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CmpSpots - 2D Database Spot Pairing pre-alpha version

Welcome To CmpSpots
( mirror)

Note: This pre-alpha level software is under construction and will change. 
Not all functionality described is fully implemented or fully debugged.    
This documentation will undergo revision as the program develops.  


CmpSpots is a Open2Dprot project Java 2D spot data pairing program for finding paired spots between two samples. A composite quantified protein expression database consisting of protein expression per (spot) for N samples may be constructred from N sample spot lists. CmpSpots is a program to aid in the construction of this type of database by pairing corresponding spots between spot lists based on their 2D (x,y) locations relative to one another.

The spot list data consists of quantified spot with location (x,y) location that varies between samples. Such data could have been created using image segmentation (e.g., 2D electrophoretic gels), derived from non-image data using clustering methods (e.g., 2D LC-MS) to define peptide "spots", or other other methods. For example, if the samples are 2D electrophoretic gels, when we refer to 'sample' we imply gel samples and the spot list of the gel could have been produced by the Open2Dprot Seg2Dgel spot segmenter and quantification program. Open2Dprot is being designed to handle data from a variety of data sources.

It is a step [4] module in pipeline analysis for the Open2Dprot project. Spot pairing is performed on data from a reference sample and another sample to be paired with that reference sample. The method uses a set of landmarks defined between the reference sample and the other sample. Landmarks could be created in a [Future] step [3] module in pipeline analysis operation.

The program may be run either interactively (-gui) with a graphical user interface (GUI) or under an OS shell command to implement batch (-nogui). In the former, after the segmentation is finished, the user has the option of interactively viewing the spot pairing. They may adjust parameters and re-pair the data.

You can currently download the pre-alpha version and install it on your computer. Currently, CmpSpots is hardwired to start with the demo samples and with the -gui switch. The remainder of this home page contains links to some screen shots of the interactive GUI. The Web site contains some initial (rudimentary) documentation.

See the Reference Manual for details. You read about downloading and installing the program on your computer. The source code will be put onto when it is a bit more stable - currently it undergoing major refactoring.

Examples - samples of screen shots

To give the flavor of running the spot pairing, we provide a few screen shots of the graphical user interfaces and some results. You can these images in the list below or view all of the screen shots in a single Web page.

Please contact us with suggestions and comments. If you make interesting changes in the source code, please send us a copy and describe your changes so we can merge them in the released version.

Contact us     CmpSpots is a contributed program available at
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         Revised: 11/07/2005