Modules and features of GelCompar II

GelCompar II consists of the Basic Software and 4 modules: Tree and Network Inference, Identification & Libraries, Dimensioning Techniques & Statistics, and Database Sharing Tools.

The descriptions below list most, but not all functions and possibilities of the GelCompar II modules. Please contact us for details.

GelCompar II Basic Software and Comparative Quantification

  • Image processing and normalization. Input of 8-bit, 12-bit and 16-bit TIFF images, densitograms, and chromatograms of unlimited filesize. Automatic lane finding on images for all types of gels. Gelstrip borders and tracking splines adjustable for each individual lane. Automated and manual alignment by pattern recognition using external reference patterns and/or internal reference bands. On-screen normalization of TIFF images with indication of reliability and possible misalignments. Direct processing of ABI, Beckman and Amersham chromatogram files with inline reference tracks. Adjustable background subtraction using rolling disk method. Adjustable curve smoothing by Arithmetic, Median and Mode filters and Least Square filtering algorithms. Adjustable Richardson-Lucy deconvolution.
  • Database. Entry description by up to 500 information fields, up to 80 characters long each. Easy drag & drop linkage of multiple experiments to database entries. Powerful search engine for combined database searches on different information fields and experiment presence, character values, and ranges. Storage and management of composite database queries. Imaging of any selection of patterns by normalized 2D-bitmap strips, densitograms or reconstructed patterns. Multi-database system, each database can contain many different fingerprint types. Direct comparison of differently normalized patterns through automatic MW remapping functions. Advanced database exchange functions using the Bundles concept and XML exchange packets. Compatibility with external databases via ODBC.
  • Quantification. Approved band-search algorithms with adjustable sensitivity for shoulder and double-band finding based on curve. Possibility to find and mark uncertain bands. Quantification of molecular sizes or any other metric unit using linear, logarithmic, combined logarithmic-third power regression, cubic spline or pole functions. Accurate expression of protein or nucleic acid quantities or concentrations based on cubic spline regression using known calibration bands.
  • Band Matching & Polymorphism Analysis. Extensive anatomy and comparative quantification of bands between groups of patterns. Generation of character tables and extensive comparative reports between unlimited numbers of patterns, with indication of molecular weight, fragment length, and binary or quantitative amount per band. Search for discriminative bands between selected groups of patterns; search for unique and common bands within selections. Binary and quantitative band matching tables of multiple combined fingerprints per entry. Binary or quantitative band matching tables are a necessary basis for Parsimony and Bootstrap (see Cluster Analysis module) and for Principal Components Analysis (see Dimensioning Techniques module).

Tree and Network Inference

  • Methods. Creation of dendrograms including up to 20,000 database entries using product-moment Pearson correlation, cosine correlation, Dice or Nei and Li, Jaccard, Jeffrey's X, Ochiai and area sensitive relatives. Categorical coefficient for multi-state character data such as VNTR. Unweighted pair-grouping (UPGMA), complete linkage (furthest neighbor), single linkage (nearest neighbor), Ward or Neighbor Joining clustering. Adjustable trace-to-trace optimization and tolerance settings for banding patterns. Statistical determination of most justified tolerance settings for banding patterns. Phylogenetic inference: Generalized Parsimony (in combination with Comparative Quantification module).
  • Interpretation. Combined display of normalized pattern images from different gel types, with similarity matrices and sorted according to dendrogram(s). Indication of statistical error at all linkage levels and calculation of cophenetic correlation. "Seaweed" and pseudo-rooted representation for unrooted trees. Bootstrap analysis for single or composite datasets, after creation of band class table (in combination with Comparative Quantification module). Display of sorted similarity matrices, shaded or with numerical similarity values. Comprehensive edit and publishing functions. Professional presentation and printing facilities, in a WYSIWYG environment. Direct interaction between database and dendrogram. Incremental and decremental clustering: new entries can be added to or deleted from existing cluster analyses, without having to recalculate the complete analysis. All features of a comparison are stored to disk.
  • Composite cluster analysis. Different fingerprint type sets can be combined into one consensus clustering. Calculation of global similarity by merging characters or by averaging experiment-related similarities. Optional weighting based on number of characters or defined by the user.
  • Plots and graphs. Creation of 2-D and 3-D bar graphs, contingency tables, 2-D and spatial 3-D scatter plots or feature plots from database fields and band characters. Professional presentation, printing and exporting tools.

Identification & Libraries

  • Database screening. Fast identification of batches of entries with entire databases or selections from databases, using all available coefficients.
  • Libraries. Creation of highly characteristic identification libraries using the open unlimited multi-library system. Specific similarity measures and settings can be defined for specific experiment types. Comprehensive identification reports showing results for each available experiment. Many different viewing options and statistical tools to facilitate interpretation.
  • Neural Networks. Neural Networks can be trained per experiment type and used for quick and accurate identification of complex groupings.

Dimensioning Techniques & Statistics

  • Principal Components Analysis. Non-hierarchic grouping by PCA (in combination with Comparative Quantification module). Spatial representation of clouds of entries in X-Y-Z coordinate system. Indication of total discrimination of axes. Real-time rotation of coordinate system to enhance perception of 3-D structures. Advanced Open-GL presentation and layout for publication. Delineation of populations using colors and/or codes. Plotting of dendrogram branches on PCA for advanced grouping comparisons.
  • Multi-Dimensional Scaling. Non-hierarchic grouping by MDS. Same presentation features as for PCA. Iterative optimization of distances according to similarity matrix.
  • Statistics. A number of parametric and non-parametric statistical tests can be performed in an easy and intuitive environment (Chi-square test, T-test, Wilcoxon signed-ranks test, Kruskal-Wallis test, ANOVA, Pearson correlation test, Spearmann rank-order test. Automatic display available tests for each input data type. Kolgomorov-Smirnov test for normality of character data.

Database Sharing Tools

  • Database connectivity. Possibility to link GelCompar II to ODBC compatible high performance database management systems such as Oracle, SQL Server and MySQL.
  • User management. Comprehensive set of user and security tools, including creation of Users with logins and passwords and User Groups defining specific privileges. Control password timeout and strength, user activity logging and data input consistency. Possibility to define access privileges for each individual database object. Create, Modify, Delete, Sign, Restore, Lock and Unlock privileges can be granted to specific users. ODBC connection string can optionally be encrypted to enhance database security. To ensure even higher security, the entire database connection and mapping settings file can be encrypted as well.
  • Client-Server setup. Client functions come with the Database Sharing Tools. Functions include querying and downloading entries from the central Server database; upload of data to the Server for identification; receipt of detailed identification report from Server. See also BioNumerics Server.
  • Geographical coding. Perform geocoding and plot database entries on an interactive geographical map based on locations present in the database.
  • Bundles. Any selected information and experiment data for selections of entries from the database can be condensed into a Bundle. Bundles can be exchanged over internet and opened in a recipient database. Automatic remapping makes full comparison between different fingerprint systems possible.

GelCompar II Network Licenses

Compatibility

  • Operating system. GelCompar II is fully compatible with Windows XP, Windows Vista and Windows 7.
  • Hardware. PC compatible with 512 MB of RAM or more and high resolution true-color graphics (1024x768 or higher)

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