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TIGR MEV Client Framework
At
the core of TIGR MEV is an extensible architecture that allows researchers to plug-in
computational microarray analysis algorithms. With the techniques to analyze microarray
data quickly evolving, TIGR needed an application that can be easily extended with new
alogrithms as they are invented.
TIGR MEV
uses a plug-in architecture to enable researchers to incorporate new algorithms and visualization
techniques. By using plug-ins researchers do not have to worry about building a
complex software application but instead focus only the developing the algorithm plug-in. To simplify
algorithm development TIGR MEV has a software framework designed to support plug-ins. The
client framework is broken into two parts, one for analysis algorithms and another for visualization.
Each part defines a set of interfaces or APIs implemented in Java.
The TIGR
MEV Analysis Algorithms API is used to develop clustering algorithms. Using the API a developer
can concentrate on mathematical aspect of an algorithm without having to worry about a user
interface. Algorithms developed with the API can run either locally on the client PC or remotely on
the TIGR MEV grid. However, writing an algorithm to run on the grid is not handled by the API and needs a
separate development effort. The API includes:
- Structure to store Microarray data,
- Structure to assign algorithm parameters,
- Cluster oriented structure to return result of a calculation,
- Supporting algorithm events in order to control calculation progress.
The
TIGR MEV Cluster View API is used for developing visualization plug-ins that can execute an algorithm
and display the result. A developer using this API does not have to be aware of the low-level math
of the algorithm but instead focus only on how to display the results in a user-friendly manner.
The API includes:
-
Structure to describe a module,
name, short description, icons. This info is used by TIGR
MEV to add items to the main toolbar and analysis menu,
-
Interface for an executable class
that should be implemented in order to run a viewer,
-
Interfaces that give access to
framework resources such as Microarray data, application
menu, status bar, amoung others,
-
Interfaces to develop result viewers,
-
Helpful GUI and utility classes.
These algorithm
and visualization plug-ins are compiled Java class files that are packaged into Java Archives and
distributed with TIGR MEV. New algorithms can be distributed easily however there is no mechanism to
distribute updates and new plug-ins over a network. Future versions TIGR MEV will use directory services
to publish plug-ins on the network or Internet.
Using
Java allows TIGR MEV to leverage many open-source, standards-based libraries to simplify development
and cross platform compatibility issues. The application uses Java 3D from Sun, Xerces from Apache
Foundation and several other open-source libraries for Base64 and HTTP support.
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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.
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