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Ingenuity Pathways Analysis 3.0, AlleleID, UniProt 6.0, Reflex, Affymetrix, Waters Analytical Workflow Manager Software 1.4.7, Jon Kleinberg, Zung Vu Tran, Neil Kipling


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Ingenuity has released Ingenuity Pathways Analysis 3.0. Features include the ability to analyze microarray and proteomics data in the context of pathways; create customized pathways for targets, biomarkers, processes, and diseases; integrate proprietary data into any pathway; and share analyses and personalized pathways with colleagues. Trials are available at

Premier Biosoft has released AlleleID, a primer-design program based on ClustalW that is designed for pathogen detection, species identification, and taxa discrimination using TaqMan and molecular beacon assays. A demo version of the program is available at

The UniProt Consortium, comprising the European Bioinformatics Institute, the Swiss Institute of Bioinformatics, and the Protein Information Resource, has released UniProt 6.0 at In the current release, UniProtKB includes 2,299,834 entries (the UniProtKB/Swiss-Prot section contains 194,317 and the UniProtKB/TrEMBL section contains 2,105,517).

De Novo Pharmaceuticals has launched Reflex, an upgrade to its SkelGen in silico drug design platform. Reflex enables SkelGen to take into account the rotational flexibility of amino acids in the target enzyme active site, the company said, which more closely mimics the dynamics of real-life protein-ligand interactions.

Affymetrix has released several updates through the Affymetrix Developer Network. These include updates to the C++ source code of the Fusion software development kit (, an update for the IGB (Integrated Genome Browser) software to include location data for the company's 10K, 100K and 500K genotyping arrays (, and a new tool called gtype_cel_to_pq, which extracts probe sets from genotyping CEL files into tab-delimited text suitable for import into other tools such as R or Matlab ( Affy has released this tool under the LGPL.

Waters has released its Analytical Workflow Manager Software 1.4.7, which administers the workflow of the order process cycle from capturing analytical requests, through instrumental measurements and result analysis, to long-term data storage. The software, formerly called Q-DIS/R, combines work-list management, sample tracking, measurement setup and triggering with data evaluation and result distribution. Scientists in analytical services laboratories can use it to share their results with colleagues.


People in the News

Jon Kleinberg, a professor of computer science at Cornell University, is among the 25 new MacArthur Fellows for 2005 named last week by the John D. and Catherine T. MacArthur Foundation. Kleinberg will receive $500,000 over the next five years. Kleinberg is best known for his research in network theory, particularly the so-called small-world concept, although his work has also touched on comparative genomics and protein structure analysis.

Bionovo has appointed Zung Vu Tran to its scientific advisory board. Tran is a research professor in the department of preventive medicine and biostatistics at the University of Colorado at Denver and Health Sciences Center in Denver and is a member of the University of Colorado Cancer Center's biostatistics and bioinformatics core.

Neil Kipling, founder, CEO, and chairman of IDBS, has been awarded the 2005 SBS Accomplishment Award for Innovation in Information Management for Scientific Software. The Society for Biomolecular Screening presented the award earlier this month at its 11th Annual SBS Conference and Exhibition in Geneva. The award carries a $1,000 honorarium, which Kipling is donating to the Sunflower Trust, a charitable organization dedicated to helping children with learning difficulties based in Guildford, UK, where IDBS is headquartered.

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The Scan

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US Survey Data Suggests Ancestry Testing Leads Way in Awareness, Use of Genetic Testing Awareness

Although roughly three-quarters of surveyed individuals in a Genetics in Medicine study reported awareness of genetic testing, use of such tests was lower and varied with income, ancestry, and disease history.

Coral Genome Leads to Alternative Amino Acid Pathway Found in Other Non-Model Animals

An alternative cysteine biosynthesis pathway unearthed in the Acropora loripes genome subsequently turned up in sequences from non-mammalian, -nematode, or -arthropod animals, researchers report in Science Advances.

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.