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NHGRI, ENCODE, Protein Structure Initiative, Isilon, Broad Institute, MD Anderson, BioDiscovery, DNAStar, US General Services Administration, Labkey, Microsoft BioIT Alliance, InforSense, Biotique, Affymetrix

Oct. 15 Deadline for Feedback on NHGRI ENCODE Data-Release Policy
The National Human Genome Research Institute is soliciting comments from the research community on an updated data release and publication policy for the Encyclopedia of DNA Elements, or ENCODE, project.
The draft policy advises ENCODE data producers to release their data in a “timely” manner. At the same time, there will be a nine-month period during which other users of that information may not publish the results of any research based on the public data without prior consent. The draft of the data release, data use, and publication policies are available here
“This will provide time for the resource producers to have a protected opportunity to publish initial analyses of the data they have generated,” NHGRI stated in the draft policy.
On its site NHGRI said the updated policy “provides more specificity” than previous guidelines, which were based on the so-called Fort Lauderdale Agreement and are a “compromise between unrestricted use of the data and unavailability of the data until publication.”
The updated policy would apply to all data generated under the ENCODE project, a large-scale effort to identify all functional elements in the human genome sequence. The project went into a second phase last year following a four-year pilot project. The policy also covers data from the modENCODE project, which is focused on the Drosophila melanogaster and Caenorhabditis elegans genomes.
According to the revised policy, “ENCODE/modENCODE resource producers will release data, as soon as they have been verified and prior to publication, to public databases.” Prior to publication of the data in a peer-reviewed journal, “NHGRI asks resource users to consider them to be unpublished and to follow standard scientific etiquette regarding the use of unpublished data.”
In order to enable the “compromise between unrestricted use of the data and unavailability of the data until publication,” NHGRI recommends a nine-month period during which researchers can freely use the ENCODE and modENCODE data as part of their research, but cannot submit for publication the results of any studies using unpublished ENCODE or modENCODE data without prior consent.
NHGRI said that this “publication moratorium” by resource users “ends either at the expiration of the nine-month protected period or when the data have been published, whichever is shorter.”
In addition to issues surrounding data release and publication for ENCODE data, the draft policy also addresses intellectual property.
Unlike the Human Genome Project and the International HapMap project, which generated raw data that did not have “utility” from a patenting perspective, “the purpose of the ENCODE and modENCODE Projects is to generate data that identify or define genomic DNA sequence elements that have biological function, and therefore might be considered to have utility and be able to be patented,” the policy states. “Therefore, the use of patents in ways that might restrict access to large amounts or broad categories of data, e.g., all transcription factor binding sites, is an issue that needs to be addressed.”
As a result, NHGRI “encourages all ENCODE/modENCODE resource producers to consider placing all information generated from their project-related efforts in the public domain.”
In cases where consortium members decide to exercise their IP rights, NHGRI said it “encourages consideration of maximal use of non-exclusive licensing of patents to allow for broad access and stimulate the development of multiple products.” NHGRI’s recommendations for licensing genomic inventions are available here.  
NHGRI added that it also encourages users of the ENCODE data to “act responsibly.” As an example, the policy states, “if a data user were to incorporate ENCODE/modENCODE data into an invention, the subsequent license should not restrict the access of others to the ENCODE/modENCODE data.”
NHGRI said that it is seeking comments on the proposal from the research community before finalizing the policy. Comments should be sent to [email protected] by Oct. 15.
Additional information about the ENCODE data-release policy is available here

NIGMS Protein Structure Initiative Partners with Nature to Relaunch Knowledgebase
The National Institute of General Medical Sciences' Protein Structure Initiative project has partnered with the Nature Publishing Group to relaunch a free database of structural genomics information.
The Structural Genomics KnowledgeBase, hosted by Rutgers University, was originally launched in March [BioInform 03-07-08] and has been reworked to include editorial content contributed by the Nature Publishing Group that is expected “to help researchers stay informed about developments in structural biology and structural genomics,” NIGMS said. 
The Structural Genomics KnowledgeBase will be “a continually updated gateway to research data and other sources” that are available through the PSI, NIGMS said.
The PSI centers launched in 2000 by NIGMS are focused on the large-scale determination of protein structures, technology, and method development. NIGMS said they have produced over 3,200 structures and published around 1,000 scientific papers so far.
The PSI-SGKB can be found here.

Isilon Clustered Storage Finds Home at the Broad
The Broad Institute of MIT and Harvard is deploying Isilon Systems’ clustered storage system to handle and manage data from DNA sequencing research projects, the company said.
The Isilon IQ system will allow the Broad to support a “five-fold increase in the volume of genomic data” that is analyzed and stored, the company said. The system will help the institute streamline data access for its next-generation DNA sequencing program, which generates several terabytes of genomic data per day.
The IQ system runs on the company’s OneFS operating system software, and it allows scientists to share their genomic data in a single scalable shared pool, without which large institutions might be forced to spread data across “multiple, disparate silos of information, creating unnecessary barriers to data access and analysis,” Isilon said. With this system, scientists will be able to access, process and store genomic data from one central storage repository, Isilon said.
No financial terms were released.

MD Anderson Expands BioDiscovery Microarray Software License
Biodiscovery announced that MD Anderson Cancer Center has expanded its license agreement for the Nexus Copy Number microarray software platform with which scientists can analyze high density arrays on their desktop computers.
The software is used to analyze and visualize chromosomal aberrations from microarray data, and the agreement allows many users in different labs to use it at the same time. MD Anderson expanded the original site license agreement to enterprise level, BioDiscovery said.
The Nexus Copy Number platform supports a variety of microarray platforms including Agilent, Affymetrix, Illumina, GenePix, BlueFuse, ImaGene, Roche NimbleGen, Empire Genomics, and custom data files. It supports Windows Win2k/WinXP and OS X platforms. 
Financial terms of the agreement were not disclosed.

DNAStar Supplies US General Services Administration
DNAStar will supply the US General Services Administration with its sequence analysis software under a new five-year agreement, the company said. GSA provides products to a number of government agencies.
The Madison, Wis.-based company said GSA will purchase its Lasergene software, which is used in DNA and protein sequence assembly and analysis, at uniform and “favorable terms.”
According to a statement the terms of the agreement will also allow researchers be able to expedite the purchase of the software.
Lasergene is for DNA and protein analysis, contig assembly, and sequencing project management and DNAStar recently added the capability to assemble and analyze second-generation sequences.
No financial terms of the agreement were released.

Labkey joins Microsoft BioIT Alliance
Seattle-based firm LabKey Software, a maker of open-source software for researchers working on large-scale, collaborative projects, announced it has joined the BioIT Alliance.
The Microsoft-led BioIT Alliance is a consortium of software and biotechnology companies working together to advance personalized medicine and drug development using the Microsoft platform.
Among LabKey’s current customers are the Fred Hutchinson Cancer Research Center, the Bill and Melinda Gates Foundation-funded Center for HIV/AIDS Vaccine Immunology, and the Statistical Center for HIV/AIDS Research and Prevention.
Labkey’s software is used for data repositories, to handle high-throughput proteomics
experiments, flow cytometry and long-running clinical studies.

InforSense Creates Partner Program PartnerSense
InforSense this week launched PartnerSense, a new partnership program designed to enable the company to increase its global market presence and strengthen its partner network and current partnerships.
The InforSense PartnerSense Program “will provide resources and support for partners to achieve their business goals and meet the advanced business intelligence and analytic mashup needs of their customers,” the company said.
 “Our customers typically use a variety of best-of-breed tools to meet their specific scientific or business analytic needs,” said David Bennett, executive vice president of worldwide sales at InforSense, in a statement. PartnerSense “allows us to work closely with industry leaders to develop and implement integrative, cross-platform solutions for our mutual customers.”
The types of partnerships available include value-added reseller, technology & OEM partner, system integrator/services provider, marketing partner, and distribution partner.

Affymetrix to Distribute Biotique's Gene Expression Analysis Software
Affymetrix will distribute Biotique’s gene expression analysis software directly to its microarray customers under a new agreement, Biotique said this week.
Biotique’s XRAY software functions as an add-in for Microsoft Excel, and requires “little or no software specific training,” the Reno, Nev.-based company said.
"Customer feedback shows that this is an intuitive and powerful way in which to analyze Affymetrix array data, offering a higher degree of flexibility and ease-of-use,” Greg Fisher, Affymetrix’s associate director of product marketing, said in a statement.
Financial terms of the agreement were not released.

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