ISCB Seeks Comments on Revised Software-Sharing Policy
The International Society for Computational Biology is soliciting comments from its members on its updated policy statement on bioinformatics software availability.
The ISCB board of directors posted a statement on the society’s blog this week outlining the revised statement, which it said has been “revised from the original 2002 statement, incorporating feedback from the ISCB membership.”
The original policy drew criticism for failing to reflect the views of the broader ISCB membership because it was issued without a poll, vote, or comment period [BioInform 08-12-02].
The revised statement, based on feedback on the original statement gathered at ISMB 2007, recommends that researchers, funding organizations, and publishers must "uphold the core principle of sharing methods and results;" grantors and publishers should "require statements of software availability in grant proposals and research reports;" and, "executable versions of the software should be freely available for research use to individuals at academic institutions."
The comment period closes April 15.
ABI Releases Human Genome Sequence Generated on SOLiD
Applied Biosystems this week said that it has completed sequencing a human genome using its next-generation SOLiD technology, and that it has deposited the sequence with the National Center for Biotechnology Information.
“The availability of this sequence data in the public domain is expected to help scientists gain a greater understanding of human genetic variation and potentially help them to explain differences in individual susceptibility and response to treatment for disease,” the company said in a statement.
ABI scientists resequenced the genome of an anonymous African male of the Yoruba people of Ibadan, Nigeria, who participated in the International HapMap Project. They generated 36 gigabases of sequence data in seven runs on the SOLiD system, resulting in 12X coverage of the genome.
The company said the researchers were able to use this data to identify millions of SNPs greater than 99.94 percent sequencing accuracy. In addition, ABI said its scientists were able to analyze regions of structural variation using 100-fold physical coverage.
ABI said that it expects the public availability of the data “will help drive innovation and speed the development of new bioinformatics tools.”
In addition to the full human dataset, ABI said it has also released “subsets” of sequence data through Genbank which “can be accessed by independent academic and commercial software developers to further enable the development of analytical tools.”
The company has released several analysis tools through the SOLiD System Software Development Community to help researchers analyze the data.
At NCBI, the human sequence data is available here or by the project name, “SOLiD Human HapMap Sample NA18507 Whole Genome Sequence,” under accession number SRA000272.
Ohio Bioinformatics Consortium Awarded $4.5M in Scholarship Funding
The Ohio Consortium for Bioinformatics will receive $4.475 million for student scholarships under the state’s “Choose Ohio First” program, which is aimed at attracting and graduating more than 2,000 students in science and technology fields in the state over the next five years.
The bioinformatics initiative was one of seven awards totaling more than $22.7 million announced this week.
The consortium includes Ohio University, 11 other colleges and universities in the state, the Ohio Supercomputer Center, and the Ralph Regula School of Computational Science. It hopes to attract and graduate an estimated 345 students over a five-year period.
Partners in the consortium will contribute an additional $4.6 million to develop programs, expand offerings, and cover other related costs, the consortium said.
University of Copenhagen Takes Site License for CLC Bio's Software
The University of Copenhagen has bought a site license for CLC bio’s Combined Workbench and Educational Suite software platforms, CLC bio said this week.
Under the agreement, the department of biology at the university has licensed access to the software for five years for “several hundred seats,” the company said.
The university’s genomics projects include retrieving DNA from fossils, gene regulation and SNP cancer research, primate genome evolution, bacterial genome sequencing, and other programs.
Financial terms of the agreement were not released.
BGI LifeTech to Sell DNAStar's Software in China, Hong Kong
The Beijing Genomics Institute’s BGI LifeTech segment will sell DNAStar’s bioinformatics software in China and Hong Kong, DNAStar said this week.
Under the agreement, BGI LifeTech has acquired the rights to sell the Lasergene, ArrayStar, Seqman Genome Assembler, and GenVision products.
The company’s software platforms are used in analyzing sequence data, microarray gene expression data, and genomic visualizations.
Financial terms of the agreement were not released.
Agilent to Embed Accelrys' Pipeline Pilot in OpenLAB Software Under OEM Deal
Accelrys and Agilent said this week that they have signed an original equipment manufacturer agreement that will allow Agilent to distribute an embedded version of Accelrys' SciTegic Pipeline Pilot workflow software with its own OpenLAB enterprise content management software.
Agilent expects to have a commercial version of the Accelrys software, called Embedded Pipeline Pilot, available in the first half of the year.
The OEM deal builds upon a resale agreement the companies signed last fall under which Accelrys has been reselling Agilent's OpenLAB, Kalabie electronic lab notebook, and GeneSpring gene-expression analysis software, while Agilent has been selling Accelrys’ Accord cheminformatics solutions and Pipeline Pilot [BioInform 09-28-07].
Financial terms of the OEM agreement were not provided.