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New Lab & IT Products for Integrated Biology: Oct 1, 2004

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BIOINFORMATICS

Scientific Software EZChrom Elite Windows XP Service Pack 2 Upgrade

EZChrom Elite Version 3.1.4 from Scientific Software, a software package designed for chromatography instrument control and data analysis, now fully supports Windows XP Service Pack 2. The August 2004 update to XP provides significant security enhancements related to network communications, buffer overflow protection, e-mail attachments and Internet Explorer security.

Scientific Software

800-588-8878

www.scisw.com

 

Lion Bioscience Target Engine 1.1

Lion Bioscience’s Target Engine 1.1 allows scientists engaged in target identification and validation to access all available life science data through a simplified Web interface. Users can retrieve gene and sequence information from multiple databases at the same time through a simple search engine-like interface, and the corresponding results are visualized in a simple to read Web-based report. The Target Engine Gene Hub, a centralized database connecting experimental, public, and proprietary data, has been extended beyond the human genome to include the mouse and rat genomes.

Lion Bioscience

+49 (0) 6221 4038 0

www.lionbioscience.com

 

Lion Bioscience LeadNavigator Lead Optimization and Prioritization Software

LeadNavigator, a component of Lion’s Lead Engine cheminformatics product suite, allows researchers to analyze large sets of chemical and numerical data through a single, intuitive interface. The LeadNavigator software relies on technology developed by Lion as part of the Bayer PIx (Pharmacophore Informatics) project, and includes a spreadsheet that provides single point access to both standard statistical methods as well as algorithms used for compound identification, prioritization, and optimization.

Lion Bioscience

+49 (0) 6221 4038 0

www.lionbioscience.com

 

NAG Data Mining and Cleaning Components Version 2.0

DMC 2.0 is the product of the Numerical Algorithms Group, a global collaborative network of 300+ computer scientists and mathematical experts that work together to solve complex mathematical problems. The software is the first commercially available data mining application development toolkit that uses results from a three-year European Union funded project, EUREDIT. The new software contains capabilities in data cleaning, outlier identification, memory-efficient multivariate statistical methods, and machine learning and pattern recognition. Written in ANSI C with simple function interfaces, NAG DMC 2.0 is ideally suited for interfacing with other programming languages such as PERL, Java, C#, and Python.

Numerical Applications Group

630.971.2337

www.nag.com

 

Partek Pro 6.0 Statistical Analysis and Data Visualization Software

Partek Pro version 6.0 is designed for statistical analysis and interactive data visualization of results from high-throughput experiments. The most recent version of the software package includes capabilities in spreadsheet analysis, data filtering, pattern visualization, and data transformations, among others. Partek Pro 6.0 is available for Windows, IRIX, Solaris, and Linux systems.

Partek

636.498.2329

www.partek.com

 

Teranode VLX Design Suite V1.4

Version V1.4 of Teranode’s VLX Design Suite, a software program for biochemical modeling, now includes support for SBML (Systems Biology Markup Language) Level 2. The suite serves as an important modeling application for extending the value of SBML models and simplifies SBML model development and collaboration through graphical visualization and editing, annotation, metadata editing and viewing, search, simulation, and experimental data management.

Teranode

206.336.5626

www.teranode.com

 

IMAGING

Alpha Innotech FluorChem SP CCD Camera Technology

Using the latest electrically cooled Charge Coupled Device camera technology, the FluorChem SP provides a real-time display, 4 million pixel resolution, and easy-to-use, versatile AlphaEase FC software. FluorChem SP is optimized for chemiluminescence, fluorescence, and visible imaging applications. Using advanced noise reduction algorithms and electronic design concepts, the FluorChem SP Imaging System delivers a high signal to noise ratio, producing a full 12-bit dynamic range for biological assays that require a wide range of analysis.

Alpha Innotech

800.795.5556

www.alphainnotech.com

 

LIMS

Ocimum Biosolutions Pharmatracker LIMS

Pharmatracker is a multi-platform, multi-user, cost-effective LIMS that enables QA/QC on all inventories, keeps accurate track of samples, reagents, instruments, processes, and output. Pharmatracker is compliant with requirements and guidelines for GxP as stipulated by US EPA, US FDA and WHO, and complies with US FDA’s 21 CFR Part 11 requirements on electronic records and electronic signatures. Pharmatracker functionalities include workflow, stability, QC batch management, and trend analysis tools.

Ocimum Biosolutions

858.646.3007

www.ocimumbio.com

 

MICROARRAY ANALYSIS

Agilent Technologies Whole-Genome Arabidopsis Oligo Microarray

Agilent’s whole-genome Arabidopsis microarray contains more than 37,000 probes, representing all Arabidopsis genes of known function and related genes of interest. The content includes probes for approximately 26,000 annotated transcripts from the ATH1v5 database of The Institute for Genomic Research. The microarray also covers more than 10,000 unannotated transcripts from the Massively Parallel Signature Sequencing database of the University of Delaware and 1,000 ncRNA (small non-protein coding) transcripts derived from the ATH1 genome.

Agilent Technologies

800.227.9770

www.agilent.com

 

5AM Solutions Microarray Enterprise Manager Software

The Microarray Enterprise Manager (MEM) from 5AM Solutions, developed in collaboration with 7GEN, Duke, and UCLA, is a Web-based software suite that manages all aspects of expression profiling laboratory workflow, data annotation, standardization, and sharing. Designed with the needs of microarray core facilities in mind, MEM simplifies data standardization through a novel method of verification (MAGEmaker), provides intuitive interfaces for data entry, batch-oriented uploads and downloads of relevant files, and allows researchers to form virtual collaboration groups.

5AM Solutions

602.595.9487

www.5amsolutions.com

 

NMR

Bruker BioSpin SampleRail

The SampleRail enables fully automated sample preparation and delivery for 24-hour, hands-off, high-throughput NMR operation. The system interfaces with a liquid handling robot, which prepares the samples in NMR tubes and then transports them on a rail system to the magnet. The liquid handler is synchronized with the NMR experiments for just-in-time sample preparation, ideal for unstable samples requiring analysis immediately after preparation. The SampleRail increases the utility of NMR in various high-throughput applications such as metabonomics, SAR (structure activity relations) by NMR, protein-ligand binding detection, and other drug discovery methods.

Bruker BioSpin

978.667.9580

www.bruker-biospin.com

 

Bruker BioSpin TCI-HPC CryoProbe

The new Triple Inverse Hydrogen Carbon Phosphorus (TCI-HPC) CryoProbe delivers enhanced carbon sensitivity by means of a cold carbon preamplifier in addition to proton-carbon-phosphorus measurement capabilities. Available for Bruker BioSpin Avance 500 and 600 MHz NMR systems, the TCI-HPC is ideal for a range of nucleic acid studies, including direct carbon observation and advanced proton-phosphorus correlation experiments.

Bruker BioSpin

978.667.9580

www.bruker-biospin.com

 

PCR

Applied Biosystems 2720 Thermal Cycler

The new, personal-sized Applied Biosystems 2720 Thermal Cycler is designed for a full range of PCR and cycle sequencing applications in a compact package. This latest addition to the Applied Biosystems family of thermal cyclers is designed with vents in the rear, allowing several thermal cyclers to be placed tightly side-by-side to conserve valuable bench space. Compact Peltier heating and cooling devices enable a wide range of features to fit in an instrument measuring only 21 x 36 cm. Included is a melting point calculator that determines the primer annealing temperature based on nearest-neighbor analysis.

Applied Biosystems

800.327.3002

www.appliedbiosystems.com

 

QIAGEN QuantiTect Multiplex PCR Kit

The new QuantiTect Multiplex PCR Kit is designed for highly sensitive, quantitative, real-time, multiplex PCR. Up to 3 cDNA or genomic DNA targets are accurately quantified in the same reaction from as few as 10 copies of starting template. The kit offers more reliable data through quantification of target and reference genes in the same tube, and minimizes pipetting tasks with the ready-to-use master mix (which includes ROX passive reference dye).

QIAGEN

800.426.8157

www.qiagen.com

 

PROTEOMICS

GeneBio Phenyx Mass Spectrometry Data Analysis Software

Phenyx, a software platform developed in collaboration with the Swiss Institute for Bioinformatics and GeneProt, is designed for the identification and characterization of proteins and peptides from PMF and tandem-MS mass spectrometry data. Phenyx is composed of two main elements, the Phenyx Virtual Desktop and the Phenyx Calculation Engine. Users who download the Phenyx Virtual Desktop from www.phenyx-ms.com can then either submit and receive results from the freely available Calculation Engine hosted at Vital-IT, a computing facility at SIB, or license the Phenyx Calculation Engine for local installation.

GeneBio

+41 22 702 99 00

www.genebio.com

 

Pall Enchant Kits for Albumin Depletion and IgG Purification

The Enchant kits for albumin depletion and the two kits for IgG (immunoglobulin G) purification remove these abundant proteins from human and animal-derived serum or plasma samples, providing the critical first step in isolating new drug targets. Each kit includes the protocol, purification columns, and necessary buffers in a complete easy-to-use package.

Pall

800.717.7255

www.pall.com

 

Waters Acquity Ultra Performance Liquid Chromatography Instrument

Waters’ Acquity UPLC system, now shipping to customers, is designed to take full advantage of the potential of proprietary, sub-two-micron particles to give scientists chromatographic run times that are up to 9x shorter than today’s fastest HPLC systems, up to 2x better peak capacity or resolution, and 3x better routine sensitivity. The Acquity UPLC system basic configuration consists of a binary solvent manager, sample manager, column chemistry, column heater module, and either tunable UV and/or photodiode array detectors. The system is controlled by Waters Empower or MassLynx chromatography/mass spectrometry software. A new graphical console designed for the Acquity UPLC system will provide control, status, and advanced diagnostic information to the scientist.

Waters

800.252.4752

www.waters.com/acquity

 

Waters Protein Expression System

The Protein Expression System is a multiplexed system to give scientists the ability to quantitatively assess changes in protein expression while performing enhanced qualitative protein identification — all within the same LC/MS run. The system consists of the new Waters Micromass Q-TOF Premier mass spectrometer, the new Waters nanoACQUITY Ultra Performance Liquid Chromatography system, columns, and new informatics tools for MassLynx 4.0. The new system uses a patented implementation of exact mass measurement UPLC/MS with parallel collision induced dissociation of tryptic peptide precursor ions to yield a complete dataset of a complex peptide mixture.

Waters

800.252.4752

www.waters.com

 

RNAi

BD Biosciences Clontech ProLabel Screening & Detection Kits

Designed to provide a functional assay for protein knockdown RNAi studies, BD’s ProLabel screening and detection kits provide sensitive chemiluminescence assays for measuring the expression levels of any gene of interest in total cell lysates. Crude cell lysates can be tested without any purification. In addition, these assays are easily run in a high-throughput screen, and cost less per sample than Western blot analysis.

BD Biosciences Clontech

tel: 650.424.8222

www.bdbiosciences.com/clontech

 

SAMPLE PREP

BD Biosciences Clontech NucleoSpin Extract II Kit

The NucleoSpin Extract II Kit, designed for both gel extraction as well as PCR purification, uses a spin column to bind DNA to a silica membrane in the presence of chaotropic salt. Once the binding mixture is loaded directly onto the column, only a single wash step using an optimized buffer is required. Obtain 75-100% recovery from PCR reaction mixtures in just 15 ML elution volume.

BD Biosciences Clontech

tel: 650.424.8222

www.bdbiosciences.com/clontech

 

QIAGEN EZ1 Bacteria Card

The EZ1 DNA Bacteria Card provides automated protocols for bacterial DNA purification from primary samples or bacterial cultures (≤200 µl) using the BioRobot EZ1 workstation. The purified DNA is suitable for use in many applications, including bacterial detection, epidemiology, infection control, infectious disease research, and PCR-based quantification and resistance profiling. Protocols on the card enable purification of bacterial DNA from primary clinical samples, swabs, biopsies, or bacterial cultures, including both Gram-positive and Gram-negative species.

QIAGEN

800.426.8157

www.qiagen.com

The Scan

WHO Seeks Booster Pause

According to CNN, the World Health Organization is calling for a moratorium on administering SARS-CoV-2 vaccine boosters until more of the world has received initial doses.

For Those Long Legs

With its genome sequence and subsequent RNAi analyses, researchers have examined the genes that give long legs to daddy longlegs, New Scientist says.

September Plans

The New York Times reports that the US Food and Drug Administration is aiming for early September for full approval of the Pfizer-BioNTech SARS-CoV-2 vaccine.

Nucleic Acids Research Papers on Targeting DNA Damage Response, TSMiner, VarSAn

In Nucleic Acids Research this week: genetic changes affecting DNA damage response inhibitor response, "time-series miner" approach, and more.