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New Lab & IT Products for Integrated Biology: Jan 1, 2005

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BIOINFORMATICS

Updated Accelrys CATALYST/CAP Reagent Databases

Accelrys has updated its CATALYST/CAP Reagents 2004 and CATALYST/CAP Complete 2004 reagent databases. The Reagents database contains 220,000 commercially available chemicals/reagents, and the Complete database contains 1.6 million reagents and screening compounds. Both are available in the 3D multi-conformation CATALYST-format.

Accelrys

800.756.4674

www.acclerys.com/catalyst/cat_dbs.html

Accelrys Discovery Studio MedChem Explorer v2.2

The new version of DS MedChem Explorer features Linux and IBM AIX server support plus two new ADME/Tox models (hepatotoxicity and cytochrome P450 2D6 enzyme inhibition). Other enhancements include scoring lists of compounds against multiple predictive and non-predictive pharmacophore hypotheses to identify potentially potent inhibitors from collections and utilization of pregenerated conformational models.

Accelrys

800.756.4674

www.accelrys.com/dstudio/ds_medchem/index.html

Accelrys Accord HTS 5.3

Accelrys has released version 5.3 of Accord HTS, the Oracle-based system for managing compounds and biological data. The enterprise informatics product now contains a number of new features and capabilities to enhance productivity and usability.

Accelrys

800.756.4674

www.accelrys.com/accord/hts.html

Bio-Rad Bio-Plex Manager 4.0 Software Security Edition

Version 4.0 of the Bio-Plex Manager software for Bio-Rad’s Bio-Plex suspension array system enables compliance with US FDA 21 CFR Part 11 regulations for electronic records. Bio-Plex Manager provides system control, system validation, calibration, data acquisition and data reduction for xMAP assays in a single application.

Bio-Rad

800.4.BIORAD

www.bio-rad.com

Synamatix SynaCompare Comparative Genomics Software

Built on Synamatix’s core IP involving SynaBASE, a structured network database which stores biological data based on sequence patterns and their co-relationships, SynaCompare compares a query sequence with DNA data from a particular organism, chromosome or whole genome stored in SynaBASE.

Synamatix

+603 8996 0984

www.synamatix.com

Teranode TDS Starter Edition

The TDS Starter Edition is a free version of the Teranode Design Suite, a program for data management and qualitative and quantitative modeling, which is limited in the size of the models that can be created. The software includes a purpose-built palette of biological species, compartments and reactions, model simulation and optimization, and the ability to fully annotate a model with papers, drawings or Web links.

Teranode

206.219.3000

www.teranode.com/download

Wolfram Research Mathematica 5.1

Featuring new string manipulation, matching, and searching capabilities, Mathematica 5.1 now allows researchers to analyze robust textual data in just one step, with performance appropriate for gigabyte sequences. With its symbolic language and computational abilities, Mathematica is now capable of text-intensive applications, such as website manipulation, data mining, and DNA processing.

Wolfram Research

800.WOLFRAM

http://www.wolfram.com

 

BIOLOGICAL ASSAYS

Bio-Rad Bio-Plex Validation Kit 4.0

Designed for validating Luminex xMAP assays, the new kit tests instrument operational qualification parameters from fluidics, optics, reporter, and classification aspects. It is designed to enable users to discriminate between an assay problem and an instrument problem.

Bio-Rad

800-4-BIORAD

www.bio-rad.com

 

BIOLOGICAL DATABASES

Global Genomics Tangerine Gene Expression Profiling Database

The newest version of Global Genomics’ Tangerine human whole-genome expression profiling technology contains more than 168,000 different transcripts derived from experimental data. The company’s mouse and rat transcriptomes for expression profiling contain 103,000 and 43,000 transcripts, respectively.

Global Genomics

+46 8 508 847 10

www.globalgenomics.com

Stratagene MegaMan Human Transcriptome Library

Designed for quick and easy cloning of rare genes without RNA isolation or cDNA synthesis, the MegaMan human transcriptome library contains full-length cDNA sequences derived from 32 different human tissues and 34 unique human cancer cell lines. By preserving rare sequences and by a unique sizing procedure for larger molecules the library is enriched for full-length cDNAs greater than 800 bp.

Stratagene

800. 424.5444

www.stratagene.com

 

DNA SEQUENCING

Applied Biosystems 3130 Series Genetic Analyzers

The new 3130 series of DNA sequencers replaces the ABI PRISM 3100 and 3100-Avant instruments. Improvements include enhanced automation, faster turnaround times, higher reliability, and higher data quality than previous generation technologies across a wide range of applications, including de novo sequencing, resequencing, mutation detection, SNP analysis, and microsatellite analysis.

Applied Biosystems

800.327.3002

www.appliedbiosystems.com

 

MICRO RNA ANALYSIS

US Genomics Direct miRNA Reagents

For use with US Genomics’ Trilogy single molecule analyzer platform, the Direct miRNA reagents are designed to detect known human and mouse micro RNA. The Trilogy platform directly detects and quantitates individual molecules of miRNAs, as well as DNA, RNA, and proteins, without the need for amplification.

US Genomics

781.937.5550

www.usgenomics.com

 

MICROARRAY ANALYSIS

Affymetrix NimbleExpress Prokaryotic Array Designs

Affymetrix has launched 179 new NimbleExpress prokaryotic array designs, expanding the company’s catalog offering of microarray expression products for basic microbiology and infectious disease. These arrays allow scientists to conduct whole-genome expression studies on a wide range of pathogenic organisms, including Bacillus anthracis, Haemophilus influenzae, and Mycobacterium tuberculosis.

Affymetrix

888.362.2447

www.affymetrix.com

Sigma-Aldrich Panorama Ab Microarray Cell Signaling Kit

First in a line of antibody-based microarrays, the Panorama cell signaling kit consists of 224 immobilized antibodies arrayed in a specialized format that maintains antibody activity and specificity within a three-dimensional structure of the nitrocellulose layer.

Sigma-Aldrich

800.325.3010

www.sigma-aldrich.com/antibody

Spectral Genomics SpectralWare CGH Analysis Software

For use with Spectral Genomics’ SpectralChip 2600 and Constitutional Chip 1.0, SpectralWare is designed for the analysis and reporting of data from array-based comparative genomic hybridization experiments. The software automatically processes data produced by standard microarray laser scanners and displays the ratios of signals produced in Spectral’s two-dye detection system.

Spectral Genomics

888.362.2441

www.spectralgenomics.com

VizX Labs GeneSifter Jumpstart Microarray Analysis Software

For use with Affymetrix GeneChip and VizX Labs GeneSifter microarrays, Jumpstart provides a written report including statistical and biological analysis of their microarray data; screenshot-based WebEx presentations that demonstrate exactly how the analysis was performed; and optionally, submission of their data to the GEO public data repository.

VizX Labs

206.283.4363

www.vizxlabs.com

 

PCR

PerkinElmer MultiPROBE II Forensic Workstation

The new MultiPROBE II forensic workstation from PerkinElmer performs automated DNA processing procedures including isolation, quantification setup (QPCR), normalization and dilution, and typing PCR setup. The workstation offers an onboard liquid handling system with bundled forensic application options.

PerkinElmer

800.762.4000

www.perkinelmer.com

 

PROTEOMICS

Agilent Technologies Second-Generation MALDI Source

For use with Agilent’s 1100 series time of flight (TOF) and ion trap MS systems, the second-generation source for matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS), a pulsed dynamic focusing (PDF) source, features highly efficient ion focusing technology, a larger, more rugged source body, and upgraded imaging optics for easier target spot selection.

Agilent Technologies

800.227.9770

www.agilent.com

Bio-Rad Experion Automated Electrophoresis System

Bio-Rad’s Experion system relies on Caliper Life Sciences’ LabChip microfluidic technology to speed 1D protein and RNA separation and analysis. Hardware includes an automated priming station, a vortex station to mix reagents and the automated electrophoresis station. Three kits are available for use in the Experion system: protein kit, standard RNA kit, and high-sensitivity RNA kit.

Bio-Rad

800.4.BIORAD

www.bio-rad.com

Bruker Daltonics Ultraflex II MALDI-TOF/TOF Mass Spectrometer

Designed for applications in expression proteomics, quantitative proteomics and biomarker discovery, the new Ultraflex II MALDI-TOF/TOF offers proprietary PAN technology for outstanding MS mass resolution over a very broad mass range measured under unchanged instrument conditions; unique T3-sequencing capability for top-down sequence analysis; significant improvements in TOF/TOF mass resolution; and tunable laser speed from 1-200 Hz for high-throughput analysis.

Bruker Daltonics

978.663.3660

www.daltonics.bruker.com

Invitrogen ProtoArray Human Protein Microarray

The new Invitrogen high-density human protein microarray contains more than 1,800 unique human proteins, representing a cross-section of gene families including pharmaceutically relevant protein classes such as kinases, membrane-associated, cell-signaling and metabolic proteins. The ProtoArray allows identification of protein-protein interactions in as little as four hours.

Invitrogen

760.603.7200

www.invitrogen.com/protoarray

 

RNAi

Stratagene GeneEraser Luciferase Suppression-Test System

The GeneEraser luciferase suppression-test system is a rapid system for identifying effective siRNAs or shRNAs, eliminating the need for gene specific reagents or QPCR reagents.

Stratagene

800.424.5444

www.stratagene.com

 

SAMPLE PREP

Agilent Technologies 5100 Automated Lab-on-a-Chip Platform

The Agilent 5100 automates the entire electrophoresis workflow, lowering per-sample analysis time by a factor of 10 and allowing unattended analysis of up to 3,840 samples per run. The first two assays, consisting of chip and reagents, are: DNA 1000 HT-4 kit for qualitative and quantitative verification of polymerase chain reaction (PCR) and multiplex PCR samples; the Protein 200 HT-2 kit for sizing and quantification of proteins during purification or protein expression experiments.

Agilent Technologies

800.227.9770

www.agilent.com/chem/5100ALP

DNA Research Innovations CST RNA Purification Kit

The CST RNA purification kits for cells and microtissues purify high quantities of total RNA and capture small molecular weight, rare, and long transcript RNA. Because of the company’s ChargeSwitch technology, the kits do not require the use of enzyme inhibitors such as ethanol, organic solvents, or chaotropic salts.

DNA Research Innovations

+44 1795 411 114

www.dri-dna.co.uk

Dynal Oligo(dt)25 Range of Dynabeads for mRNA Isolation

Based on superparamagnetic separation technologies, Dynabeads Oligo (dT)25 and associated kits can consistently isolate poly A+ mRNA with or without prior total RNA preparation. The source of RNA can be controlled using Dynal Biotech’s cell specific Dynabeads to select cells based on distinctive surface marker proteins.

Dynal Biotech

800.558.4511

www.dynalbiotech.com

QIAGEN BioRobot MDx DSP Nucleic Acid Purification System

Designed for purifying viral nucleic acids in clinical laboratories, the BioRobot MDx DSP is a CE-marked system that provides exact performance specifications for applications in in vitro diagnostic procedures. Precision pipetting minimizes the risk of cross-contamination, and an automated load check ensures high process reliability and error-free worktable setup.

QIAGEN

800.426.8157

www.qiagen.com

Perkin Elmer TotalChrom Chromatography Data System Version 6.3

Among other improvements, the latest version of PerkinElmer’s TotalChrom software now includes IRIS 3-D spectral processing software, a next generation software package that offers a fully 21 CFR Part 11 compliant architecture, automated processing and a modern, intuitive interface.

Perkin Elmer

800.762.4000

www.perkinelmer.com/totalchrom

Scientific Software EZChrom Elite Version 3.1.6

The newest version of EZChrom provides support for Windows 2003 servers and Windows XP Native Mode Active directories. In addition, the new release incorporates enhancements to user programming, audit trailing of projects, and support for new chromatography instruments.

Scientific Software

800.588.8878

www.scisw.com

 

To tell GT about new recently released products, e-mail John MacNeil, Senior Editor, at [email protected]

 

The Scan

Guidelines for Ancient DNA Work

More than two dozen researchers have developed new ethical guidelines for conducting ancient DNA research, which they present in Nature.

And Cleared

A UK regulator has cleared former UK Prime Minister David Cameron in concerns he should have registered as a consultant-lobbyist for his work with Illumina, according to the Financial Times.

Suit Over Allegations

The Boston Globe reports that David Sabatini, who was placed on leave from MIT after allegations of sexual harassment, is suing his accuser, the Whitehead Institute, and the institute's director.

Nature Papers on Esophageal Cancer, Origin of Modern Horses, Exome Sequencing of UK Biobank Participants

In Nature this week: genetic and environmental influences of esophageal cancer, domestic horse origin traced to Western Eurasian steppes, and more.