VIMIDA


VIMIDA - is a Java-applet for VIsualization of MIcroarray DAta using linear and non-linear principal components analysis (PCA)
keywords: visualization; microarrays; principal components analysis; elastic maps; visual clustering

Description

VIMIDA allows two-dimensional visualization of a data file with vectorial data (tab- or space- delimited table with a simple header, look at a sample). The basic features of the applet are the following: For further details go to the TUTORIAL

Examples

You can test VIMIDA immediately with a sample data file

Screenshot of visualization of CGH array data

Refer for other examples to the TUTORIAL


References

Other software implementing elastic maps algorithm: Publications:
  1. Gorban A., Zinovyev A. Elastic Principal Graphs and Manifolds and their Practical Applications. Computing, 2005 (PDF)
  2. Gorban A, Zinovyev A. and Wunsch D. Application of the method of elastic maps in analysis of genetic texts. Proc. International Joint Conference on Neural Networks (IJCNN), 2003 (PDF)
  3. Gorban A, Zinovyev A. Visualization of Data by Method of Elastic Maps and Its Applications in Genomics, Economics and Sociology. IHES Preprint, 2001 (PDF)
Web-pages:

Implementation

The applet is a part of VDAOEngine package which is implemented using the core java classes. For solving systems of algebraic linear equations with big sparse matrices in the algorithm of principal manifold construction, COLT library is used (it is included in the applet jar file). The applet is signed by Andrei Zinvoyev and Bioinformatics Service of Institut Curie. This is done to allow the applet to have access to the local filesystem.

Downloads


Contacts

Bioinformatics service of Instiute of Curie
Andrei Zinovyev