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AVADIS®

AVADIS® is Strand's award winning application development platform that enables Strand to build data and text mining solutions in life sciences. AVADIS® brings the power of analytics to extract value from the vast amounts of data available and which continues to become available in life sciences research. AVADIS® is at the core of many solutions and products that Strand has developed.

 

AVADIS® platform has a rich collection of data/text mining algorithms, data visualization libraries, workflow/application automation layers, and enterprise data organization functions. These functions are available as libraries that allow developers to rapidly build software prototypes, applications and off-the-shelf products.

 

The collection of algorithms and visualizations in AVADIS® grows as new applications using the platform are developed. Currently, the algorithms that AVADIS® platform contains range from general purpose statistical mining and modelling algorithms, to text mining algorithms, to very application-specific algorithms for microarray/NGS data analysis, QSAR modelling and biological networks analysis. AVADIS® has a collection of powerful mining algorithms like PCA, ANOVA, T-test, clustering, classification and regression methods.

 

The range of visualizations includes most statistical and data modelling related graphing views, and very application-specific visualizations. Some of the statistical views include 2D/3D scatter plots, profile plots, heat maps, histograms and matrix plot; data modelling relevant views include dendrograms, cluster profiles, similarity images and SOM U-matrices. Application-specific views in AVADIS® include pathway network views, genome browsers, chemical structure views and pipe-line views.

 

Functionality and workflows can be customized for an application or a user job role or customer-specific requirements using XML-driven configuration files and Python-based scripts. The look-and-feel of software developed on AVADIS® can also be controlled via these XML configuration files. This ability of the platform allows technical groups at clients to manage theAVADIS®-based applications, themselves.

 

There are several functions in AVADIS® that enable applications developed on this platform to be implemented enterprise-wide. AVADIS® has data/information management server modules to enable collaborative research environments. AVADIS® also has compute server function that allows distributed computing ability for support very compute intensive applications build on the platform.

 

AVADIS® is trademarked in several key jurisdictions. Products powered by AVADIS® are marketed world-wide by Strand and partners like Agilent Technologies.


AVADIS® features include
Intuitive Visual Analysis

  • All analysis results are accompanied by a graphical output

  • Interactive visualizations that allow for dynamic changes

  • Multiple graphical representations to help identify patterns in the data

  • Selections on one view are propagated to all other open views

  • All views can be customized for publication quality image or transferred to Word, PowerPoint etc.

Projects & Workflows

  • AVADIS® offers many different project-types, and each project is associated with one such project-type

  • Each project-type has a specific pre-defined workflow. Workflows can be edited/customized through configuration files and interfaces.

  • Each workflow is organized in an user-friendly manner, with simple url-type links in the workflow browser

  • The subsets and data views relating to each workflow are organized into a hierarchical tree structure for easy recall

  • AVADIS® is highly customizable and allows for the creation of new customer or process specific workflows very easily.

User Interface Organization

  • The AVADIS® interface supports three main areas: the Desktop, the Navigator and the Workflow Browser. The Desktop accommodates all the views and algorithm results pertaining to each project, the Navigator displays all currently open datasets, views and algorithm result reports in a hierarchical tree structure, while the Workflow Browser allows application specific workflows to appear as a sequence of user clickable links.

  • AVADIS® makes it very easy for users to edit, analyse and save datasets. It allows users to work on and save multiple data sets as well as to share data easily.

 

Powerful Statistical Algorithms

  • AVADIS® has a range of data pre-processing algorithms like normalization, background/noise correction and transformations. Depending on the application, these algorithms are extended and optimized.

  • The three kinds of normalization supported: Mean/Median Shifting , Linear and Non-Linear Lowess Regression and Quantile Normalization for Replicates

 

Cluster Analysis

  • Cluster analysis is a powerful way to organize rows in the dataset into groups or clusters of similar rows using the power of algorithms; different algorithms work on application-specific data.

  • To cater to the needs of various applications, AVADIS® provides many different kinds of algorithms and distance measures. This includes algorithms such as k-Means, Hierarchical, EigenValue, Self Organizing Maps (SOM), Random Walk and Principal Components Analysis (PCA) along with many distance functions such as Euclidean, Square Euclidean, Manhattan, Chebychev, Differential, Pearson Absolute and Pearson Centered

Classification & Regression

  • AVADIS® has the widest range of classification and regression algorithms in its class - a set of powerful tools that allow researchers to build prediction models.

  • AVADIS® classification algorithms include four powerful machine learning algorithms - Decision Forest, Support Vector Machines, Neural Networks, Naïve Bayes and Axis-Parallel Decision Trees.

  • Regression algorithms in AVADIS® include Multiple Linear Regression, Neural Network, Support Vector Machines, Regression Forest and Partial Least Squares.

  • Algorithm-specific visualizations guide users to build best possible models for their data.

  • AVADIS® allows nesting and ensemble of multiple models to create more fine grained models that cover a wide range of prediction space.

Enterprise Functionalities

  • AVADIS® helps organizations deal with application data by providing a client-server architecture where access and integration of data can be set up at the server and automatically inherited by all clients applications.

  • AVADIS® enables collaboration by allowing users to easily share analysis and results with others.

  • It also allows administrators to setup role-based access to information, projects and applications.

  • By capturing Workflows and managing them on the enterprise server, AVADIS® allows implementation of ‘best practices' or SOPs.

Case Studies