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Waters, Hitachi, Shimadzu, Current BioData, BioDiscovery, NCI, NIH, NHGRI, NIMH, SGI, BioWisdom, OmniViz, Symyx, Microsoft

Hitachi, Shimadzu to Distribute Waters’ Chromatography Software
Shimadzu and Hitachi High-Technologies will distribute Waters’ Empower 2 chromatography data software, a company official said this week.
The distribution agreements build upon deals that Waters signed with the two firms last year to support the Hitachi and Shimadzu high-performance liquid chromatography product lines, Mary Ellen Goffredo, senior director of systems product marketing at Waters.
“So we’re not only opening up the control [of the instruments] from within Empower, but we’re also opening up our channels and Hitachi and Shimadzu are both going to resell Empower 2 as their chromatography data systems as well,” she said.
Empower 2 lets scientists collect data, control multiple instruments, and report on their findings through a single user-friendly interface.
Goffredo said that the agreements are the latest step in a strategy Waters began several years ago “to really open up the architecture … of Empower 2.”
The firm signed its first integration deal for the software with Agilent Technologies in 2005, and “by the end of 2008, will have control over most major LCs and GCs from all the major vendors from within Empower 2,” she said.
Goffredo noted that informatics is “central” to Waters’ business and is “one of the key driving factors” in the company’s future growth.
“When you think about the modern analytical laboratory, it’s really the software that people interact with, and the software is where they get their results,” she said. “So we see software growing in importance, both to ourselves and to the market that we compete in, because as we watch our customers — and particularly our big pharma customers — move toward the need to be ever more efficient, finding ways to make it easy to systemize their workflow, and make their day-to-day operations more streamlined and more efficient is critical.”

Current BioData Opens Research and Publishing Center in Wales
Scientific database provider Current BioData said this week that it is opening a new research and publishing center in Wales to serve customers in the US, Europe, and the rest of the world.
The company, which has research centers in Geneva and London, was formed in 2005 as a joint venture between Geneva Bioinformatics and the Science Navigation Group (formerly Current Science Group) — the parent company of BioMed Central and several other independent scientific publishing companies.
The firm markets the Targeted Proteins Database, a curated protein information resource that is updated daily with new data published in the scientific literature.
"We have been growing so rapidly that we wanted to double our existing staff and looked around the world for a suitable location," said Ian Tarr, CEO of Current BioData, in a statement.
The firm considered Singapore as a low-cost option, Tarr said, but ultimately decided that “Wales makes more sense and is a lot easier to manage than Singapore.”
The company intends to recruit 45 new staffers for the facility from the University of Wales, Swansea, and Cardiff University.

NCI Signs Site License for BioDiscovery's Nexus Software
BioDiscovery said this week that the National Cancer Institute has obtained a site license for its Nexus Copy Number software, which is used to analyze and visualize chromosomal aberrations from microarray data.
Nexus Copy Number can integrate data from thousands of arrays along with their clinical annotations in a single project, the company said.
Financial terms of the licensing agreement were not disclosed.

NIH to Host Data from MJFF-Funded Parkinson's GWAS, Agrees to Support Future 'Orphan' Data Sets
The National Institutes of Health said this week that it will host data from a genome-wide association study focused on Parkinson’s disease and funded in part by the Michael J. Fox Foundation for Parkinson’s Research.
The National Human Genome Research Institute and the National Center for Biotechnology Information have released the data through dbGaP, the database of Genotypes and Phenotypes.
The study was conducted by researchers at the Mayo Clinic and Perlegen Sciences and funded by MJFF’s Linked Efforts to Accelerate Parkinson’s Solutions, or LEAPS, initiative.
Because the project was primarily supported by a private foundation, NIH said that it is considered an “orphan” data set because it doesn’t meet NIH requirements for access to GWAS data, which can contain details that could be used to identify study volunteers and potentially violate their privacy.
NIH requires that projects submitting GWAS data remove identifying information, such as names and social security numbers. In addition, researchers who want to use the data must ask for permission and agree to certain limitations in order to ensure patient privacy. These requests are reviewed by a data access committee, or DAC. While several NIH institutes have DACs, few private foundations do.
In this case, NHGRI’s data access committee agreed to “adopt” the study and manage the data access approval process, NIH said.
“Until now, the individual-level data from this study had been available only to a few researchers,” Teri Manolio, director of the NHGRI Office of Population Genomics, said in a statement. “This is the first orphan data set NHGRI is adopting to make public through NCBI, but it certainly will not be the last.”
NIH said that NHGRI’s DAC will manage data access for all GWAS studies submitted to dbGaP that are not associated with other NIH institutes, “including studies submitted by corporate entities.”

NIMH Commits $2.5M for Analysis of Mental Health GWAS Data
The National Institute of Mental Health has earmarked around $2.5 million to support the analysis of data from mental health-related genome-wide association studies.
NIH plans to issue five awards through individual R01 grants and through the collaborative R01 mechanism to support one year of secondary statistical analysis on existing GWAS data sets for major mental disorders, including attention-deficit hyperactivity disorder, bipolar disorder, autism, major depression disorder, and schizophrenia.
Applicants are required to be participants in the Psychiatric GWAS Consortium. They are also expected to propose methods for analyzing combined data sets across different genotyping platforms and across phenotypes using either existing or new statistical methods.
NIMH said in its program announcement that while several large mental health GWAS have been conducted involving thousands of cases and controls, “the analyses of these data and data from studies in different disease areas have shown that to successfully determine the contribution of common alleles to the genetic architecture of mental disorders, it may be necessary to have sample sizes in the tens of thousands.”
Other challenges that NIMH noted include the fact that study subjects need to be carefully phenotyped and the likelihood that common risk alleles underlying mental disorders “are of modest effect size and prone to estimation errors and confounding and are thus highly model dependent.”
The agency said it expects combined data sets across various studies to “provide the opportunity to test association between genetic variants and sub-phenotypes for specific mental disorders and … also improve the precision of estimates for the effect size for a single allele or a set of jointly interacting alleles.”
The program is based on existing data and NIMH said it will not fund new sample collection or genotyping. In addition, applicants must have appropriate consent in place for study subjects and must submit a data-sharing plan that makes all genotype and phenotype data available through the NIMH Human Genetics Initiative and the NIH dbGaP database.

Dresden Center Deploys 11.9-Tflop SGI Altix for Bioinformatics, other Apps
SGI said this week that Germany’s Technische Universitat Dresden has deployed an SGI Altix cluster that is being used in a range of disciplines, including bioinformatics, physics, chemistry, engineering, and nanotechnology.
One group at the center is using the system to semantically analyze 16 million scientific articles to “efficiently grasp the world's combined understanding of gene expression and protein structures,” SGI said in a statement.
The 11.9-teraflop SGI Altix 4700 system includes 2,048 Intel Itanium 2 processor cores and has 6.5 terabytes of memory. The center has also built a data-management infrastructure with SGI InfiniteStorage 6700 systems.

J&J PRD Extends License for OmniViz Software
Johnson & Johnson Pharmaceutical Research and Development has extended a licensing agreement for BioWisdom’s OmniViz visualization and data-mining software, BioWisdom said this week.
The OmniViz software offers visualization of text, numerical, and categorical data as well as genome sequences, chemical structures, and text files.
Financial terms of the agreement were not released.

Symyx Joins BioIT Alliance
Symyx Technologies said this week that it has joined the BioIT Alliance, a Microsoft-led consortium of companies focused on developing data-management strategies that could help advance drug discovery programs and personalized medicine.
Symyx, based in Santa Clara, Calif., is a provider of electronic lab notebooks and other scientific decision-support software. Last fall, it acquired MDL Information Systems from Elsevier for $123 million, adding the ISIS and Isentris platforms, MDL Draw, MDL Direct, the Available Chemicals Directory, and DiscoveryGate products to its portfolio.

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