ViDaExpert - is a software for multidimensional vectorial data visualization (ViDa stands for VIsualization of DAta).
Development of ViDaExpert software is a continuous process which was started in 2000 by Dr. Andrei Zinovyev
for his PhD thesis
at the Institute
Of Computational Modeling of
Russian Academy of Science, was continued at IHES and
moved to Bioinformatics service of Institut Curie. For the moment, it is actively used by researchers
of Institut Curie for exploratory data analysis (mainly, microarray data).
ViDaExpert implements a number of methods for exploratory data analysis:
- Principal Components Analysis
- Weighted Principal Components Analysis
- Method of Elastic Maps for construction of Non-linear Principal Manifolds with Different Topologies
- PCA-based bi-plots
- Visualization of Functions by Coloring (non-linear analogue of bi-plots and visualization of density estimations)
- K-means clustering
- Hierarchical clustering
- Linear discriminant analysis
- Linear regression analysis
- Linear desicion tree construction machine
In ViDaExpert there is a well-developed set of tools to browse, annotate and mark datapoints with colors, shapes and sizes.
ViDaExpert is equiped with fast and convenient OpenGL-based 3D-viewer, which creates an integrative environment
for exploratory data analysis.
ViDaExpert was shown to be a useful tool, in particular, in analysis of microarray data. There are special
panels integrated to support analysis of microarray data (for example, dot-plots).
In the nearest future we plan to integrate into ViDaExpert several data analysis techniques, including
a version of Independent Component Analysis.
You can also have a look at the following Powerpoint presentation:
- Gorban A., Zinovyev A. Elastic Principal Graphs and Manifolds and their Practical Applications. Computing, 2005 (PDF)
- Andrei Zinovyev. Method And Software For Fast Construction Of Principal Manifolds Approximations. (PDF)
- Alexander Gorban, Andrei Zinovyev. Visualization of Data by Method of Elastic Maps and Its Applications in Genomics, Economics and Sociology. (PDF)
- Alexander Gorban, Andrei Zinovyev and Donald Wunsch. Application of the method of elastic maps in analysis of genetic texts. (PDF)
VidaExpert tool was also used in the following publicaitons:
- Non-linear Principal Manifolds - elastic maps approach. (PPT)
Method of elastic maps is also used in development of VIMIDA Java-applet.
- Gorban A., Popova T., Zinovyev A. Four basic symmetry types in the universal 7-cluster structure of microbial genomic sequences. In Silico Biology, 2005 (HTML)
- Carbone A., Kepes F., Zinovyev A. Codon Bias Signatures, Organization of Microorganisms in Codon Space, and Lifestyle. Mol.Biol.Evol., 2005 (PDF)
- Carbone A., Zinovyev A., Kepes F. Codon Adaptation Index as a measure of dominating codon bias. Bioinformatics, 2003 (PDF)
- Gorban A., Zinovyev A., Popova T. Seven Clusters In Genomic Triplet Distributions. In Silico Biology, 2003 (PDF)
Here you can find several tutorials to start with ViDaExpert.
Look also at the description of elmap method.
ViDaExpert was implemented in Borland Delphi version 5. The installation does not require any additional
Bioinformatics service of Instiute of Curie
Dr. Andrei Zinovyev