • Binary executable file for Windows (zip format or tar.gz format) (tested on Windows XP).

  • Binary executable file for Linux/Unix I386 Architecutre (zip format or tar.gz format) (tested on : Linux fedora core 3 kernel 2.6.12, Linux Debian 3.1 kernel 2.6.12, Linux Gentoo kernel 2.6.12, Linux Slackware 10.2 kernel 2.6.13).

  • Binary executable file for Mac Os X (zip format or tar.gz format) (tested on Mac Os X 10.4 Darwin 8.0 PPC).

  • Documentation files.

  • Examples about input files for Genclust (zip format or tar.gz format).

     

    Links to dataset :

    Links to available datasets used for the experimentation are provided here while references and credits are given in the manuscript. To download the dataset file ready to be processed from genclust, choose the link "Dataset in an input format suitable for genclust".

  • CNS-RAT dataset

  • REDUCED YEAST CELL CYCLE dataset

  • YEAST CELL CYCLE dataset

  • PERIPHERAL BLOOD MONOCYTES dataset

  • REDUCED PERIPHERAL BLOOD MONOCYTES dataset (see manuscript for details)

     

    Experiments : 

    Here we report on experiments for Genclust-random-best and Genclust-avLink-best on all datasets. Figure 1, provides experiments with the adjusted Rand index, while Figure 2 provides the ones with FOM. Comparision with Kmeans-random and AvLink is also included.

    The discussion is in the second subsection of the experiment section of the manuscript.

 

Page by Lo Bosco Giosuč