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Bioinformatics Solutions for Gene Expression
 

Data Acquisition and Basic analysis

Affymetrix GeneChip® Command Console (AGCC) provides comprehensive data collection and analysis tool for the Affymetrix GeneChip Platform. The suite provides automated data collection and instrument control for the GeneChip® Fluidics Station 400 and the GeneChip Scanner 3000. Using advanced scientific algorithms, the suite provides several different analysis applications. Analysis options include conversion of intensity data into expression results, allele detection, singular nucleotide polymorphism detection, and nucleotide analysis. 

ArrayAssist® Expression Software

ArrayAssist® Expression Software, powered by avadis™, is easy to use, while still offering a full spectrum of advanced analytical features such as new statistical tests (multi-way ANOVA and non-parametric statistical tests), data mining tools (classifiers for machine learning-based prediction) and sophisticated, dynamic, interactive visualization options.

For advanced users, a new scripting engine is featured in all products of the ArrayAssist line. The engine allows scripting of complex functions and user-defined workflows and is fully integrated with external programs such as the R statistical software. The scripting capabilities enable creation and deployment of automated workflows significantly extending ArrayAssist expression software functionality, ease of use, and its usefulness for the research team. ArrayAssist Expression software is Mac, Windows and Linux compatible and is integrated with the PathwayArchitect™ software, allowing seamless data transfer between the products.

PathwayArchitect® Software

100 manually curated pathways*

Large biological interaction database with over two million biological facts*

Guided workflows for ease of use

Relevance Interaction Network algorithm helps find most important interactions

Support for Mac® OS X, Linux® and Windows®

Stratagene’s PathwayArchitect® software, powered by avadis™, is the new standard in pathway analysis. With its easy to use biology-focused workflow and a vast database of over two million biological interactions, PathwayArchitect® software is designed with the life scientist in mind.The PathwayArchitect® software also features a new method to explore biological interactions—the Relevance Interaction Network. Relevance Interaction Network analysis begins with a protein list and identifies the network of proteins and small molecules, which are most statistically related to the biology of the protein list. This algorithm makes it possible to easily identify binding complexes, transcriptional regulation networks, and even small molecules that regulate the biology of a group of proteins.

PathwayArchitect® integrates powerful data management tools with analysis options that enable scientists to determine both the statistical and biological significance of microarray data, all in a single convenient system. Support for common platforms (Affymetrix, Illumina, etc.) as well as custom arrays, makes PathwayArchitect® the most effective and accessible microarray data analysis system available today.

GeneMaths XT

GeneMaths XT is perhaps the most complete and professional software for microarray analysis currently available. Its advanced concept of layers and subsets makes it is possible to work with different layers for different data outputs, for example Cy3 and Cy5, standard deviations, error values, etc., as well as different subsets of genes and/or arrays. Also unique is the full error handling through all analysis, mining, and statistics functions. Further features include:

Active history concept: record and repeat all steps of the analysis through history files and templates

Reliable data normalization for all types of arrays

Interactive querying and pattern matching

Easy plot wizard for all types of plots and graphs

Unsupervised learning through transversal clustering, hierarchical k-means partitioning, PCA, Discriminant Analysis, self-organizing maps

Supervised learning using neural networks, support-vector machines, k-nearest neighbor

Analysis of variance, multivariate analysis, and a large number of statistical tests

Special analysis tools for time-course experiments

Seamless interaction between all analysis applications

Interactivity with databases on the internet

Automation and customization through powerful script language

Advanced Data Analysis For Genotyping

ArrayAssist® Expression Software

ArrayAssist® Expression Software, powered by avadis™, is easy to use, while still offering a full spectrum of advanced analytical features such as new statistical tests (multi-way ANOVA and non-parametric statistical tests), data mining tools (classifiers for machine learning-based prediction) and sophisticated, dynamic, interactive visualization options.

For advanced users, a new scripting engine is featured in all products of the ArrayAssist line. The engine allows scripting of complex functions and user-defined workflows and is fully integrated with external programs such as the R statistical software. The scripting capabilities enable creation and deployment of automated workflows significantly extending ArrayAssist expression software functionality, ease of use, and its usefulness for the research team. ArrayAssist Expression software is Mac, Windows and Linux compatible and is integrated with the PathwayArchitect™ software, allowing seamless data transfer between the products.

PathwayArchitect® Software

100 manually curated pathways*

Large biological interaction database with over two million biological facts*

Guided workflows for ease of use

Relevance Interaction Network algorithm helps find most important interactions

Support for Mac® OS X, Linux® and Windows®

Stratagene’s PathwayArchitect® software, powered by avadis™, is the new standard in pathway analysis. With its easy to use biology-focused workflow and a vast database of over two million biological interactions, PathwayArchitect® software is designed with the life scientist in mind.The PathwayArchitect® software also features a new method to explore biological interactions—the Relevance Interaction Network. Relevance Interaction Network analysis begins with a protein list and identifies the network of proteins and small molecules, which are most statistically related to the biology of the protein list. This algorithm makes it possible to easily identify binding complexes, transcriptional regulation networks, and even small molecules that regulate the biology of a group of proteins.

PathwayArchitect® integrates powerful data management tools with analysis options that enable scientists to determine both the statistical and biological significance of microarray data, all in a single convenient system.

Exemplar Genotyping Solutions from Sapio Sciences

Exemplar for Genotyping is an innovative, advanced genetic analysis tool. The Exemplar Genotyping Analysis Suite was devised to model the genetic roots of disease using advanced machine learning technology combined with traditional statistics. Our analysis solution takes raw genotype data all the way through the analysis pipeline to biological interpretation. The Suite is constructed of numerous analysis modules that take different approaches toward the understanding of genetic affectations.

Exemplar provides a consistent and easy-to-use approach of creating projects and grouping experiments within those projects. New experiments are created with the help of a wizard to walk through the options for various types of experiments, which can then be run at the click of a button. Exemplar can analyze both genotyping and clinical data together to better classify complex genetic disorders.