Bio Saga Blog - A Chronicle of Life Sciences & Informatics

- GSK becomes first company to freely share chemical structures on 13,500 molecules from its compound library - Alliances formed with leading scientific research communities from private industry and public-domain data provider courtesy CDD Blog GlaxoSmithKline (GSK) had teamed up with leading public-domain data providers European Bioinformatics Institute (EMBL-EBI), the U.S. National Library of Medicine (NLM) and the US-based informatics service provider Collaborative Drug Discovery (CDD) to make freely available key scientific information on more than 13,500 compounds that could ultimately lead to new treatments for malaria. The release of this data marks the first time that a pharmaceutical company has made available the structures of so many compounds and is made possible through the collaboration of the web hosts and their specialist research tools, which will be available at no cost to researchers. The information, which is hosted on websites regularly used by researchers, incl

Here is something I came across recently, a relatively old article which I found on Bioinformatics Zen by Michale Barton. Simple, practical and worldly wise. Bioinformatics usually involves shuffling data into the right format for plotting or statistical tests. I prefer to use a database to store and format data as I think this make projects easier to maintain compared with using just scripts. I find a dynamic language like Ruby and libraries for database manipulation like ActiveRecord makes using a database relatively simple. Using a database however stops being simple when you have to deal with very large amounts of data. Here I’m outlining my experience of analysing gigabytes of data with millions of data points and how tried to improve my software’s performance when manipulating this data. I’ve ordered each approaches with I think is the most pragmatic first. The simple things Obvious but sometimes overlooked. 1. Use a bigger computer Using a faster computer might seem like a la

Abbott May 21 announced a definitive agreement with Piramal Healthcare Limited to acquire full ownership of Piramal's Healthcare Solutions business (Domestic Formulations), a leader in the Indian branded generics market, for an up-front payment of $2.12 billion , plus $400 million annually for the next four years, giving Abbott the No. 1 position in the Indian pharmaceutical market. This further accelerates Abbott's emerging markets growth following the recent acquisition of Solvay Pharmaceuticals and announcements last week of Abbott's collaboration with Zydus Cadila as well as the creation of a new stand-alone Established Products Division to focus on expanding the global markets for its leading branded generics portfolio. "This strategic action will advance Abbott into the leading market position in India , one of the world's most attractive and rapidly growing markets," said Miles D. White , chairman and chief executive officer, Abbott. &quo

Nick Loman at Pathogens: Genes and Genomes says that the key players emerging third-generation sequencing market are comparable to the Intel x86 family and its famed competitor, reduced instruction set computing — or RISC — chips in the early 1990s. "Despite the seeming obvious killer advantages … RISC chips resoundingly failed in the desktop PC market, never challenging Intel’s dominance," Loman recalls. He writes that labs considering which third-gen sequencing instruments to invest in is "very similar to the common nerd dilemma: buy a new laptop now, or wait for the next model?" Loman wonders whether the theory behind Moore's law will hold true for the transition from second- to third-generation sequencing technologies. "I propose that Illumina are Intel, and the Genetic Analyzer family — GA1, GA II, GAIIx, HiSeq 2000 — are x86. Life Tech is AMD, producing similar technology with much reduced market share," Loman writes, adding that "the thir

The Ontario Genomics Institute has started a new fund that will be used to make genomics research papers available as open access from the date of their publications in journals. The OGI Genomics Publication Fund (GPF) will contribute up to C$3,000 ($2,900) per publication to genomics researchers in Ontario who want to make their papers available. The GPF will be open to researchers at Ontario-based academic, industry, or government institutions, and its goal is to maximize access to important genomics publications and to increase the visibility and citations of genomics research conducted in the province. OGI expects to support up to 35 open access publications over the next 12 months, and it will either reimburse special fees charged by traditional publishers to make individual manuscripts open access or to defray publication costs for manuscripts published in open access. "OGI's program is targeting those publications with the greatest potential reach. Open sharing of knowl

Pfizer UK-Kent-Sandwich Computational Biologist Computational Sciences are integral to Pfizer’s strategy to accelerate the discovery of important new medicines. This is your opportunity to join a dynamic, innovative team, focusing on the development and use of novel computational methods and algorithms to enhance the efficiency and effectiveness of drug discovery. We are looking for a Computational Biologist with skills in working with genomics data, developing novel algorithms and generating new biological hypotheses to join our Computational Sciences Center of Emphasis in Sandwich, UK. Specific areas of interest include: • Identification of new datasets and data mining techniques relevant to drug discovery • Developing and testing novel methods and algorithms, working with academic collaborators where opportunities arise • Building and testing prototype systems (both interfaces and algorithm libraries) • Working with scientists to apply tools to every day problems • Awarded or

In a major advancement in influenza science, India is ready with its first indigenous vaccine against H1N1 swine flu. Pune-based Serum Institute of India (SII) has developed a H1N1 vaccine — not a painful syringe shot but a harmless nasal spray — which can be used by anybody above the age of three except pregnant women. To cost around Rs 150, SII will apply to the drug controller general for licensure of its product next week. Scientists, who are presently completing tabulation of results from the vaccine’s phase-III clinical trial, say it is safe and effective with side-effects being runny nose and a bout of sneezing. Interestingly, the breakthrough comes exactly a year after India reported its first case of swine flu (May 15, 2009). Confirming this to TOI, SII’s executive director (operations) Adar Poonawala said, “Our nasal mist vaccine is now ready. We will apply for licensure next week. It had no side-effects which are synonymous to injectible vaccines like fever, swelling or conv

Agilent Technologies said after the close of the market Friday that it has completed the roughly $1.5 billion acquisition of Varian. Completion of the deal was announced a day after Agilent said that the European Commission has informed the firm that it had met the conditions set forth in January for the acquisition of Varian. Those conditions included the divestiture of certain product lines, which were recently sold to Bruker. Agilent said today that the majority of Varian's product lines will become part of the Chemical Analysis Group, with some key businesses being housed in Agilent's Life Sciences Group. Adding to Agilent's portfolio of mass spectrometry, liquid and gas chromatography, and array products, the firm's life sciences business gains Varian's nuclear magnetic resonance, MRI, and X-ray products. "These technology platforms will open new doors for Agilent and its customers," Nick Roelofs, Agilent's senior VP and president of LSG, said in

Senior Bioinformatics Analyst Requirements: - PhD or equivalent experience in life science / biology. - 4+ years demonstrated success in working in the life sciences, preferably in an industry research settings. -In-depth understanding, analysis and processing of data from various post genomic technologies and their applications. - In-depth knowledge in gene expression (genotyping, chromosomal copy number, SNPs, gene signatures) and sequencing -Wide understanding of commercially available bioinformatics/clinical genomics tools and databases -Ability to handle complex / multi projects in rapidly changing environment. - Good knowledge on Perl, C / java and any relational databases. Responsibilities: - Analyzing and documenting project requirements. -Developing biocomputing algorithms for tools development and data analysis. -Performing biological analysis on data from various domains like gene expression, sequencing , molecular lab. -Co-ordination with sales team on projects to understan

Lockheed Martin is working with researchers at Johns Hopkins University and medical informatics firm Sage Analytica to mine a "unique" set of medical records with the aim of integrating clinical and genomic data for prostate cancer research. The researchers are using Lockheed Martin's rule-based natural language processing platform, called ClinRead, to extract phenotypic descriptors from a set of clinical records tracking 33 men with metastatic prostate cancer for over 15 years before they succumbed to the disease. (Read Full Article)

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

BioTorrents, a website that allows open access sharing of scientific data and uses the popular BitTorrent peer-to-peer file sharing technology. BioTorrents allows files to be transferred rapidly due to the sharing of bandwidth across multiple institutions and provides more reliable file transfers due to the built-in error checking of the file sharing technology. BioTorrents contains multiple features, including keyword searching, category browsing, RSS feeds, torrent comments, and a discussion forum. AVAILABILITY: BioTorrents is available at http://www.biotorre nts.net/ REFERENCE: A complete description of BioTorrents is described in the manuscript at http://www.plosone. org/article/ info:doi/ 10.1371/journal. pone.0010071

Computercraft seeks a highly motivated Molecular Biologist to join the Gene Expression Omnibus (GEO) curation team onsite at the National Institutes of Health (NIH) in Bethesda, MD. GEO is the largest fully public repository for functional genomic data, primarily microarray and next-generation sequence datasets. More information on GEO can be found on the web site http://www.ncbi.nlm.nih.gov/geo . RESPONSIBILITIES: We are currently looking for someone with a background in molecular biology , genomics, or biomedicine that is capable of working with large datasets. This person will be a member of the GEO curation team, helping to review and process incoming data submissions. The successful candidate will work at NIH's National Center for Biotechnology Information (NCBI) in the National Library of Medicine (NLM). The successful candidate will perform the following tasks: - Review and evaluate data submissions for structural integrity and content. - Communicate extensively with rese

BioSLAX is a new live CD/DVD suite of bioinformatics tools that has been released by the resource team of the BioInformatics Center (BIC), National University of Singapore (NUS). Bootable from any PC, this CD/DVD runs the compressed SLACKWARE flavour of the LINUX operating system also known as SLAX . SLAX is becoming the live CD/DVD of choice because of its ability to modularize almost any application and plug it into the system on the fly. The system can also be installed to USB thumb drives or directly to the PC as a regular Linux using the BioSLAX installer provided. It consists of commonly used Bioinformatics Applications, Software and Algorithms. For Download, http://www.bioslax.com/downloads.shtml

Various positions are open at Biocon-India currently (even for fresh graduates) Please go through this link: http://www.biocon.com/biocon_careers_job.asp Submit your resumes at careers@biocon.com Manager Sr Manager/Deputy General Manager - HR Senior Scientist - Process development cell culture-R&D Scientist / Sr. Scientist - RND - ANF Manager / Sr. Manager - Production Sr. Manager - Phamacovigilance Jr. Executive - Production Executive - Production Junior Executive Toxicology

R&D - BioinformaticianReputed client of GlanzHR Services Private Limited Summary Experience: 5 - 10 Years Location: Bengaluru/Bangalore Education: UG - Any Graduate - Any Specialization PG - M.Sc - Microbiology Industry Type: Pharma/ Biotech/Clinical Research Role: Research Scientist Functional Area: Healthcare, Medical, R&D Posted Date: 28 Apr Desired Candidate Profile M Sc. / Advanced diploma in Bioinformatics or Genetics / Biotechnology / life sciences with good bioinformatics knowledge with analytical and reasoning skills,Knowledge of population genetics is a plus.Job Description Analyze genomics data from multip le perspectives to derive new knowl edge,Understand, benchmark&imple ment tools available for above t ask,Develop new genomics data analy sis methods,Understd,implement& maintain quality control Keywords: M Sc. / Advanced diploma in Bioinformatics or Genetics / Biotechnology / life sciences with good bioinformatics knowledge.population genetics is a plus.A