SyncPro

Introduction
Working Environment
Change Log
Downloads
ScreenShots
Acknowlegdement

SyncPro is a visualization package targeting on processed mass spectrometry data. It uses synchronization and layering techiques in graphics to simultaneously visualize groups of MS datasets.

The major features of SyncPro are :

synchronizing different datasets and different kinds of plots in visualization
facilitating data exploration through selection and extraction
providing a quick judgment tool for the quality of selected features

Working Environment return to index

Recommended hardware configurations

Central Processing Unit : 2GHz or above
Memory : 2GB or above

Required system configurations

Java Runtime Environment : version 1.6 or above ( freely avaliable at http://www.java.com/ )

Change Log return to index

Version 1.04 -- 20/08/2010

Implement Level of Detail for 2D intensity plot to impore rendering speed.
Rewrite synchronization related class to improve synchronization speed and simplify extension steps of implementing new synchronization features.
Support loading configurations from file.

Version 1.03 -- 20/01/2010

Feature statistic tool window tab is avaliable for evaluating features with statistic scores.

Version 1.02 -- 25/11/ 2009

Support MZML(version 1.1.0) file format.
Minor bug fixs in ProjectManagenment and FileChooser.
Panning mode is avaliable for 2D-intensity plot.

Version 1.01 -- 17/ 08 / 2009

Undo/Redo functions for selections in intensity plots and features in feature window tool tab are avaliable now.
Minor bug fixs in selections of Intensity plots.
Minor bug fixs in check loops of types of files supported.

Version 1.00 -- 07 / 08 / 2009

First release of demo version of SyncPro

Downloads return to index

SyncPro (version 1.04) is avaliable for free.

Java executable : HERE, Source code : HERE.

Sample datasets and a sample project can be found HERE.

A quick start manual for SyncPro can be found HERE.

All related files and older version of SyncPro can be found in the mirror site of SyncPro in SourceForge : HERE.

Screenshots of SyncPro return to index

Synchronization

click the graph to enlarge

Fig. 1 2D-intensity plots for 20 unknown samples

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Fig. 2 Spectrum plots of 120 unknown samples (each spectrum plot shows 20 samples)

Layering

click the graph to enlarge

Fig. 3 Spectrum plots of 80 unknown samples (each spectrum contains 40 samples, 10 of 40 samples in the spectra are the same)

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Fig. 4 Spectrum plots of 80 unknown samples (each spectrum contains 40 samples, 5 of 40 samples in the spectra are set to be invisible)

Miscellaneous Plots

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Fig. 5 Screenshot for a feature scatter plot

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Fig. 6 Screenshot for showing various visualization types of SyncPro

Acknowlegdement return to index

Core software packages used :

Program logging �C Log4j and Xerces from the Apache Software Foundation http://www.apache.org
MZXML file parsing �C JRAP mzXML parser in the Trans-Proteomic Pipeline software developed by the Seattle Proteome Center http://tools.proteomecenter.org/wiki/index.php?title=Software:JRAP
XML file parsing �C Dom4j in the apache Maven Project http://www.dom4j.org/index.html
Chart drawing �C JFreeChart from JFree.org http://www.jfree.org/
Graphical user interface docking framework �C MydoggyFramework http://mydoggy.sourceforge.net/
Internal desktop management �C Swing Desktop extensions by Guy Davis http://www.guydavis.ca/log/view.jsp?id=893
Statistical Score Calculation �C The Apache Commons Mathematics Library http://commons.apache.org/math/

Miscellaneous source codes and resources used :

Relative path generator �C A java class written by David M. Howard http://www.devx.com/tips/Tip/13737
Magnifier len and memory monitor �C Java classes written by Angelo De Caro and included in the package of MyDoggyFramework
Silk icon set �C A set of icons provided by Mark James http://www.famfamfam.com/lab/icons/silk/