Melanie - 2D gel analysis software
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Transcript of Melanie - 2D gel analysis software
Department of Bioinformatics
SAMPLE GEL IMAGES
Melanie is a feminine given name derived from the Greek (melania), "blackness
Melanie is 2D Gel Analysis Software
Visualize, Explore and Analyze
MelanieTM software is continuously at the fore-front of 2D gelanalysis. During the last 30 years, it has constantly beenimproved and maintained by a team of the renowned SIB SwissInstitute of Bioinformatics. This access to world class talent,expertise and technology allows us to offer you the mostrelevant solutions.
MelanieTM lets you detect real differences in protein expressionwith high objectivity, sensitivity and confidence. This is madepossible through image quality control, 100% spot matching andthe use of statistical tests that take into account the design ofyour experiment. With less false positives, you save time andmoney otherwise wasted on downstream analysis of proteinchanges that are merely due to biological variation.
Your analysis time will be significantly reduced with the intuitivestep-by-step workflow and powerful strategies which increaseefficiency of alignment with no need for spot editing.
Clear image analysis guidance and robust default settings willgive new users an easy start. However, MelanieTM lets you stayin control of your analysis. It offers unequaled flexibility at alllevels, from image display choices, through normalizationoptions and advanced workflow settings.
MelanieTMs free viewer functionality permits you to easily shareyour work and scientific discoveries so you can collaborate withcolleagues all over the world.
Microsoft Windows XP, Vista, 7 or 8
Administrative permission to install Melanie
At least 500 MB RAM
Recommended: Intel dual-core processor with 2GB of RAM
Color Resolution 24 bit
Screen Resolution 1024 x 768
Input formats - .gel, .mel, .tiff, .img, .isc
Resolution: 150 300 dpi
Image Depth: Min 28 - 256 gray shades
Calibration - More than 100,000 encode the grayvalues using a nonlinear calibration curve to conserveas much information as possible
Image editing: General purpose graphics softwaresuch as Adobe PhotoshopTM ignore or even removecalibration information
A spot delineates a small region in the gel whereprotein is present.
Non-DIGE images - Melanie algorithm
DIGE images - GE Healthcares DeCyder 2Dalgorithm & Melanie algorithm
Smooth - It fixes the number of times Melanie smoothsthe image before detecting spots, using a smooth-bydiffusion algorithm
Saliency - It indicates how far a spot stands out withrespect to its environment.
Min Area - It eliminates spots that have an area smallerthan the specified threshold.
Spot quantification: The software automaticallycomputes the amount of protein present in each spot.
Spot detection parameters
To study the variations in protein expressionamong a series of gels, the gels should bematched together
Analyze Gels: Study protein expression changeswithin a set of gels.
The analytical methods used include scatterplots, descriptive statistics, and histograms
Table, Histogram and Scatter Plot