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NCBI, caGrid, Tripos, Lion, Cresset, InforSense, Rosetta, Ingenuity, ACD/Labs, Genomatix


NCBI Adds Flowgram Format to Trace Archive

The National Center for Biotechnology Information has added a new submission format for its Trace Archive to accept data from 454 Life Sciences' sequencing technology, 454 said this week.

The new format, called Standard Flowgram Format, represents "the first new sequence trace format adopted by the NCBI since the Sanger method," 454 said.

"We hope that the extraordinary amount of data being generated with our technology will be placed into the public domain, thereby fostering research in a variety of areas including medicine, biology, and paleontology," said Christopher McLeod, president and CEO of 454, in a statement.

Further information on SFF is available at

NCI Seeks Subcontractors for caGrid Client Demo Project

The National Cancer Institute Center for Bioinformatics has issued a request for proposals for "professional service experts" to work on the cancer Biomedical Informatics Grid.

The goal of the project will be "to demonstrate the usefulness of caGrid infrastructure as a platform to perform scientifically challenging investigations involving integration of data and analytical services from diverse research communities."

The NCICB is seeking experts with previous experience in grid computing, n-tier architecture design, and software design.

Interested parties can request a copy of the request for proposal from Jennifer Thomas (301-228-4004, [email protected]). SAIC-Frederick, the operations and technical support services contractor for NCI, will be responsible for awarding the contract.

Further details are available at

Tripos Lays off Half its Discovery Research Staff…

As expected, Tripos has cut staff at its UK-based Discovery Research business.

The company said this week that it has laid off 76 of its 161 employees at Tripos Discovery Research, based in Bude, UK. Tripos warned that it would have to cut staff at the UK facility in December [BioInform 12-26-05].

As of Dec. 31, the company employed 314 employees worldwide.

The company said that more than half of the affected employees are leaving under a voluntary separation plan. Tripos is offering all affected employees severance packages and is assisting them with outplacement services.

The reduction in force is "an integral part of Tripos' plan to streamline and refine its Discovery Research business and associated cost structure," the company said in a statement.

Tripos said it also plans to close a 6,000-square-foot temporary laboratory facility in Bude and explore "alternate uses for or disposition of the excess property."

Tripos expects to post restructuring charges of around $1.8 million associated with the layoffs in the first quarter of 2006. This includes $900,000 for severance and related employee costs and a $900,000 asset write-off associated with the closure of the temporary laboratory building.

… But Signs Five New Discovery Collaborations

One day after it announced layoffs at it UK-based Discovery Research unit, Tripos said that it had signed discovery research collaborations in the fourth quarter of 2005 with CeNeS, Gemin X Biotechnologies, Genzyme, GlaxoSmithKline Research and Development, and Schering-Plough Research Institute.

Tripos said that the partnerships encompass "a range of research activities including medicinal chemistry programs, the development of new LeadQuest compounds, follow-up libraries based on hits from LeadQuest, provision of synthetic protocols, [and] fragment-based screening and LeadHopping(R) projects."

Further details of the agreements were not disclosed.

Lion to Gather SRS Feedback from EMBL Researchers

Lion Bioscience said this week that the European Molecular Biology Laboratory will deploy its SRS data integration platform across all of its research staff.

Under the terms of the agreement, EMBL researchers will provide "end-user feedback on SRS-related products and input on new requirements."

SRS was originally developed at EMBL, and researchers there have had access to the product in the past, but there was previously no "official collaboration" related to the product, Martina Fortin, director of global marketing at Lion, told BioInform.

Fortin said that EMBL researchers previously had access to an older version of SRS, and the new agreement involves an upgrade to the most recent version, SRS 8.1.

Bayer CropScience to Use Cresset's FieldScreen Software

Cresset BioMolecular Discovery said this week that Bayer CropScience will use its FieldScreen software to identify early-stage active compounds as part of its computational chemistry pipeline.

The agreement is the first application of Cresset's molecular field technology in the agrochemical arena, the company said.

FieldScreen is based on an approach that models compounds in terms of their molecular fields rather than their atom and bond representations, Cresset said. The company's software can be used to create and visualize fields around a molecule that can be used to model binding interactions.

Syngenta Licenses InforSense's KDE

Syngenta has purchased a license for InforSense's software suite, including its KDE workflow platform, which will be deployed throughout its R&D activities.

InforSense will also provide professional services to Syngenta under the agreement "to build up its workflow-driven bioinformatics computational platform," InforSense said. Syngenta will also use the BioSense and TextSense add-ons for KDE.

Financial terms of the multi-year deal were not disclosed.

Rosetta and Ingenuity to Integrate Software

Rosetta Biosoftware and Ingenuity Systems said this week that they are collaborating to establish interoperability between the Rosetta Resolver gene-expression analysis system and the Ingenuity Pathways Analysis system.

Further details were not disclosed.

Université Joseph Fourier Installs ACD/Labs' NMR Software

Advanced Chemistry Development said this week that France's Université Joseph Fourier has installed its suite of NMR prediction, verification, and data management software tools at the Centre Grenoblois de Résonance Magnétique.

The agreement includes ACD/Labs' 1H and 13C NMR Predictors for calculating chemical shifts and coupling constants; 1D and 2D NMR Processors for vendor-neutral processing and analysis; and the NMR database modules of ACD/SpecManager, a spectroscopic processing and data management software package.

Financial details of the agreement were not provided.

Genomatix to Launch ChipInspector for Exon Arrays in Q2

Genomatix Software said this week that it plans to launch a new version of its ChipInspector software for analyzing data from Affymetrix exon arrays in the second quarter of 2006.

The company said that the new version of ChipInspector "will considerably improve analysis of the exon array data including transcript separation and promoter identification of the relevant transcripts."

Filed under

The Scan

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.

Mitochondrial Replacement Therapy Embryos Appear Largely Normal in Single-Cell 'Omics Analyses

Embryos produced with spindle transfer-based mitochondrial replacement had delayed demethylation, but typical aneuploidy and transcriptome features in a PLOS Biology study.

Cancer Patients Report Quality of Life Benefits for Immune Checkpoint Inhibitors

Immune checkpoint inhibitor immunotherapy was linked in JAMA Network Open to enhanced quality of life compared to other treatment types in cancer patients.

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.