DataNaut Services - Case Studies

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TIGR Multiple Experiment Viewer

DataNaut delivers Information Technology solutions that enable our clients to save time and money by optimizing workflows and providing tools to analyze data in new and compelling ways. By understanding both the science and IT sides of the equation, DataNaut can focus on enhancing the productivity of the scientist and speed of genetics research by applying complex Information Technologies to real world problems.

For more detailed information about MEV we invite you to read our technical white paper at http://www.datanaut.com/serv_articles_tigrwp.asp.

Approach

The Institute for Genomic Research (TIGR) consulted with DataNaut to build the next generation of TIGR's Multiple Experiment Viewer (TIGR MEV). The TIGR MEV project is an example of how DataNaut has applied IT technologies to develop a complex gene expression analysis system that optimizes analyses performed by scientific researchers.
Some of the problems were:

The use of gene expression analysis in research is dramatically increasing.
Many researchers end up using spreadsheet programs to analyze microarray data. These programs don't offer complex analysis algorithms or data visualization needed for deeper research.
Experiments can generate expression data that includes hundreds to 32,000 genes, and the ability to test more genes per experiment continues to rise.
There is no open source platform for gene expression analysis.
TIGR desired to upgrade their gene expression analysis software to meet researcher's needs.

Benefits

Following DataNaut's software development approach, TIGR MEV was completed in eight months in June 2002 taking over 4000 man-hours to complete. TIGR MEV is implemented using Java and Swing for the client application and web services built using Java and XML and a computational grid built using Parallel Virtual Machine. The TIGR MEV client application operates on any platform that supports Java. The software’s web server components run on Windows, Linux and UNIX.

Value

Valuable features of the application include:

Multi-platform gene expression analysis system to offers nine sophisticated analysis algorithms and normalization features.
Powerful computational grid seamlessly integrated with the TIGR MEV client application that harnesses the power of hundreds computers to crunch gene expression data.
Extensible plug-in framework that allows new analysis algorithms and visualization techniques to added to the system dynamically.
Flexible user interface to visualize analysis results.
Low-cost implementation that used only open source third party software reducing cost of ownership.
Built as an open source platform that can be licensed by any public or private organization.

Success

More then ever the life sciences community is relying on microarrays as a key tool for research but the lack of a comprehensive, low-cost gene expression analysis tool still remains. TIGR MEV represents a significant step to solving this problem by offering an open source platform that is being used by one of the most sophisticated microarray processing facilities in the world. TIGR MEV also offers very high performance using grid technology reducing processing time from hours to minutes making researchers more effective. Built by TIGR's microarray software experts who collaborated with DataNaut computer scientists and mathematicians, TIGR MEV stands to be the key building block of genetics research for many years to come .

Figure 1 - The TIGR MEV client application running on Microsoft Windows 2000. ^*

Figure 1 is a screenshot of the TIGR MEV client graphical user interface ("TIGR MEV client"). The TIGR MEV client supports hundreds of experiments with up to 32,000 spots per slide used in each experiment. On the left is a navigation tree that organizes analysis performed across experiments. On the right is the primary view of the application and in this screenshot is a Relevance Network View. The Relevance Network Algorithm builds a network in which nodes correspond to genes and chains correspond to the degree of similarity between them. Researchers can select spots with specified gene ID or feature degree value and zoom each network. Clicking a spot displays a dialog with detailed information about the selection. For more information, go to the TIGR MEV software page (http://www.tigr.org/software/tm4/mev.html ).

View additional TIGR MEV screenshots:

1. TIGR MEV HCL Viewer ^*
The TIGR MEV viewer used to display results of hierarchical clustering the loaded experiments. Currently, the display is similar to the main display but similar genes and experiments are connected by a series of ”branches.” Labels are displayed on the right side. Clicking near a branch intersection selects that branch and all branches to the right. Right clicking in the selected area displays a pop-up menu where the user sets the highlighted area as a cluster. A cluster can have a name and properties and can be saved for further use in other TIGR MEV Viewers. For more information, go to the TIGR MEV software page (http://www.tigr.org/software/tm4/mev.html).

2. TIGR MEV KMC Viewer ^*
The TIGR MEV viewer used to display the result of k-means or K-medians clustering. TIGR MEV KMC Viewer updates expression views to show centroids for each cluster and experiment, individually or as a group, and gene expression levels, which are displayed alongside the centroids. For more information, go to the TIGR MEV software page (http://www.tigr.org/software/tm4/mev.html) .

3. TIGR MEV PCA Viewer ^*
Older versions of TIGR MEV viewer displayed only the results of principle component analysis. The new TIGR MEV PCA Viewer uses a 3D-view as the primary PCA display. The display can be rotated and shifted by left dragging or right dragging. Right clicking on the 3D view node will display a popup menu that allows the user to change the 3D views display options and create a selection area (essentially a cube) to define a cluster. For more information, go to the TIGR MEV software page (http://www.tigr.org/software/tm4/mev.html) .

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TIGR MEV is an open source bioinformatics system used for computational microarray analysis. Portions of this software were developed by DataNaut Inc.; however, all rights and title in and to this software are owned and retained by The Institute for Genomic Research. If you are interested in obtaining the software visit the TIGR web site.

DataNaut provides software development consulting services with extensive expertise with microarray technologies. Organizations that are interested in using DataNaut consulting services or having TIGR MEV customized for specific research applications can send email to info@datanaut.com.