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 Home : Products : Bionumerics 2D : Features
Features of BioNumerics 2D

With the incentive to realize a global bioinformatics platform for the integrated management and analysis of all genomics, metabolomics, and proteomics data, the BioNumerics Platform, Applied Maths has released the powerful and innovative 2-D analysis module of BioNumerics.
BioNumerics 2D is characterized by a large number of automation features, powerful and fast normalization, ease of use, and above all, professional databasing and unparalleled analysis and statistics tools.

Being part of the BioNumerics Platform, which includes powerful sequence and microarray databasing and analysis solutions, BioNumerics 2D offers analytical and interpretative features that no other package can offer. The entire system can run on its own database or on a powerful Oracle, SQL Server, MySQL, PostgreSQL, or Access database, driven by the software.



BioNumerics 2D offers the following main features:

  • Analysis of 2-D gel TIFF files of any size, resolution and complexity

  • Automatic and interactive tools for
    • Non-linear background removal
    • Spike removal
    • Streak removal
    • Tone-curve optimization
    • Noise filtering (Median, Gaussian)

  • Powerful automatic spot detection algorithm, with adjustable parameters for
    • Estimated spot size
    • Minimal profiling
    • Minimal spot area
    • Constriction sensitivity (separation of conglomerate spots)
    • Depression sensitivity (separation of conglomerate spots)

  • Real-time preview window for all above edit functions: finding optimal settings is greatly facilitated

  • Ergonomic shortkey functions for comprehensive manual editing, including
    • Adding spots
    • Deleting spots
    • Splitting spots
    • Merging spots
    • O.D. calibration

  • Calibration tools for spot concentration

  • 2-dimensional non-linear regression for molecular weight and IP determination

  • Various graphical display functions, including
    • Multicolor or rainbow palettes
    • Emboss view for easily detecting conglomerate spots or oversaturated areas
    • Movie-like rotatable 3-D view with differential color according to intensity

  • Powerful automatic gel matching algorithm for quick and reliable normalization

  • Convenient real-time drag-and-drop normalization tools based upon
    • Overlay mode: red and blue gels with overlapping spots black
    • Dynamic switching mode

  • Adjustable automatic spot identification algorithms based upon the use of synthetic or real reference gels

  • Possibility of merging gels with different pH ranges into a single composite analysis

  • Possibility of co-analyzing images of the same gel after different exposure times, with automatic detection of spots with optimal intensity

  • Powerful database environment for proteins (BioNumerics)

  • Smart and intuitive query tool for designing spot queries of any complexity

  • Extensive protein spot description with possibility of storing full Swissprot, EMBL or GenBank information (in conjunction with Kodon), plus a number of additional user-defined information fields

  • Interactive analysis tools including joint comparison of different gel images with comprehensive documentation of spots/proteins

  • Very powerful and unique analysis tools to identify groups of spots with similar or dissimilar behaviour, using the variety of grouping, identification and statistical tools of BioNumerics

  • Co-analysis of 2-D protein gels and microarrays using BioNumerics 2D and GeneMaths applications

  • Complete analysis of any protein or EST at nucleic acid or amino acid level using BioNumeric's powerful "Molecular Analysis module" (Kodon software)

The new BioNumerics Platform software with integrated 2D gel, microarray (GeneMaths), and sequence analysis (Kodon) interacting on one single powerful database engine, forms the first complete bioinformatics platform available, with high-end applications for 1D gel analysis, 2D gel analysis, microarray analysis, sequence analysis, and phenotype analysis.


Network Licenses of BioNumerics 2D
 Compatibility

© 2008 Applied Maths NV