BGI Licenses CLC Bio’s Genomics Workbench
CLC bio said last week that it has licensed its Genomics Workbench sequence analysis and visualization software to the Beijing Genomics Institute.
According to the terms of the agreement, for which financials were not released, all BGI researchers inside and outside of China can now use CLC’s Genomics Workbench, which analyzes data from several next-generation sequencing platforms, including Illumina’s Genome Analyzer, Applied Biosystems’ SOLiD, Roche Applied Science’s 454 platform, and the Helicos HeliScope.
In a statement, Ruiqiang Li, BGI’s head of bioinformatics, said that the organization selected CLC Genomics Workbench “after testing several commercial solutions.”
The Aarhus, Denmark-based bioinformatics company said BGI will use the software for several sequencing projects, including the Giant Panda Genome Project and the 1000 Genomes Project.
CLC Genomics Workbench is available for Mac OS X, Windows, and Linux.
CLC said the software utilizes paired end data and supports tasks including reference assembly, de novo assembly, SNP detection, multiplexing, and high-throughput trimming.
Axxam Licenses Genedata's Screener Software
Drug discovery research services provider Axxam has licensed Genedata’s data analysis and management software for its high-throughput screening programs under a multi-year agreement, Genedata said last week.
Axxam will use Genedata’s Screener software to analyze, integrate, and manage assay data and combine it with chemical, pharmacological, and in vivo information to identify lead compounds for drug discovery.
Financial aspects of the agreement were not made public.
Axxam CEO Stefan Lohmer said the agreement with Genedata extends beyond the actual license agreement to “a comprehensive, long-term partnership in high-throughput screening.”
UT Health Sciences Center Taps GenoLogics for Translational Informatics System
The University of Texas Health Sciences Center in Houston said last week it will use GenoLogics’ informatics platform for its clinical and translational research efforts.
Powered by a Clinical and Translational Science Award from the National Institutes of Health, UTHSC is partnering with the University of Texas MD Anderson Cancer Center and the Memorial Hermann Hospital System in the newly created Center for Clinical and Translational Sciences.
Peter Davies, executive vice president of research for UTHSC, said in a statement that the center chose GenoLogics’ platform because it will improve information flow between researchers in core laboratories and the clinic and will help to “effectively integrate our omics data and healthcare information into a common platform across multiple facilities and collaborators.”
GenoLogics said that its platform is “highly configurable” for working arrangements with multiple collaborators and can “support the complex workflows of organizations conducting translational research outcomes.”
NIH Roadmap to Fund Informatics, Computational High Risk Research
The National Institutes of Health last week announced a pair of bioinformatics grant opportunities under its “Exploratory Collaborations with National Centers for Biomedical Computing” program, an NIH Roadmap initiative.
The R01 program will support direct costs of up to $500,000 per year for up to five years, and the R21 program will grant up to $275,000 over two years in total funds.
The program will fund researchers working with the National Centers for Biomedical Computing, or NCBCs, on innovative, high-risk, and high-impact applications “in new areas that are lacking preliminary data or development,” NIH said in a program announcement.
Because the size and scope of the research may vary, NIH said, the award amount will fluctuate depending on the projects. The total amounts will also depend on the number and duration of the applications received.
The NIH NCBCs are partnerships that bring together three types of computational scientists: those who invent and develop efficient and powerful languages, data structures, software architectures, hardware, and algorithms for solving biomedically significant computing problems; biomedical computational scientists who adapt and deploy resources from computational science to solve significant biomedical problems; and experimental and clinical biomedical and behavioral scientists, who generate data that can be transformed into knowledge by computational simulation, analysis, modeling, data mining, and visualization.
These partnerships are designed to produce, validate, and disseminate tools and computational environments that will be useful to a broad spectrum of biomedical researchers across the nation, NIH said.
As examples of how funding may be used, the NIH said that the collaborations could yield software tools that would be integrated in computing environments under development at the NCBCs; they might extend the realm of an application to a different data type; or they may be basic algorithmic efforts that could make software at the NCBCs run more efficiently.
Collexis, JISC Partner on Online Collaboration Tool
Collexis and JISC Collections said last week that they are partnering to provide researchers in the UK access to Collexis' Expert Profiling, a system that lets researchers identify, locate, and collaborate with experts within their own institutions and elsewhere.
JISC Collections is an offshoot of the UK’s Joint Information Systems Committee that negotiates with publishers of online information in order to guarantee affordable access to these resources for education and research.
Through Collexis, subscribing institutions create expert profiles of investigators, researchers, and departments to disseminate research results. These profiles are generated using researchers' publications and grants. Once an institution subscribes, Collexis' Expert Profiling is available to all staff and students within the institution.
Collexis said that researchers can use Expert Profiling to build applications to search, index, and aggregate information as well as prioritize, trend, and predict data based on sources in multiple industries without the limitations of language or dialect.
UC Riverside Installs ‘Biocluster’ Supercomputer
The University of California at Riverside’s Bioinformatics Facility of the Institute for Integrative Genome Biology said last week that it has installed a Verari Systems supercomputer for bioinformatics applications that it has named “Biocluster.”
According to a statement, the Linux blade cluster system is the most powerful computer at UCR and will “significantly” reduce the computing time for large-scale genome analysis, drug discovery, and simulation studies for many research projects on campus. The system cost $280,000.
Biocluster has 256 cores and runs 64x Xeon Quad Harpertown processors. The system has 12 MB cache, 640 GB of total RAM, and an Infiniband interconnect with a total of 64 GB of usable memory available for a single process. If needed, the memory on this node can be expanded to a total of 192 GB, UCR said.
“It changes not only the nature of science at UCR but its quality as well, making UCR more competitive for large federal grants,” said Thomas Girke, the director of the Bioinformatics Facility. According to a release, he is also assistant professor of bioinformatics in the Department of Botany and Plant Sciences and who oversees Biocluster’s use.
“With Biocluster, we don’t have to wait for days before we can run our simulations,” said Chia-en Chang, an assistant professor of chemistry at UCR, who performs computer-aided drug design.
The computer is currently located in the Computing and Communications data center and will be moved in December into a server room in the university’s new Genomics Building.
The supercomputer also has made possible the hiring of new faculty at UCR. “The university just hired three faculty members in computational biology,” Girke said. “Hiring them would have been very difficult — if not impossible — without a state-of-the-art infrastructure for high-performance computing.”
Sanger Institute Sequences 1 Terabase in Six Months
The Wellcome Trust Sanger Institute said last week that it has sequenced one terabase of genomic data, or the equivalent of 300 human genomes, in just over six months.
Every two minutes, the institute produces as much sequence as was deposited in the first five years of the international DNA sequence databases, which started in 1982.
The institute attributed the rapid rise in sequence data to its fleet of next-generation sequencing platforms, including Roche/454, Illumina, and AB SOLiD machines, which are currently generating more than 50 terabytes of quality-filtered data per week.
MD Anderson Automating Workflow with Stone Bond's Enterprise Enabler
MD Anderson Cancer Center is automating laboratory workflow at its new Small Interfering Ribonucleic Acid Facility with a laboratory information management system by Stone Bond Technologies.
Stone Bond's Enterprise Enabler integration platform, EE-LIMS, automates laboratory workflows, invoicing, data and sample tracking, collections and other business processes to help laboratories reduce overhead and administrative costs.
According to a statement, Stone Bond said the system will increase throughput, while reducing the risk of errors in siRNA research in which scientists need to document exactly what tasks go into producing genetic data that corresponds to the RNA in a given sample.