Bio Saga Blog - A Chronicle of Life Sciences & Informatics

BIBI automates DNA sequence analysis for bacterial identification in the clinical field. BIBI relies on the use of BLAST and CLUSTAL W programs applied to different subsets of sequences extracted from GenBank. These sequences are filtered and stored in a new database, which is adapted to bacterial identification. For further details refer : http://umr5558-sud-str1.univ-lyon1.fr/ lebibi/lebibi.cgi

Here is the climax of the stories  Life Technologies to Acquire Ion Torrent for up to $725M  and  The Argument Continues - Blue Ray or HD, Intel or AMD and now Illumina or Life Tech?   Life Technologies has completed its acquisition of Ion Torrent for $375 million in cash and stock.  The total value of the deal could rise by another $350 million if certain technical and time-based milestones are met through 2012. The acquisition adds Ion Torrent's semiconductor chip-based sequencing platform, which measures the release of hydrogen ions as nucleotides get incorporated by DNA polymerase. Unlike other existing second-generation sequencers, it does not require lasers, cameras, or labels.  The first system based on the technology is the Personal Genome Machine sequencer, which will be launched in the fourth quarter of this year. Life Technologies said that the transaction is expected to be $.02 dilutive to its earnings per share in 2010, neutral in 2011, and ac...

"Protein Structure and Drug Discovery" Workshop – Sept 30th to Oct 1st 2010 La Jolla, CA. Please join us at MolSoft's (   www.molsoft.com   ) "Protein Structure and Drug Design" Workshop in La Jolla, California USA. For more information and a registration form see:   www.molsoft.com/training.html This workshop is suitable for chemists and biologists who would like to learn more about computational drug discovery and bioinformatics. No prior knowledge in this field is required to participate. The workshop is presented by Prof. Ruben Abagyan (University of California San Diego) and Dr. Maxim Totrov (MolSoft). Price: $349 (Academics) $749 (Commercial) The workshops will consist of lectures, demonstrations, and "hands-on" computational experiments and will cover the following topics: - How To Display Fully Interactive 3D Molecules in PowerPoint and the Web - Sequence and Protein Structure Analysis - Protein Modeling and Simulations - Structure...

The European Molecular Biology Laboratory (EMBL) has launched a genomics resource called the European Nucleotide Archive (ENA) that consolidates three DNA and RNA sequence databases. EMBL's European Bioinformatics Institute (EMBL-EBI) will host the ENA resource, which is made up of the EMBL Nucleotide Sequence Database, the European Trace Archive, and the Sequence Read Archive (SRA). The European Trace Archive, formerly maintained at the Wellcome Trust Sanger Institute, contains raw data from electrophoresis-based sequencing machines, while the SRA is a new repository for raw data from next-generation, array-based sequencing platforms. The ENA research team plans to launch new features for the resource over the coming year, including enhancements for the browser, improved interactive submissions tools and organism and project-centered portals into ENA data. "ENA has been designed to provide our users with improved access both to annotated and to raw sequence data through the s...

Canadian-based GPU maker Tycrid Platform Technologies has just announced the launch of the Prometheus Alliance , a collaborative effort aimed at developing cutting edge HPC applications for bioinformatics, with a specific emphasis on next-gen sequencing data and personalized genomics. Chris Heier, President of Tycrid Platform Technologies, stated in a release that "Alliance is being established to address a specific challenge that continues to impede the progress of scientific discovery – the lack of scalable, purpose-built appliances. I feel this is critical as we can virtually eliminate the need for scientists to become computer scientists. Our goal is to take a fresh, innovative approach to developing HPC solutions that do one thing really well – address specific computational challenges for bioinformatics .” XTractor Premium - A Platform for discovery , knowledge sharing, analysis and modelling of published biomedical facts. The only Knowledgebase which provides "...

Mutations in the protein tyrosine kinase gene ERBB4 contribute to — and may provide hints about treating — a subset of melanoma, according to a paper by researchers from the National Institutes of Health and Johns Hopkins University that appeared in the advanced, online edition of Nature Genetics this week. The team sequenced protein tyrosine kinase or PTK genes in 29 individuals with melanoma. Their search uncovered dozens of somatic mutations affecting the kinase domain of 19 different PTK genes. When they looked at the same 19 genes in another 79 melanoma patients, the researchers found that almost a fifth of those tested harbored mutations in ERBB4 . And, they reported, knocking down the mutated form of ERBB4 or using a drug that targeted the gene slowed the growth of melanoma cell lines, suggesting it might be useful to evaluate ERBB4 status in melanoma patients. Researchers at the NIH Intramural Sequencing Center sequenced all 86 PTK family genes in tumor samples from 29 ...

Complete Genomics emerged from stealth mode today brandishing an audacious service model for wholesale next-generation sequencing, with its first human genome already assembled and the CEO’s pledge to reach the magical “$1000 genome” price point as early as spring 2009. Based in Mountain View, Calif., Complete Genomics has raised $46 million in three rounds of financing since its incorporation in 2006. Unlike its commercial next-gen sequencing rivals – Roche/454, Illumina, Applied Biosystems (ABI) and Helicos – Complete Genomics will not be selling individual instruments, but rather offer a service aimed initially at big pharma and major genome institutes. “Our mission is to be the global leader in complete human genome sequencing,” chairman, president and CEO Clifford Reid in a briefing last week. “We are setting out to completely change the economics of genome sequencing so that we can do diagnostic quality human genome sequencing at a medically affordable price. Essentially, [we’ll...

In Heidelberg, Germany, today researchers from eight countries and the European Commission announced the formation of a new research enterprise, the International Human Microbiome Consortium (IHMC), which will sequence the genomes of tens of thousands of microorganisms that live in and on the human body and that influence human health. Initial funding of more than US$200 million is being provided by the U.S. National Human Genome Research Institute (NHGRI) and the European Commission (EC). Jane Peterson, associate director of extramural research at the NHGRI, said international collaboration is very important in advancing science, and that “the sum is more than the parts.” Participants in the IHMC have agreed in principle to the free and open release of data and resources, and the coordination of research plans, as well as to sharing innovative developments, she reported. Data from microbiome research already being conducted by the NIH Human Microbiome Project and the EC Metagenomics ...

Leading scientists discuss DNA database at April 7-8 Meeting For a quarter century, GenBank has helped advance scientific discovery worldwide. Established by the National Institutes of Health (NIH) in 1982, the database of nucleic acid sequences is one of the key tools that scientists use to conduct biomedical and biologic research. Since its creation, GenBank has grown at an exponential rate, doubling in size every 18 months. In celebration of this vital resource and its contribution to science over the last 25 years, the National Center for Biotechnology Information, National Library of Medicine (NLM), NIH, is holding a two-day conference on GenBank. The conference will take place April 7-8, 2008 at the Natcher Conference Center on the main NIH campus in Bethesda, Maryland. For details on the meeting, see the conference Web site, at http://www.tech-res.com/GenBank25 . The conference is open to the public and also will be available via live and archived webcast; the April 7 proceedin...