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Dell Latitude XT, CERF, GenBank Release 166.0, Ingenuity Pathway Analysis 6.3, BIOMARKERcenter, Field Programmable Gate Array Accelerator Kit

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Dell and Columbus, Ohio-based LIMS company Rescentris have partnered to offer a “solution bundle” combining the convertible Dell Latitude XT tablet with Rescentris’ Collaborative Electronic Research Framework, CERF.
 
Dell combines servers and support with its convertible Latitude XT tablets to allow scientists to manage research lab documents and images through a laptop computer.  
 
To accompany the solution, Dell is offering its PowerEdge 2900 scalable server.  The system includes CERF seat licenses for up to 10 users along with a fully configured CERF server.  The data is stored on the network rather than on the notebook.
 
Rescentris said that it provides remote configuration and one day of onsite training to allow a lab to “get up and running quickly.” The system is scalable and can support between 50 and 75 users. CERF software is a secure, 21 CFR part 11-compliant system for electronic records and signatures that centralizes scientific content management and record keeping.
 

 
GenBank Release 166.0 is available via FTP from the National Center for Biotechnology Information here
 
The new release contains 92,008,611,867 base pairs of non-whole-genome-shotgun sequence and 113,639,291,344 of WGS sequence.
 
Uncompressed, the release 166.0 flat files require roughly 343 GB for sequence files only. The ASN.1 data require approximately 314 GB.
 
With this release, GenBank has surpassed the 200-billion basepair threshold, with a total of 205,647,903,211 bases.
 
NCBI said that it has discontinued the single, comprehensive protein FASTA file due to the availability of divisional protein FASTA files as of GenBank Release 164.0. The size of this file has grown to exceed 4 GB, which is unmanageable for many users, NCBI said.
 
Users should make plans to convert to the new divisional files, available here, by August.
 

 
Ingenuity Systems has released Ingenuity Pathway Analysis 6.3. IPA now supports Affymetrix GeneChip exon arrays and several new animal and plant species.
 
Users can now upload transcript IDs from all probes that map to genes, letting scientists interpret data in the context of Ingenuity’s Knowledge Base, for example, to look at pathways and networks.
 
The release includes nine new species in addition to human, mouse, and rat: cow, chimp, chicken, Rhesus macaque, fruit fly, worm, zebrafish, yeast, and Arabidopsis.
 
This release also includes content updates for drug information from manufacturers and the dates of clinical trial updates; over 80,000 findings on protein-protein interactions; and new pathways such as BMP, 14-3-3-mediated signaling, and the role of BRCA1 in DNA damage response.
 
The protein interaction content is from various sources such as the Biomolecular Interaction Network Database and IntAct and can be filtered in the pre- and post-analysis stages, Ingenuity said.
 

 
Thomson Reuters has launched BIOMARKERcenter, a database of information on biomarkers that alerts uses to status changes of biomarkers of interest.
 
BIOMARKERcenter, developed by Thomson Reuters subsidiary Prous Science, covers biomarkers identified in the scientific literature, patents, conferences, clinical trial information, and from other sources for various therapeutic areas such as oncology, cardiovascular diseases, diabetes, respiratory disorders, autoimmune diseases and neurological disorders.
 
For each therapy area, the records include not only biomarkers with established clinical usage, but also emerging uses for the biomarker. Each manually created report on the biomarker uses a novel lifecycle model, the company stated.
 
Other data includes the name, classification, biological entities/processes connected to the biomarker, associated drugs, role or utilities, measurement techniques, regulatory status and related diagnostic kits.
 
The database is available as an integrated module for Prous Science's Integrity platform or as an XML feed to internal customer databases. The standalone web solution will be delivered later this year.
 

 
Mitrionics and Nallatech have released the Field Programmable Gate Array Accelerator Kit, which is targeted at the defense and bioinformatics sectors.
 
The kit encompasses an 8-lane PCI Express card featuring a Xilinx FPGA directly coupled to multiple independent banks of SDRAM and SRAM memory. It also includes Mitrionics’ FPGA development platform.
 
Mitrionics said the kit is a “powerful, flexible, and low-cost” commercial-off-the-shelf solution for organizations seeking FPGA-accelerated applications.
 
Nallatech, a Mitrionics partner for the last several years, said in a statement that the improved bandwidths offered by the PCI Express card along with Mitrionics tool flow will deliver “the ideal platform” for customers to accelerate their applications.

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