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



Accelrys INSIGHT II 2000.3L

Insight II 2000.3L is the first release of Insight II on Linux. Insight II 2000.3L is certified on Red Hat Linux WS 2.1 and NVidia Quadro4 980 XGL graphics cards using NVidia Linux drivers. Select modules may also be run on IBM AIX servers. Insight II is a 3D graphical environment for molecular modeling.



Ariadne Genomics and Stratagene PathwayAssist 2.5 Software

Ariadne Genomics and Stratagene have released an updated version of PathwayAssist 2.5, a software suite designed for visualizing and analyzing biological pathways. New features in the PathwayAssist 2.5 version include the addition of molecular network databases for four model organisms (Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Arabidopsis thaliana), the capability to map gene expression data onto KEGG pathways, and the ability to save pathways in HTML format as interactive, clickable maps.



Ariadne Genomics MedScan TextMiner

Ariadne’s MedScan TextMiner software is designed for automatically processing MEDLINE abstracts, articles, and other scientific texts, and extracting biological facts along with references to the original source of information. The software can be integrated with corporate information systems as a component of their bioinformatics toolset. Among other information, MedScan TextMiner extracts functional associations between proteins, cell processes and small molecules, recognizes types of regulatory mechanisms involved, and the effects of regulation. Captured data is presented as a datasheet or an XML file.

Ariadne Genomics

(240) 453-6296

Bioinformatics Solutions PatternHunter 2.0 Homology Search Tool

The updated PatternHunter 2.0 now has the full functionalities of BLAST (BLASTn, BLASTp, tBLASTx, tBLAST, BLASTx) and input and output formats compatible with BLAST, but can perform searches faster. PatternHunter 2.0 does gapped alignments, and the program’s new algorithm explicitly avoids 6 frame translations, allowing frame shift gaps. PatternHunter 2.0 can now search against arbitrarily large databases without running out of memory.

Bioinformatics Solutions


Silicon Genetics Varia Software for Genetic Variation Analysis

Designed as a standalone workbench for handling millions of SNP measurements generated by whole-genome genotyping measurement platforms, the Varia software includes validated algorithms for the association of variation-to-variation or of variation-to-disease, including linkage disequilibrium and transmission disequilibrium tests, genetic linkage scores, and case control calculations. In addition, the program features navigable displays of the complete human genome at the nucleotide scale, automated tools for building haplotype maps and constructing pedigrees from user-supplied data, flexible visualization tools, and patent-pending algorithms for identifying regions of autozygosity likely to represent transmissible markers of recessive diseases.

Silicon Genetics


Vivísimo ClusterMed MedLine Search Software

Designed to allow researchers to search the MedLine database more productively and efficiently, ClusterMed organizes the long list of results returned by PubMed into hierarchical folders allowing researchers to hone in on the most relevant results quickly. By organizing results into categories, users discover the main themes relating to the subject of the query and can easily reach relevant articles buried deep in the chronological list. In addition, similar articles are grouped together, rather than scattered throughout the results.




Ambion Human Tumor RNA

Ambion now offers FirstChoice brand tumor and normal adjacent tissue RNA. Each sample includes 5 mg each of total RNA isolated from individual tumors and the normal adjacent tissue. Each sample is derived from a single donor and has not been pooled with other RNA. Ambion’s human RNAs have been prepared from tissue donated with the fully informed consent of the donor, or the informed consent of the donor’s family.



Molecular Devices IMAP Substrate Finder

The latest addition to Molecular Devices IMAP platform for developing and running kinase screens, the IMAP substrate finder is a tool for accelerating the task of finding new substrates for unique or proprietary kinases. The substrate finder enables researchers to quickly test one or more kinases against dozens of peptides included in a 384-well microtiter plate to identify potential substrates for subsequent IMAP screens. 56 of the 59 peptides have been previously published as kinase substrates; the remaining three peptides are already phosphorylated for positive controls.

Molecular Devices



Applied Biosystems SQL*LIMS Version 5.0

The latest version of ABI’s SQL* LIMS includes an enterprise-accessible productivity solution for pharmaceutical manufacturing organizations. Additionally, the new SQL*LIMS software includes enhancements such as instrument calibration, user qualification and reagent inventory tracking. The new, open-platform Web services application was built using the Oracle Application Server 10g, Database 9i and provides a J2EE standards-based application.

Applied Biosystems


LabVantage Solutions SafeData Data Management Software

LabVantage has released SafeData, a secure and accessible scientific data management solution for the live data phase of a project. The software automates the storage of operational data in its native format, and maintains easy access to files during the iterative analysis period, with versioning, to protect intellectual property. In environments where high levels of compliance to GLP/GMP regulations are required, SafeData is a secure method for archiving raw data within seconds of its creation or change.

LabVantage Solutions



Affymetrix GeneChip Rat Genome 230 2.0 Array

Affy’s new GeneChip Rat Genome 230 2.0 array provides the transcribed rat genome on a single microarray, consolidating all the data from the previous two-array Rat Expression Set 230. This new array represents over 30,000 transcripts, including 28,000 well-substantiated rat genes from several leading public rat genome databases. All probe sequences and annotations are freely available through Affymetrix''''s online NetAffx Analysis Center. Affymetrix uses 22 independent probes to quantitate the levels of each of the transcripts on the array.



Nugen Technologies Ovation Biotin System for RNA Amplification and Labeling

Optimized for use with Affymetrix GeneChip arrays, the Ovation Biotin System performs sensitive and rapid expression analysis with as little as five nanograms of RNA starting material. The system incorporates a fast and robust method for post-amplification fragmentation and direct chemical attachment of biotin to the cDNA amplification products.

Nugen Technologies


Parallel Synthesis Technologies Silicon Microarray Printing Technology

The new pins from Parallel Synthesis Technologies for microcontact printing applications feature the ability to print from 96, 384, and 1536 source plates. Highly precise volumetric uptake, combined with the elimination of prespotting phenomena and the ability of these pins to print to dryness, greatly reduces waste of precious samples, and has print tip sizes from 50-100 µm, uptake volumes of 25-250 nL, and print volumes of less than 250 pL per spot.

Parallel Synthesis Technologies


QIAGEN BioRobot Gene Expression System GeneChip Target Preparation Pack

The GeneChip target preparation specialist pack from QIAGEN provides an automated solution for standardized preparation of cRNA targets for Affymetrix GeneChip arrays. The system automates the steps from first strand cDNA synthesis to cRNA fragmentation, reducing hands-on time. The system processes up to 96 samples per run. Starting with 5 µg total RNA per sample, the system generates cRNA targets with yields of at least 20 µg and concentrations of at least 0.625 µg/µl. The system comprises a robotic workstation that is integrated via a robotic arm with external hardware required in the GeneChip target preparation process.




MJ Research Tetrad 2 Thermal Cycler

The Tetrad 2 thermal cycler is a redesigned and updated version of its DNA Engine Tetrad cycler. The new version of the instrument features an advanced graphical interface with an on-board touch pad that allows rapid input of protocols, and real-time monitoring of sample, block, and lid temperatures. The Tetrad 2 accepts up to four Alpha unit heat-block assemblies; up to eight independent protocols can be run simultaneously when the cycler is outfitted with four dual-block Alpha units. For higher-throughput environments, Tetrad 2 software facilitates protocol transfer between instruments.

MJ Research


MWG Biotech THEQ LifeCycler Thermocycler

The new THEQ LifeCycler thermocycler features eight peltier heating units and four independently controlled temperature zones. Active sample protection cools samples until the lid is fully heated to avoid unspecific binding, and a lifting block design hermetically seals the sample plate to ensure temperature and pressure distribution. All systems are robot compatible format for integration into MWG Biotech’s range of THEONYX lab automation systems.

MWG Biotech



Agilent Technologies 1100 Series Liquid Chromatography Micro Collection/Spotting System

Designed as a separation tool for proteomics, Agilent’s new 1100 Series liquid chromatography micro collection/spotting system enables separation of small sample amounts at low flow rates for the subsequent collection of very small fraction volumes. The system features direct spotting on matrix-assisted laser desorption/ionization mass spectrometry targets, and provides flexibility for multidimensional separations.

Agilent Technologies


EMD Biosciences ProteoPlex 16-Well Human Cytokine Array Kit

The ProteoPlex 16-Well human cytokine array is designed for multiplex detection and measurement of 12 important human cytokines in parallel from up to 16 experimental samples. The 12 cytokines measured in the kit are pro- and anti-inflammatory cytokines important for the study of immune system regulation and diseases such as asthma and arthritis. Each well on the slide contains a microarray of spotted antibodies with four spots for each of the 12 cytokines plus additional spots for positive and negative controls.

EMD Biosciences


MDS Sciex ProteoSpin Protein Purification Product Line

MDS Sciex’s new ProteoSpin protein purification product uses processed silicon carbide as a chromatographic matrix. The product is available in three different kits, each able to process samples of up to 50 mg of protein: ProteoSpin CBED Micro Kit, which simultaneously concentrates, provides buffer exchange and removes salts using a rapid procedure; ProteoSpin Detergent Clean-up Micro Kit, which provides a fast and effective procedure to remove detergents including SDS, Triton X-100, CHAPS, NP-40 and Tween 20; and ProteoSpin Inclusion Body Isolation Micro Kit, which facilitates screening by providing the rapid isolation, solubilization and purification of inclusion body proteins from up to 1.5 mL bacterial culture.

MDS Sciex

(905) 660-9005

Schleicher & Schuell BioScience FAST Quant Mouse Th1/Th2 and FAST Quant Human II Kits

Designed as an alternative to running multiple ELISAs, the new FAST Quant Mouse Th1/Th2 and FAST Quant Human II kits contain 64 individual arrays — up to 10 cytokines arrayed in triplicate, 16 arrays per slide, and four slides per kit. Each array requires as little as 50 µL of sample to generate up to 10 quantified results.

Schleicher & Schuell


Zyomyx Murine Cytokine Biochip

Zyomyx has released its murine cytokine biochip, which allows research to multiplex the quantitative analysis of 30 mouse cytokines, chemokines, and growth factors using small sample volumes of 40 µL. The chip is compatible with Zyomyx’s protein expression profiling platform, which includes the Assay 1200 biochip workstation and Scanner 100 biochip reader.




Ambion Phosphodiesterase siRNA Library

The Silencer phosphodiesterase siRNA Library is designed for inhibiting specific phosphodiesterases to generate phenotypes in high throughput. This library includes 108 siRNAs, with three siRNAs targeting each of 36 human phosphodiesterases. All of the siRNAs have been designed using a highly validated algorithm and are provided individually with full sequence information.



SuperArray Bioscience siRNA Array Plates

The patent-pending design for SuperArray Bioscience’s siRNA array plates includes validated siRNAs for six related, pathway-specific genes on one 6-well plate with a unique reverse-transfection agent. The six siRNAs on each siRNA Array Plate have been functionally proven to decrease target mRNA levels by > 70%. The first three siRNA Array Plates announced are specific for Human Caspase, Human NFkB I and Human Cell Cycle I.

SuperArray Bioscience



Paracel AGENT 2.0 Automated Genotyping Tool

Version 2.0 of the AGENT software for automated genotyping now includes technology for accurately handling the intricacies of trace file datasets. AGENT incorporates Paracel''''s advanced TraceTuner MX base calling and quality value assignment algorithms. TraceTuner MX is optimized for heterozygous and mixed bases and is able to distinguish between noise peaks and even low-level mixed bases seen in pooled samples and in viral samples such as HIV. AGENT is built upon a client/server architecture, and is compatible with a variety of server platforms.



Jurilab DrugMEt Genotyping System

Based on microarray technology, Jurilab’s DrugMEt genotyping and SnpRater software genotypes all the variations proven to play a critical role in the metabolic pathways of most known drugs. DrugMEt can process up to 48 samples and includes 27 variations in eight genes that code for major drug metabolising enzymes. The test contains 3 microarrays (up to 48 samples total), 2 PCR multiplex mixes (x6 vials), RT mix (x3 vials), CYP2D6 deletion/duplication PCR mix, DNA controls (with known SNP content), 4 PCR plates plus sealing tape, and SnpRater software and manual.


+358 (09) 3193 6470



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


The Scan

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.

TB Resistance Insights Gleaned From Genome Sequence, Antimicrobial Response Assays

Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.