KnowItAll Metabolomics Edition

Category Metabolomics/Metabonomics>Metabolic Profiling/Analysis Systems/Tools

Abstract The KnowItAll Informatics System, Metabolomics Edition covers the full range of steps from raw data processing to biomarker identification.

By combining spectroscopic, cheminformatics, and chemometrics tools, with a resource of metabolic pathways, KnowItAll allows researchers to analyze and manage clinical/biological data in the search for relevant biomarkers.

Spectral Processing Toolbox --

ProcessIt NMR - NMR Spectrum Processing - With KnowItAll Informatics System’s ProcessIt NMR, researchers can seamlessly import, process, and analyze NMR spectra from various sources to improve the quality of archived data and search results. With this application, one can execute multiple-step processing either step-by-step or by using a macro capability to accomplish it in batch mode.

ProcessIt NMR is easy to use, yet offers a comprehensive set of processing features to correct experimental artifacts and improve the appearance of NMR spectra. Features in ProcessIt NMR include:

1) Import 1D processed or free induction decay (FID) spectra from multiple formats;

2) Processing features: Zero filling, interactive window functions and Fourier transform;

3) Automatic and manual phase correction;

4) Automatic and manual baseline correction, includes polynomial, spline, linear, and FaceLift algorithms;

5) Automatic and manual peak picking;

6) Automatic and manual integration;

7) Addition and subtraction of spectra;

8) Automatic alignment of multiple spectra by correcting reference offsets;

9) Interactive suppression of solvent peak(s);

10) Overlay multiple spectra for easy comparison;

11) Macro capability for quick and efficient processing;

12) Export in the International Union of Pure and Applied Chemistry Joint Committee on Atomic and Molecular Physical Data (JCAMP) format;

13) Spectrum handling tools, such as horizontal zoom, box zoom, hand cursor, and scaling;

14) Customizable display integrated with MineIt (see below...) for easy batch processing and archiving of processed spectra, ReportIt (see below...) to create reports containing spectra, peak, and integral tables, and SearchIt (see below...) for spectral searches;

15) Local and global spectral alignment; and

16) Peak distance measurement.

Spectral Analysis Toolbox --

AnalyzeIt MVP - Multivariate Processing - AnalyzeIt MVP, which incorporates Infometrix’ chemometrics technology for principal component analysis (from the well-known Pirouette® software), is a complementary addition to Bio-Rad's KnowItAll data analysis environment.

The integration provides an advanced tool for expert and non-expert users alike to perform multivariate analysis of spectroscopic, chromatographic, or numeric data.

It enables a user to:

1) Gain insight into hidden patterns and relationships in the user’s data;

2) Explore data correlations to answer critical research, development, or production questions; and

3) Facilitate the storage of analysis results for subsequent reference, reporting, or investigation.

Database Projection Analysis - In order to find prominent factors or differentiation within large databases of chemical, analytical (including spectra and chromatograms), and biological data, a researcher can use the loadings plot from a multivariate analysis of that data as a query to search against a “standard” dataset.

However, depending upon the correlation of the experimental dataset to the standard dataset, this method does Not always yield accurate answers.

In response, Bio-Rad Laboratories, Inc. has introduced a new method known as ‘Database Projection Analysis’ within the KnowItAll Informatics System.

This method, which is complementary to other analytical approaches, can be quite successful in helping researchers to identify differentiation factors or “markers” hidden within a dataset.

ValidateIt - Model Validation - Validation of prediction is an essential step in the successful use of prediction tools in a regulated environment. Standalone prediction models and consensus models are easily validated by using the ValidateIt application in Bio-Rad's KnowItAll Informatics System.

Conveniently, the ValidateIt application also serves as the control center for viewing and evaluating the suitability of a model or consensus model.

ValidateIt allows you to:

1) Plot one database variable against another;

2) Validate the prediction of an existing model; and

3) Create and cross-validate Consensus Models.

Data Included -- NMR Metabolite Database - A database of CNMR and HNMR spectra of proteins, peptides, and nucleic acids.

Data Toolbox --

SearchIt - Database Searching - Database Searching of Spectra, Chromatograms, Structures, and More - The SearchIt application allows structures and/or spectra to be imported and searched against reference databases, as well as against user-created databases.

Searches are fully customizable and are driven by state-of-the-art algorithms. Searching can be performed by structure, substructure, name and properties, spectra, or any combination thereof.

Multi-Technique Spectral Searching – KnowItAll’s spectral search system is capable of searching spectra in multiple analytical techniques simultaneously from one or many databases.

MineIt - Database Display & Mining - MineIt is a deceptively simple application. Like Microsoft Word®, it is easy for beginners, but has many advanced features that more sophisticated users will appreciate. With MineIt, users can view reference databases, user-created databases, or hit lists generated by the companion SearchIt application.

This interface allows the user to access databases containing many types of data, such as IR, NMR, MS, UV-Vis, Raman, NIR, structures, chromatograms, physical properties, and more.

Since analytical databases can contain one or more analytical techniques in the same record, this application is ideal for accessing databases of reference spectra.

Advanced Data-mining Capabilities - MineIt includes sophisticated data-mining capabilities that allow users to convert masses of uninterruptible data into actionable information. The unique, fully user-definable color coding and weighted scoring scheme allows users to rank-order their datasets according to the priorities of a particular project, and then readjust the scheme for different projects.

Database Building Option - Build Searchable Databases with Spectra, Chromatograms, Structures, & Properties - Chemists and spectroscopists produce valuable data every day within their organizations.

With KnowItAll’s MineIt Database Building option, researchers can capture these resources and build searchable databases that include multiple analytical techniques (NMR, MS, IR, Near IR, Raman, UV-Vis, and chromatography), chemical structures, and alphanumeric data. With this option, users can:

1) Centrally store & share critical data;

2) Customize & protect databases;

3) Import experimental data even if laboratories have instruments from multiple vendors;

4) Add hyperlinks to web pages and other documents;

5) Cross-reference to other datasets; and

6) Deploy at the desktop or enterprise-wide.

Overlap Density Heatmaps - Visual Data-mining & Analysis - Patented Technology for Visual Data-mining and Analysis of Spectra, Chromatograms, and Other Resources -

Bio-Rad’s Informatics Division has introduced this new technology for visual data-mining and analysis to assess the similarities and dissimilarities in massive amounts of spectral, chromatographic, or other graphical data.

This patented technology, called Overlap Density (OD) Heatmaps and OD Consensus Object displays, will allow scientists to visualize the common features of the overlapped objects (such as spectra or chromatograms) by color coding the areas from highest to lowest overlap.

This technology can be used to analyze the large amounts of graphical data from such disciplines as cheminformatics, analytical informatics, metabolomics, chemometrics, genomics, and/or proteomics and has applicability in all branches of scientific research, including chemistry, the life sciences, and diagnostics.

Pirouette Model Support - Use models built in Infometrix Pirouette software; feature of MineIt.

Batch Property Calculation - Calculate properties for entire databases; feature of MineIt.

CompareIt - Data-mining - KnowItAll’s CompareIt application is a data analysis and visualization package built upon a cheminformatics software platform: chemical intelligence is its foundation, Not an afterthought.

With this application, researchers can visualize and compare numeric data within a single database or between multiple databases. Using CompareIt, users can select any two property fields from multiple databases for comparison.

Once the researcher selects the fields to be compared, CompareIt generates a scatter-plot diagram of one variable versus the other. From this scatter plot comparison, the researcher can then visualize trends and segregate data that follows a desired trend from that which does Not.

Selecting any point or group of points on the scatter plot will immediately display the compounds associated with that record, including a convenient view of all the data associated with the compound.

AssignIt - HNMR, CNMR, & XNMR - Add Assignments to NMR Databases for 1H, 13C, & Other Nuclei - The AssignIt application allows KnowItAll users to increase the power of the databases they build using KnowItAll’s Database Building option (see above...).

With this tool, users can add assignments and other information to the structures in 1H, 13C, 19F, 31P, 15N, 17O, 11B, and 22Si NMR databases.

AssignIt’s easy-to-use interface allows quick database information input, such as peak shift assignments, intensities, coupling constants, and multiplicities - all linked to the relevant chemical structure or proposed structure.

Basics Toolbox --

DrawIt - 2D Structure Drawing - With DrawIt, users can draw any chemical structure with just a few clicks and drags. It has all the tools users need to draw rings, bonds, atoms, chains, arrows, and chemical symbols. With programmable hot keys, users can quickly label common groups by typing a single key. (DrawIt uses familiar ChemWindow technology).

DrawIt recognizes stereochemistry and automatically specifies R/S centers and E/Z double bonds. Complex mixtures of diastereomers including relative and absolute stereochemistry can be represented with a single structure.

ReportIt - Custom Publishing - With ReportIt, users can create standard reports, presentations, and web publications that fit specific communication needs. Reports are easy to lay out by using one of the predefined templates or creating custom ones.

ReportIt also includes an annotation tool to create links between objects like structures, formulas, captions, tables, graphics, etc., allowing the user to present clear graphical comments for key elements of experiments.

And because some research results need to be presented in tables, a ‘Table Tool’ has been added so users can enter and organize their data quickly. Users can design their own tables or choose from a number of predefined table styles.

ReportIt also provides the ability to incorporate spectral data, chromatograms, and peak tables. With this tool, users can directly import IR, NMR, MS, NIR, Raman, and UV-Vis spectra and chromatograms, using common native file formats.

Once spectra or chromatograms are imported, users can annotate them with text and structures, select peaks, generate peak tables, produce and edit property tables, zoom in to focus on specific peaks and regions, change colors and fonts, annotate peaks, and do whatever users need to improve both the understanding of their data and the presentation of their work.

BrowseIt - An Integrated Web Browser - BrowseIt is a web browser built into the KnowItAll Informatics System, which provides access to a website designed especially for KnowItAll users.

This site also offers demo movies, tips, and the latest KnowItAll product information.

System Requirements

Contact manufacturer.

Manufacturer

Manufacturer Web Site KnowItAll Metabolomics Edition

Price Contact manufacturer.

G6G Abstract Number 20673

G6G Manufacturer Number 104313