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



GenePattern 1.2

Researchers at the Broad Institute have released GenePattern 1.2, an enhanced version of the GenePattern microarray analysis package that is freely available to the scientific community. New features of GenePattern 1.2 include an online module repository, a Java programming environment, and batch analyses.

Broad Institute

Geospiza FinchTV Trace Viewing Software Update

Geospiza announced an update to Geospiza FinchTV, a free, cross-platform trace viewing software utility for use in DNA sequencing analysis. The newly-enhanced version of the freely downloadable FinchTV software now incorporates sequence editing, insert and delete capabilities, selection and copying of bases for use in another application, and the ability to search for a given sequence. The newest version, FinchTV 1.2, now also runs on the Sun Solaris platform, in addition to Mac OS X, Windows, and Linux.


InNetics PathwayLab 1.0

PathwayLab is InNetics’ product suite designed to analyze, visualize, and document biochemical pathways. By building pathway models that can integrate kinetic, gene expression, and functional data, PathwayLab is an efficient hypothesis test bench for prediction and analysis of disease pathways.


Elsevier MDL and Partek Statistical Visualization Tool

Elsevier MDL and Partek have introduced a new statistical visualization tool to help drug researchers analyze plate-based biological data. The new MDLAssay Explorer Visualizer software module allows scientists to visualize plate-based data in predefined, interactive views, and apply powerful statistical tests to validate experiments, thereby saving time, reducing false positive results and identifying better quality leads faster.


Rosetta Resolver Version 5.0

Version 5.0 of the Rosetta Resolver system for expression analysis provides enhanced customization, biological knowledge, and productivity. Scientists have a broad choice of analysis options enabling fully customized processing and manipulation of data according to the specific needs of any user or research group. In addition, version 5.0 of the Rosetta Resolver system provides scientists with enrichment tools for extracting biological meaning from expression data.

Rosetta Biosoftware

GeneSpring Version 7

Version 7 of Silicon Genetics’ flagship application GeneSpring includes the following enhancements: new support vector machines algorithms, project-based organization, a new genome wizard for genome import and management, new algorithms to find associations and correlations between parameters and expression profiles to help determine causative relationships, and Java API for extending GeneSpring with custom analyses or visualizations.

Silicon Genetics

Tripos Sybyl 7.0

SYBYL 7.0, the latest version of Tripos’ molecular modeling environment for drug discovery research, is compatible with multiple platforms and includes a Linux operating system upgrade, Red Hat Enterprise Linux 3.0. The new SYBYL software contains numerous enhancements and expanded functionalities to existing applications, and is available in DVD and CD-ROM formats.


Scientific Software New Software Control of Varian 3900 GC

Scientific Software has released new control software for the EZChrom Elite Chromatography Data Systems and the OpenLABLaboratory Software Framework to control the Varian 3900 GC. The new control software allows EZChrom Elite or OpenLAB to fully control the 3900 GC with instrument control of the GC and related autosamplers. Software control of the 3900 GC allows users to create a single software method to provide data analysis and reporting as well as control of instrument running conditions.

Scientific Software

ToolBus/PathPort 2.0

ToolBus/PathPort is a collection of open source web services that allows for the analysis and visualization of data. The software can perform sequence alignment, annotation, and comparison; gene prediction; probe design; phylogenetic trees; and microarray data analysis. ToolBus is domain and platform independent, and client-side interconnect enables easy access to Web-services with inter-active visualization of their results. A simple drag-and-drop interface allows researchers to perform a wide variety of data analyses without data reformatting or command line executables.

Virginia Bioinformatics Institute



Beckman Coulter Biomek Assay Workstation

The new Biomek Assay Workstation can be configured with either the Biomek FX or NX liquid handlers, providing multiple pipetting and configuration options for different capacity, throughput, and lab space requirements. The system integrates Beckman Coulter’s new DTX Series multimode detector, which offers absorbance, fluorescence, and luminescence detection for a complete solution to a range of applications. The workstation has been optimized for cell-based screening and ELISAs. The system’s SAMI Workstation EX Software incorporates new dynamic scheduling capabilities that allow the user to create methods and run multiple assays.

Beckman Coulter

BioTrove OpenArray Transcript Analysis System

BioTrove has launched its OpenArray transcript analysis system for high-density, quantitative PCR (qPCR) analyses. The OpenArray platform, which enables massively parallel qPCR using nanoliter scale quantities of reagents and samples, allows researchers to study 9,000 transcripts simultaneously in about two hours.


NuGen Launches the Ovation RNA Amplification System for Gene Expression Analysis

NuGEN Technologies has launched its Ovation RNA Amplification System, a technology designed for gene expression experiments, especially those based on real-time quantitative PCR (QPCR). Use of the system prior to QPCR analysis amplifies mRNA in potentially limited, biologically important samples such as small biopsies or flow sorted cells. The Ovation RNA Amplification System offers a standardized 3.5-hour protocol in a complete kit format that works equally well with large or small total RNA sample amounts, allowing experimentation from samples as small as 5ng of total RNA.

NuGen Technologies



Applied Biosystems LS*LIMS Software

LS*LIMS software is a new workflow management and process automation solution that integrates data from many different sources for genomics and proteomics laboratories. The software increases lab productivity by integrating an expanding library of Applied Biosystems and third-party instrument interfaces, including the Applied Biosystems 3730 and 3730xl DNA Analyzers, the ABI PRISM 7900HT Sequence Detection System, and the GeneAmp PCR System 9700.

Applied Biosystems

NextGen Sciences OrchestratorIMS

The OrchestratorIMS, based on the software powering NextGen’s Expressionfactory protein expression platform, is an information management system that links experiments planned virtually with those performed manually in the laboratory, enabling the user to plan, coordinate, execute, monitor, and track successful cloning and expression strategies.

OrchestratorIMS is fully compatible with cloning techniques such as Gateway and TOPO. The software has been designed to enable the users to plan their experiments at a PC, and then carry out the research using either manual techniques or laboratory robotics.

NextGen Sciences



PerkinElmer ProScan-Array and ScanArray GX series of microarray scanners

The ProScanArray and ScanArray GX series of microarray scanners utilize confocal technology that delivers a high signal-to-noise ratio. PerkinElmer has designed these microarray scanners to integrate image acquisition and analysis for proteomic and genomic applications through PerkinElmer’s exclusive ProScanArray Express software. For higher-throughput applications, the ProScanArray HT features a patented 20-slide autoloader. ScanArray GX, a two-laser microarray scanner ideal for genomic applications, is optimized for traditional array applications and is driven by the latest release of the feature-enhanced ScanArray Express software.


Telechem Microplate Microarray Hardware, Surface Chemistry and Manufacturing Technology

Now available in a 96-well microarray format, these tools allow over 1,000 spots per each 96-well subarray and various surface chemistries are available for both DNA and protein microarrays. The new microarray microplate hardware contains 96 separate wells for microarrays. The glass plate is detachable from the rest of the chamber for superior spotting and scanning flexibility. Each subarray measures 7.7mm x 7.7mm, providing maximum printable real estate as well as conforming to robotic liquid handling.

Telechem International



Qiagen Quantitect Multiplex PCR Kit

Designed for quantitative, real-time, multiplex PCR of cDNA or genomic DNA targets using sequence-specific probes. The detection limit is as low as 10 copies of each target sequence, and target and reference genes are quantified in the same well or tube. The ready-to-use master mix is compatible with a wide range of real-time block cyclers.


Epicentre High-Performance Real-Time PCR Master Mix

The TAQurate Real-Time PCR Master Mix is designed for routine and high-throughput real-time PCR applications. Add your primers and template to the Master Mix, mix thoroughly, and begin your PCR thermal cycler. The TAQurate Real-Time PCR Master Mix contains SYBR Green I Dye for the detection and quantification of real-time PCR products, the TAQurate Real-Time PCR Enzyme blend for highly specific and reliable amplification of templates, and the patented PCR Enhancer (with betaine) for high amplification efficiencies and fewer nonspecific PCR products.




Roche X-tremeGENE siRNA Transfection Reagent

Designed for co-transfection of siRNA and plasmid DNA, Roche’s X-tremeGENE reagent enables high levels of gene expression and effective knockdown. Over 90% gene knockdown efficiency (in several cell lines) proven at Roche Pharmaceuticals and external laboratories. Available in 1 ml for 400 transfections in 24-well plates.




Agencourt Bioscience RNAPrep Kit

The RNAPrep kit is optimized for isolating total RNA from eukaryotic cultured cells. The kit leverages the company’s SPRI (Solid Phase Reversible Immobilization) magnetic bead technology that delivers high yield and purification for quality nucleic acid retrieval. The RNAPrep kit method has been formatted to work in a single tube through fully automated plate formats with streamlined processing times of under 20 minutes.

Agencourt Bioscience

BD Biosciences Clontech NucleoSpin Extract II Kit

The NucleoSpin Extract II Kit is suitable for both gel extraction as well as PCR purification. The spin column binds 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 µl elution volume.

BD Biosciences Clontech

Matrix Technologies 384-Well Small Volume Microplates

Matrix Technologies has released a portfolio of 384-well small volume microplates that combine the low volumes of a 1,536-well microplate with the practical benefits of the popular 384-well format. These plates are offered in clear, white, or black, standard height or low-profile, and offer working volume ranges of 2 ¯ 20µL.

Matrix Technologies

BD Biosciences Discovery Labware Falcon 96-Multiwell Insert System

The BD Falcon 96-multiwell insert system is a cell culture insert platform suitable for both manual and robotic screening of compounds in cell-based assays. The system has been tested for its ability to produce a differentiated monolayer of Caco-2, LLC-PK1, and MDCK cells, making it ideal for in vitro bioavailability and permeability studies. This automation-compatible platform is composed of a 1.0 µm pore size PET (polyethylene terephthalate) membrane-based 96-multiwell insert plate, a media feeder tray, and a lid.

BD Biosciences


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


The Scan

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.