VeraCode Assay Designer software

The VeraCode Assay Designer software streamlines the development of low- to mid-plex genotyping assays using VeraCode Universal Capture Beads. Simply import list of desired targets in FASTA format by dbSNP accession number, or directly insert sequence information and select the design parameters. The software outputs multiple allele-specific primer extension assay designs scored on multiplex compatibility, GC content, melting temperature, likelihood of primer dimmers, and folding. Results are easily exported for straightforward purchasing of consumables and running on the BeadXpress Reader.

VeraCode Assay Designer Highlights
Streamlined Interface: Simply input target sequences and the software automatically designs multiplex assays
Flexible Assay Design: Automatically incorporate capture bead sequence or manually assign bead codes
Customizable Design Parameters: Manually select parameters for increased control, use pre-set criteria, or allow the software to use preset design parameters.

Software Link:  VeraCode Assay Designer software
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SNP & Variation Suite - Genomic software

SNP & Variation Suite is the most powerful and integrated collection of high-performance analytic tools for managing, analyzing, and visualizing large-scale, complex genomic data. It's fast, easy-to-use, and runs on conventional desktop computers enabling you to interact with your data as never before. Both statistically and visually, you can explore the relationships among vast amounts of clinical patient data, environmental factors, and genetic variants to understand the cause of disease and other traits - without writing a single line of code (unless you want to).
Details
YOUR DATA. YOUR ANALYSIS. YOUR DISCOVERY.

SNP & Variation Suite is the most powerful and integrated collection of high-performance analytic tools for managing, analyzing, and visualizing large-scale, complex genomic data. It's fast, easy-to-use, and runs on conventional desktop computers enabling you to interact with your data as never before. Both statistically and visually, you can explore the relationships among vast amounts of clinical patient data, environmental factors, and genetic variants to understand the cause of disease and other traits - without writing a single line of code (unless you want to).

ANALYTIC SOLUTIONS

SNP Analysis
Get the most out of your microarray data with the most complete set of SNP analysis tools.

Genome-Wide Association
Take GWAS to a new level with unparalleled performance on large-scale data.

Next-Generation Sequencing Analysis
Latest tertiary analysis methods for DNA
next-generation sequencing.

Copy Number Analysis
Optimal results with a complete set of quality assurance, CNV detection, and analysis tools.

LD and Haplotype Analysis
Powerful new plotting and analytics for linkage disequilibrium and haplotypes.

Family-Based Analysis
Cutting-edge analytics for virtually any family study design and ascertainment condition.

Data Management
Easily manage data of any size and type on a conventional desktop computer.

Data Editing and Enrichment
Real-time data editing, manipulation, and enrichment on large-scale data.

Quality Assurance
A robust toolset for quickly assessing and remedying sample and marker issues.

Genome Browser and Visualization
Explore data and results with unprecedented whole genome navigation and visualization.

Scripting and Integration
Innovate, integrate, and automate with a fully-programmatic Python scripting interface.

Runs of Homozygosity Analysis
Identify patterns of extended homozygosity and run statistical tests for association.

SVS MODULES

HelixTree
HelixTree is the core module of the SNP & Variation Suite. Its unique set of conventional and leading edge analytic tools empower you to quickly and easily perform a broad array of workflows for genetic association studies.

CNAM
CNAM, in conjunction with other SVS 7 modules, offers a complete set of tools for processing raw intensity data, identifying regions of copy number variation (CNV), visualizing copy number data, and performing association analysis on a variety of copy number covariates.

Whole Genome Analysis Module
The Whole Genome Analysis Module incorporates several technologies and methods designed to overcome the statistical and computational challenges of large-scale whole genome analysis.

Sequence Analysis Module
Rare variants require new methods that don't work in traditional common variant studies. With the introduction of an entirely new Sequence Analysis Module you now have access to the latest tertiary analysis methods to help you make the most sense of all that next-gen sequencing data.

PBAT
Developed in collaboration with Dr. Christoph Lange of Harvard's School of Public Health, Golden Helix PBAT delivers an exclusive and extensive array of advanced statistical routines for the design and analysis of family-based SNP and CNV association studies.

Regression Module
Perform advanced linear and logistic regression, stepwise regression, and permutation tests with numeric variables and recoded genotypes.

SVS Viewer
SVS Viewer makes collaboration easy, and it's completely free. Load projects or individual datasets created by someone with SVS 7. Then you can manipulate spreadsheets, edit node annotations, augment existing plots, or create entirely new ones.



Software Link: SNP & Variation Suite

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GenomeQuest - Sequence data management (SDM) platform

At the core of GenomeQuest is the GQ-Engine - a database engine that is purpose-built for storing, managing, and analyzing sequence data at NGS scale.

GenomeQuest is the world's leading sequence data management (SDM) platform. Researchers use state-of-the-art tools to store, manage, and analyze genomic data. Bioinformatics teams get a development platform to customize workflows, build applications, and unify their sequence data environment. IT and business managers can efficiently scale to NGS across discovery operations.

Science Applications
GenomeQuest provides cutting-edge computational, querying, and visualization tools along with applications that accelerate research and discovery.

Built-In Collaboration
A web-based dashboard offers easy access to everything your team needs - including compute resources, sequence datasets, and discovery tools.

High Performance Infrastructure
GenomeQuest is purpose-built for large-scale sequence data management and analysis, utilizing cloud-based, embarassingly parallel" computing.

Unified Database for all Sequence Data

Sequences

Software Link: GenomeQuest
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Sequencher 5.0 - DNA sequence data anaylsing Software

Sequencher 5.0 from Gene Codes Corporation takes you from DNA sequence data to results easier and faster than ever! Over 20 years of daily use by biologists in labs around the world have refined Sequencher's tools and interface. You get the power and speed to get accurate results from your DNA analysis, and get back in the lab more quickly. Whether you need DNA sequence assembly and analysis tools for next-generation or traditional (Sanger or Capillary Electrophoresis) DNA data sets, Sequencher 5.0 will guide you toward results.

Next-generation DNA data sets:
  • Maq and GSNAP alignment algorithms
  • SNP analysis and methylation studies
  • Tablet Viewer

Traditional DNA data sets:
  • Multiple, configurable DNA Assembly algorithms
  • Comprehensive DNA sequence editing tools
  • Full support of sequence data confidence values

Next-generation or Traditional DNA data analysis features:
  • Powerful reference sequence alignment
  • Variance Table to discover SNPs quickly and easily
  • Extensive data import and export capabilities
  • NCBI BLAST search
  • Forensic mtDNA profiling

Software Link:  Sequencher 5.0

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DNAnexus - Sequence Data analysing software


DNAnexus provides solutions for both DNA sequencing centers growing their next-gen capacity, and researchers working with next-gen sequence data. Our web-based platform solves the data management and analysis challenges common to both with a single, unified system.

DNAnexus is built from the ground up to run on Amazon Web Services, the world's leading cloud computing provider. Our solution delivers not just software, but also all the computing and storage infrastructure. 100,000s of CPUs and 100s of petabytes of storage are available to you through DNAnexus, which acquires those resources on demand, allowing our pricing to mirror your usage. We support sequencing operations and research organizations of virtually any size, with absolutely no upfront hardware investment needed.

For core facilities with one instrument or sequence centers with 100 instruments, you can connect your sequencing output to DNAnexus in as little as 10 minutes. Learn more about what DNAnexus can do for your next-gen data management.

For researchers with a single lane of data, or for large commercial life science research organizations, DNAnexus can give you the right tools for your work, and the ability to scale up your research instantly in the future. Get started immediately without any setup or configuration.

Software Link: DNAnexus - Sequence Data analysis




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CLC Main Workbench

CLC Main Workbench aggregates user friendly gene expression analysis with all features of CLC Protein Workbench, CLC RNA Workbench, and CLC DNA Workbench in one integrated software package.
Details
A comprehensive workbench for advanced DNA, RNA, and protein analyses

CLC Main Workbench aggregates user friendly gene expression analysis with all features of CLC Protein Workbench, CLC RNA Workbench, and CLC DNA Workbench in one integrated software package.

CLC Main Workbench creates a software environment enabling users to make a large number of advanced DNA, RNA, and protein sequence analyses, combined with gene expression analysis, smooth data management, and excellent graphical viewing and output options.

CLC Main Workbench is available on Windows, Mac OS X, and Linux platforms.
Detailed Pricing
Static single computer license: $1999 for industrial customers, $399 for academic customers
Network licenses: $3999 for industrial customers, $799 for academic customers

Software Link: CLC Main Workbench
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CLC Science Server

CLC Science Server is an advanced Next Generation Sequencing focused three- tier solution offering secure, powerful, and flexible bioinformatics computing on a server located centrally in your organization.

Details
An advanced & powerful three-tier solution

CLC Science Server is an advanced Next Generation Sequencing focused three- tier solution offering secure, powerful, and flexible bioinformatics computing on a server located centrally in your organization.

The three main components are:

CLC bio offers installation, customization, and integration
Server software running on all major platforms (Windows, Mac OS X, and Linux)
Database backend: Either your existing database(s) or CLC Bioinformatics Database (Microsoft SQL Server 2003 & 2008, Oracle, mySQL, PostgreSQL, or H2)
Client software: Any CLC Workbench, any Web browser, and any custom developed clients can access the server concurrently

Among others, CLC Science Server provides you:
A powerful and modern three-tier server architecture
Flexible options of executing centralized services
Easy integration with other applications and services
Powerful database communication and data integration
Secure access control framework and central action logging

Software Link: CLC Science Server
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CLC Assembly Cell - Genomics Software

CLC Assembly Cell is a high-performance computing solution for read mapping and de novo assembling of Next Generation Sequencing data.

Details
CLC Assembly Cell is a high-performance computing solution for read mapping and de novo assembling of Next Generation Sequencing data.

The command-line interface of CLC Assembly Cell enables the functionalities to be easily included in scripts and other Next Generation Sequencing work-flows.

CLC Assembly Cell is utilizing SIMD instructions to parallelize and accelerate the assembly algorithms, making the program the fastest Next Generation Sequencing assembler at present.

The main functionalities of CLC Assembly Cell are:

Read mapping
Read mapping of Illumina Genome Analyzer, SOLiD, and 454 sequencing data
Support for native Color Space assembly
Support for both short read and long read assembly, including 454/Titanium data
Support for both gapped and ungapped alignments when doing short read assemblies
Support for assembly of paired end reads

De novo assembly
De novo assembly of Illumina Genome Analyzer and 454 sequencing data
Support for both short read and long read assembly, including 454/Titanium
Support for de novo assembly of paired end data

Other analyses
Fast analysis of raw data, including reporting
Option of joining data from different sources into the same analysis (including data generated by different kinds of sequencing technologies)
Extraction of data from part(s) of an assembly. Examples are extraction of contig and reads from an area of interest, or extraction (exclusion) of data from a specific sequencing lane that is suspected not to be of acceptable quality.
Find variations (simple SNP detection)
Support for input file formats Fasta, Sff, GenBank, csfasta, and scarf
A number of output options, including tables with assembly info
A "graphical" (ASCII art :-)) assembly viewer to get quick overview
Full integration with CLC Genomics Workbench. Output data from CLC Assembly Cell can be imported and further analyzed in CLC Genomics Workbench.

Software Link: CLC Assembly Cell
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CLC Genomics Machine - Genomic Software

CLC Genomics Machine is a turnkey solution including a lightning fast hardware platform with pre-installed enterprise software focusing on High-Throughput Sequencing data analysis - ready to function straight out of the box.
Details
Turnkey solution for large full-genome analyses

CLC Genomics Machine is a turnkey solution including a lightning fast hardware platform with pre-installed enterprise software focusing on High-Throughput Sequencing data analysis - ready to function straight out of the box. In addition, CLC Genomics Machine comes with several CLC Genomics Workbenches for user-friendly NGS data analysis on your own desktop.

Features
CLC Genomics Machine is a turnkey solution providing your organization with a wide range of High-Throughput Sequencing data analysis tools. Some are shown below:

Genomics
Read mapping of Sanger, 454, Illumina Genome Analyzer and SOLiD sequencing data
De novo assembly of genomes of any size (only limited by RAM available)
Color space mapping
Advanced visualization, scrolling, and zooming tools
SNP detection using advanced quality filtering
Support for multiplexing with DNA barcoding

Transcriptomics
RNA-seq including support for paired data and transcript-level expression
Small RNA analysis
Expression profiling by tags
EST library construction
Advanced visualization, scrolling, and zooming tools
Gene expression analysis

Epigenomics
Chromatin immunoprecipitation sequencing (ChIP-seq) analysis
Peak finding and peak refinement
Graph and table of background distribution and false discovery rate
Peak table and annotations


Software Link: CLC Genomics Machine
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CLC Genomics Server

CLC Genomics Server is an advanced High-Throughput Sequencing focused three-tier solution offering secure, powerful, and flexible bioinformatics computing on a server-architecture located centrally in your organization.
Details
Centralized Bioinformatics Analyses

CLC Genomics Server is an advanced High-Throughput Sequencing focused three-tier solution offering secure, powerful, and flexible bioinformatics computing on a server-architecture located centrally in your organization.

Available bioinformatics analyses
Read mapping of Sanger and High-Throughput Sequencing data
De novo assembly of Sanger and High-Throughput Sequencing data
SNP detection on whole genomes of any size
DIP detection on whole genomes of any size
ChIP-seq analysis
RNA-seq analysis
Small RNA analysis
Trim Sequences

Main reasons to invest in CLC Genomics Server
Compute Resource Management:
Central execution platform with flexible queuing system, designed for your bioinformatics analysis and services.
Flexible:
Based on a 3 tier system architecture to offer maximum security and intractability within fields of biology and bioinformatic computing.
Premium System-Clients:
Offers maximum client-flexibility with support for our user-friendly and award winning CLC Genomics Workbench as a premium system-client.
Customizable:
Highly customizable on both client-side and server-side using our SDK or various Command Line Tools.
Scalable:
Highly scalable with support for CLC Server Nodes.
Advanced Data I/O:
Offers an advanced and customizable data-import/export framework, that also can be used for data conversion.
Shared Data:
Store your data on central storage. This can be either a File System, the CLC Bioinformatics Database or on a custom designed database scheme.

Design custom workflows to support your science
With the Command Line Tools of the CLC Genomics Server, it is possible to define your own workflows. This is done in terms of scripts that interact with the CLC Command Line Tools. With the solution a sample script workflow is given, that imports NGS reads, maps the reads to a reference, followed by SNP and DIP detection:

Software Link:  CLC Genomics Server










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CLC Genomics Workbench


We have overcome the challenge to analyze High-Throughput Sequencing data faster than it is produced by implementing a SIMD-accelerated assembly algorithm in our Next Generation Sequencing solution, CLC Genomics Workbench - a cross-platform desktop application with a graphical user-interface.
Details
Dominating the High-Throughput Sequencing data analysis challenge

We have overcome the challenge to analyze High-Throughput Sequencing data faster than it is produced by implementing a SIMD-accelerated assembly algorithm in our Next Generation Sequencing solution, CLC Genomics Workbench - a cross-platform desktop application with a graphical user-interface.
CLC Genomics Workbench, for analyzing and visualizing Next Generation Sequencing data, incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow.

Some of the key Next Gen Sequencing applications of CLC Genomics Workbench are listed below

Genomics
Read mapping of Sanger, 454, Illumina Genome Analyzer and SOLiD sequencing data
De novo assembly of genomes of any size (only limited by RAM available)
Color space mapping
Advanced visualization, scrolling, and zooming tools
SNP detection using advanced quality filtering
Support for multiplexing with DNA barcoding

Transcriptomics
RNA-seq including support for paired data and transcript-level expression
Small RNA analysis
Expression profiling by tags
EST library construction
Advanced visualization, scrolling, and zooming tools
Gene expression analysis

Epigenomics
Chromatin immunoprecipitation sequencing (ChIP-seq) analysis
Peak finding and peak refinement
Graph and table of background distribution and false discovery rate
Peak table and annotations

Cross-platform
CLC Genomics Workbench is available for Windows, Mac OS X, and Linux platforms, and includes all features of CLC Main Workbench for carrying out a wide range of downstream analyses.

Benchmarking
In benchmark tests we have assembled half a million 454 reads against the full E. coli reference genome in around 2 minutes on a two-core laptop with 2 gigabyte RAM. This speed-up, based on integrated SIMD high-performance computing technology, increases even more when using a computer with more CPU-cores and RAM.

454, SOLiD, Illumina Genome Analyzer - no problem!
We support all the major Next Generation Sequencing platforms, such as SOLiD, 454, Illumina Genome Analyzer and of course also Sanger. We are working closely together with all the instrument vendors to ensure full integration in the ongoing development.







Software Link: CLC Genomics Workbench
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Mascot Cluster - Spectroscopy Software

Mascot Cluster is a complete, turn-key solution for high throughput protein identification.

Mascot has been designed to be embarrassingly parallel, which means that each search can be divided to run in parallel on multiple processors. Support for parallel execution is built-in to Mascot, and does not require any special operating system or grid engine. If you wish, you can license the software and set up a cluster using your own hardware. On this page, we describe the other option: a turn-key system with Mascot pre-installed on reliable, high performance IBM hardware.

Hardware

Any current IBM server that uses Intel or AMD processors can be used as the hardware platform. For a small cluster, up to around 6 processors, the most cost-effective solution is to use a number of dual processor servers, either tower or rack mount. For larger systems, we recommend the IBM BladeCenterTM, which is more compact and easier to manage than a large number of standard servers.

Mascot licensing is socket based. That is, if a processor has multiple cores, Mascot will use all of them for searching. For a given architecture, search speed (or throughput) goes as the processor clock speed multipled by the total number of cores.

Only the processors used for searching require a Mascot licence. It is often a good idea not to run searches on the master (head) node of the cluster, but leave it free to run the web server, handle database updates, and generate reports. This makes the server very responsive even when there are several searches running, using all the processor time on the search nodes. Having a non-searching master node also gives you a spare node, in case one of the search nodes has a hardware failure.

Result files are stored on the master node, so this needs access to plenty of disk storage. Search nodes only need local storage for program files and the compressed sequence database files; a single hard drive of modest size is usually sufficient. All nodes should have at least 2 GB RAM.

Software Link: Mascot Cluster - Spectroscopy Software
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PharmaExpert - Pharmacology Software

PharmaExpert analyzes the relationships between biological activities, the interactions of drugs and the multiple targeting actions of chemical compounds. As a pharmacological knowledge-based tool, it provides in silico screening of compounds using PASS prediction results.

Details
Key features of PharmaExpert:
• Mechanism-effect relationship (MER) base, manually curated by experts, contains 11,049 mechanism-effect relationships
• Selection of compounds with required therapeutic but without side effects
• Comparative analysis of compounds with similar structures
• Selection of compounds with multiple mechanisms of action
• Analysis of drug-drug interactions with regard to their pharmacokinetic, pharmacodynamic and adverse effects

PharmaExpert is an addition to the PASS (Prediction of Activity Spectra for Substances) tool. It provides a comfortable solution for data mining of the PASS prediction results to find the best drug-like candidates from a set of compounds. The core of the program is a mechanism-effect relationship (MER) base, manually curated by experts, which is used to determine cause-effect relationships for the compounds. Like PASS, the software runs under Windows.

PharmaExpert has been developed by Vladimir Poroikov, Dmitry Filimonov & Associates currently working in the Department for Bioinformatics at the Institute of Biomedical Chemistry, Russian Academy of Medical Sciences in Moscow.

A free demo version, as well as further information, is available upon request.

Software Link: PharmaExpert - Pharmacology Software
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Mascot Daemon - Spectroscopy Software

Mascot Daemon is a client application which automates the submission of data files to Mascot server. It runs under Microsoft Windows 2000, XP, Server 2003, Vista, Server 2008, and 7. Daemon functionality includes:

Batch mode, in which an arbitrary group of files can be defined for searching, either immediately or at some pre-set time.
Real-time monitor mode, in which new files on a pre-defined path are searched as they are created.
Score dependent follow-up tasks. For example, automatically repeating a search at a later date or against a different sequence database.

Multiple Daemon clients can submit searches to a single Mascot server. If you have several mass spectrometers, you can install separate copies of Daemon on each instrument data system or just have a single copy of Daemon somewhere on the LAN marshalling searches for all instruments.

The functional unit of Mascot Daemon is a task, which is defined by the data source (a list of data files or a file path), how the data are to be searched, when the searches are to take place, and any follow-up activities, such as conditional repeat searches.

Search parameters are defined in the Parameter Editor, which closely resembles the HTML form used for interactive Mascot searches. Fields can also contain HTML-like tags which are automatically substituted at run time with information such as a file name or a sample description.

Every time a new task is run, it creates a task node on the status tree. The results from each task are attached to the task node, just like directories and sub-directories in Windows Explorer. Key information for each result can be displayed by clicking on the result node. The full result report can be displayed in a web browser by clicking on the blue hyperlink.

Daemon's follow-up function is extremely powerful and can be used in many different ways. A couple of simple examples would be:

A batch of data files can be searched at specified intervals against database updates. Each data file will stay in the loop until it's score exceeds a pre-set level.
Sequence databases of increasing size or decreasing quality can be searched serially. For example, a small database of common contaminants such as keratins might be searched first. Spectra which are unmatched can then be searched against a comprehensive non-redundant protein database, such as NCBI nr. Data which still fail to find a match can then proceed to a search of dbEST.

Arbitrary numbers of follow-up tasks can be chained together to implement complex decision trees. This is only possible because Mascot scores reflect true probabilities, permitting rule based software to determine whether a match is significant according to user specified criteria.

The default database engine used by Mascot Daemon is Microsoft Jet 4.0, the engine used by Access 2000. Alternatively, Daemon can be configured to use any database engine which supports either OLE DB or ODBC, such as Microsoft SQL-Server or Oracle, enabling multiple Daemon clients to share a common task database.

 Software Link: Mascot Daemon - Spectroscopy Software
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Metabase - laboratory data management software

Metabase is a laboratory data management software system designed specifically to meet the needs of laboratories conducting ADME metabolism, pharmacokinetics, and toxicokinetics studies. Starting with the generation of a sample list for an entire study, Metabase serves as the basic tool to acquire, organize, manage, calculate, store, and report study results. Key features of the program are its clear organization (which follow standard laboratory workflow procedures), its flexible and powerful data handling, its ease of use, and its integration with other productivity software. The flow sheet on the right illustrates the overall process of using Metabase as your primary data handling and management system.

Metabase is a practical, low cost, user-friendly, laboratory-oriented tool. The program is based on Microsoft Excel® and can be easily custom tailored to fit each client's work place or modified to meet changing needs and requirements. And to make sure that it does the job the right way, it was designed and operated in radio-analytical metabolism research laboratories.

Metabase comes as a turn-key system for radio-analytical sample processing and liquid scintillation counting data, but it can be custom modified for other analytical methods. Metabase is designed to meet GLP guidelines and comply with FDA, EPA, EEC software development and validation requirements. The system is provided with complete system life-cycle documentation. Test files are supplied for use in validation. Metabase is a cost-effective solution for comprehensive management of metabolism information in a well organized, flexible, and user-oriented manner.

Benefits

Specifically designed for sample handling of ADME metabolism and pharmacokinetic studies.
Excel-based software providing wide flexibility in a familiar spreadsheet environment.
An exceptionally affordable LIMS system for radioanalytical lab.
Helps you define, collect, manage, calculate, and report entire study protocols.

Features

Excel-based for Reliable Performance

Metabase is based on Microsoft Excel® and can run in any version of Excel in versions of Microsoft Windows. Excel provides a familiar working environment for using Metabase. Additionally, Metabase can take full advantage of all the functions, features and power of Excel.

Flexibility

The need for flexibility is an overriding requirement for any metabolism data handling system. No two studies are exactly alike. Therefore, every function of Metabase is designed with flexibility in mind. Added to this, the "open architecture" afforded by Excel spreadsheet operations allows user control over such features as formatting and appearance, significant figures, and exporting of results. Input functions and calculations can be modified or added, as needed.

Lab Smart

Metabase is a "lab smart" tool. It was developed by researchers with extensive experience in metabolism studies and is designed to provide assistance through all phases of a typical metabolism study.

Protocol and Study Designs

Metabase can handle any type of study design, whether the study involves serial sampling of individual animals, time-based composites from groups of animals, multiple dose levels, or even variable specific activities. Metabase helps the user set up a clear one-page overview of the study design and sampling strategy and uses this to develop a master sample information database.

Variable Dose Methods

Metabase supports dose computations based on individual dose measurements or nominal dose amounts per group. Additionally, different specific activities can be used for each dose group, such as employed in EPA's guidelines for dermal absorption studies.

Automated Data Entry

No hand entries of data. Metabase automatically reads data files obtained from a liquid scintillation counter or it can be directly connected for on-line data transfer. Similarly, Metabase automatically prepares a Sample Processing spreadsheet that can be linked to auto-balances for direct transfer of weight measurements.

Sample Processing

Metabase incorporates unique features to help you manage both your samples and your data from collection to counting. Special algorithms summarize laboratory processes and provide a consistent method for gathering and processing quantitative measurements, regardless of the number and complexity of sample processing procedures. Automated balances and robot-controlled processing stations can serve as data inputs. Volumetric measurements can be gathered electronically or entered directly into electronic forms.

Adaptable and Expandable

The primary design is to provide acquisition of LSC and auto-balance or robot-processing data. However, Metabase can be extended or modified to acquire quantitative results from other analytical instruments. In fact, due to its modular nature, the program can be customized to provide data management support for other disciplines besides metabolism.

High Throughput

There are practically no limits to the number of study animals, sample types, or time points that can be assembled in a single study. A single data file can handle approximately 16,000 records, and multiple files can be used in a study

Radioactivity Calculations

A built-in calculation module provides initial dose calculations such as the amount of total dose and radioactivity required, the limit of detection and analytical sensitivity for a given specific activity, and other useful values.

Pharmacokinetics

Metabase results can be passed directly to PK Solutions, Summit's powerful pharmacokinetics data analysis program. This program generates all commonly reported PK parameters from blood levels obtained after single, multiple, and infusion dose regimens.

Report Generation

Automatically prepares data tables with appendix and report quality formats, including color, if desired. User-selectable output choices and data arrangement. Metabase data outputs can be custom tailored for specific analysis routines or for advanced document preparation.

Custom Design

Metabase is designed to fulfill core functions associated with metabolism sample management and data acquisition, analysis and reporting functions. Typical installation in the client laboratory involves custom modifications to insure that the program fits with individual client procedures, needs, and requirements.

QA and GLP Compliant

Metabase is designed to comply with GLP guidelines and to facilitate QA data reviews. In addition to built-in data protection and automatic audit trails, the laboratory may choose among several alternatives for managing authorized entry and use.

SDLC Documentation

Metabase comes with a complete system development life cycle documentation package to make validation a breeze. The minimum validation documentation set includes Requirements Analysis, System Design Specifications, Version History, Source Code, User Manual, Test Procedures, and Test Files. All documentation is also supplied both in hard copy and as a formatted Word file for on-line viewing in color.

Usability

Metabase is a colorful, fast and fun application to use. It was designed to give you maximum control over your data in a logical and straight forward manner.

Portability

Metabase files can easily be transported on diskettes or other portable medium (or via e-mail) to be worked on anywhere.

Economical

The cost of equipping a laboratory with a custom installed Metabase system is a fraction of the cost of competing systems. The reason is because we take advantage of the power and breadth of Excel to both maximize your options and minimize your costs.

Software Link:  Metabase - pharmacokinetics/ toxicokinetics Software
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Mass Spec Tools - Mass Spectrometry Software

Mass Spec ToolsTM
Exact-mass spectra and common calculations related to mass spectrometry

An essential toolkit of 11 programs for the mass spectrometrist, Mass Spec (MS)Tools process exact-mass spectra and perform common calculations related to mass spectrometry. Display and processing functions are intended to make use of exact-mass data, but integer mass spectra can also be displayed.

Listed below are brief descriptions of each program

MS Tools includes
Elemental Composition Workshop
Individual masses or an entire high resolution mass spectrum may be rendered to generate a list of elemental compositions that can be used to assist spectral interpretation or to search NIST or other nominal mass spectral libraries for compound identification.

Calculate elemental compositions from exact masses, isotopic abundances, or both. This utility has a direct link to the NIST MS Search Program if present and will search for the best match based on the number of synonyms and presences in other databases.

SearchFromList
Search exact-mass spectra against your own custom mass spectral database or identify components in a complex spectrum by exact mass measurements. Lists are easily created in comma-delimited text or Microsoft Excel format.

Mass Spec Periodic Table
A periodic table with information that is relevant to mass spectrometry. Clicking on an element produces a graphical display of the isotopic abundances for that element along with a table of exact masses and abundances for each element.

MassSpec To Metafile
Generate vector graphic (metafile) displays from mass spectra or mass chromatogram files saved in text format. The output can be imported into reports, presentations, or graphic editors for preparing publication-quality figures.

Isotope Ratio Calculator
A means for simulating the isotopic abundances and masses average mass and the appearance of single-charge or multiple-charge isotopic clusters at any given resolving power. Supports isotope enrichment calculations and simulates overlapping isotopic distributions.

Mass Series Calculator
Useful for calculating reference tables based on polymers or clusters with repeating subunits. The program can also calculate ionic clusters and multiple-charge ions (including multimers).

Simple ESI Calculator
Calculate multiple-charge ion m/z's for a given composition, or estimate molecular weight from two successive charge states or a measured m/z and a known adduct.

Interactive Peak Integrator
Permits manual peak integration for text-format chromatograms or peaks in a segment of a mass spectrum.

PPM Calc
Interactively view the relationship between parts-per-million, resolving power, and mass differences.

Batch Composition to Mass Converter
Rapid calculation of monoisotopic average, nominal, and/or lowest m/z for large compound lists. Convert thousands of elemental compositions in spreadsheet form within seconds.

Subtract Composition
Subtract one elemental composition from another and view the resultant composition and masses for each composition.

 Software Link: Mass Spec Tools - Mass Spectrometry Software
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LabWare ELN - Electronic Laboratory Notebook ELN

LabWare ELN is an experiment and workflow driven software application designed to give the laboratory scientist the ultimate platform to electronically document their experiments including relevant scientific content and observations, instrument results, and attachments such as spectra, chromatograms and, if appropriate, chemical structures. LabWare ELN works seamlessly with LabWare's flagship product, LabWare LIMS, allowing any data within LIMS to be accessible by ELN and vice versa. Integrating ELN products from different suppliers has significant practical challenges and limitations, and very often requires the creation of a customized interface to achieve even simple data exchange between ELN and LIMS. The benefit of LabWare ELN is the inherently elegant interface that exists between the two systems and the simplicity by which both LIMS data and LIMS functionality can easily be shared and leveraged from within LabWare ELN.

Software Link: LabWare ELN - Electronic Laboratory Notebook ELN
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Agilent Mass Profiler Professional - Mass Spectrometry software

Explore relationships in complex mass spectral data

Agilent Mass Profiler Professional software is the only chemometrics software package designed to exploit the high information content of mass spectrometry data. Researchers can easily import, analyze and visualize GC/MS, LC/MS, CE/MS and ICP-MS data from large sample sets and complex MS data sets.

Mass Profiler Professional integrates smoothly with Agilent MassHunter Workstation and ChemStation software, and is ideal for any MS-based application where you need to determine relationships among sample group and variables, including metabolomics, proteomics, food safety, environmental, forensics and toxicology.

For metabolomics and proteomics studies, the optional Pathway Architect helps you evaluate MS data in biological context.

Features:
  • Allows comparison of multiple samples and/or multiple MS analysis platforms in a single project
  • Designed for both scientists and statisticians, with guided and advanced workflows
  • Provides comprehensive statistical tools including ANOVA, PCA, t-tests, volcano plots, hierarchical trees, SOMs, QT clustering, and SVMs for class prediction
  • Generates inclusion list for subsequent MS/MS-based analyses to facilitate protein and metabolite identification
  • Integrated ID Browser mirrors MassHunter Qualitative Software to allow identification using LC/MS Personal Compound Databases (METLIN, pesticides, forensics) and GC/MS libraries (NIST and Agilent Fiehn Metabolomics)
  • R Scripting compatibility within Mass Profiler Professional allows you to further extend and customize statistical analysis and visualization capabilities 
Software Link: Agilent Mass Profiler Professional - Mass Spectrometry software
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PASS - Pharmacology Software

The acronym PASS stands for Prediction of Activity Spectra for Substances. After entering structural formulas of organic compounds - either a single structure or a big library - the program instantly gives a list of predicted bioactivities, accompanied by estimated mathematical probabilities.
Details

Key features of PASS:
• Chemical structures are represented with Multilevel Neighborhood of Atoms (MNA) descriptors
• Activity spectra for libraries of compounds can be predicted within minutes
• Atoms of every structure are colored according to their contribution to the chosen activity
• Possibility to create and train own SAR bases and to modify the included SAR base
• Currently, 4,444 bioactivities can be predicted with the included SAR base
• Mathematical algorithm based on Bayesian estimates of probabilities

PASS can quickly predict biological activity spectra for organic drug-like compounds qualitatively. The activities that can be predicted range from pharmacotherapeutic effects, biochemical mechanisms and toxic and adverse effects to influence on the metabolism, gene regulation and transporter-related activities. The software runs under Windows.

PASS has been developed by Vladimir Poroikov, Dmitry Filimonov & Associates currently working in the Department for Bioinformatics at the Institute of Biomedical Chemistry, Russian Academy of Medical Sciences in Moscow.

A free demo version, as well as further information, is available upon request.

Software Link :  PASS - Pharmacology Software
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SmileMS - Mass spectrometry Software

Mass spectrometry is a recognized powerful analytical technique used to screen and identify a wide range of chemical compounds. It is used routinely in many laboratories in fields such as Laboratory Medicine, Forensic Toxicology, Doping Control, Food Testing, and Metabolomics research. The rapid introduction of LC-MS and LC-MSMS provides access to an extended range of molecules, complementing the well-established GC-MS methods. Current identification methods for both targeted and unknown screening increasingly rely on MSMS spectra library searches. A number of challenges are however still to be addressed:
Fragmentation spectra of a given compound can vary a lot depending on the selected instrument and acquisition method.
Currently available MSMS spectral libraries only cover a subset of these experimental conditions for the available molecules.
Algorithms offered in dedicated software solutions originate from the GC-MS development and do not show appropriate performances for LC-MSMS data.
In routine applications, there is a need for a robust, easy-to-use, MS vendor-independent and integrated solution for rapid screening of large sets of molecules with confidence.

SmileMS meets these needs and proposes a unique LC-MSMS library search solution.
SmileMS software is designed to identify analytes from MS spectra of fragmented molecules via a spectral library search approach. It can be used both for targeted and untargeted screening methods.

The intuitive interface makes SmileMS appropriate for routine applications and allows experts to evaluate the results in detail.
Results are delivered in aggregated lists of identified analytes, supported with chromatogram and annotated spectra.
A robust and innovative algorithm allows for confident identification of molecules across different instrumental architectures and acquisition methods.
The software can handle MSMS and MSn data from a wide range of LC-MSMS vendors and takes advantage of accurate mass MSMS.
Different spectral libraries can be uploaded and queried simultaneously or separately, e.g. from NIST, AB SCIEX, Wiley-VCH, etc., as well as privately created libraries.

Key Features:
Outstanding compound identification with highest levels of confidence
Easy to use and intuitive interface
Two-step workflow designed for routine technicians
Interactive result review for in-depth analysis
Filters for identification of metabolites and other unknown compounds
Compatible with LC-MSMS instruments from major vendors (AB Sciex, Agilent, Bruker, Thermo, Waters)
Library search against multiple LC-MSMS libraries, provided by NIST, AB Sciex, Wiley, as well as home made libraries

Advanced Functionalities:
Take advantage of accurate mass MSMS from high resolution instruments, e.g. QqTOF, FT, etc.
Efficient spectra library management (edition, visualization, sharing, etc.)
Analysis workspace for organization of results and analyses
Login system and user rights for enhanced traceability and privileges
Automation with SmileMS submission module" for greater productivity with Bruker and Thermo instruments"

 Software Link: SmileMS - Mass spectrometry Software
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