Bio Saga Blog - A Chronicle of Life Sciences & Informatics

A few of Bruker’s top executives will take pay cuts in the range of 10 percent to 25 percent in 2009, the firm reported in a filing today with the US Securities and Exchange Commission. The 2009 salary for Bruker Chairman, President, and CEO Frank Laukien will decrease 25 percent to $318,750 from his 2008 salary of $425,000. CFO and Treasurer William Knight will receive a 2009 salary of $288,000, down 10 percent from his 2008 salary of $320,000. Brian Monahan, corporate controller and EVP of Bruker Daltonics, will receive a 2009 salary of $180,000, down 10 percent from his 2008 salary of $200,000. The firm said in the filing that the salary reductions were temporary, but it didn’t provide any other details. At the end of October, Bruker reported flat third-quarter revenue growth. During its Q3 conference call Laukien noted that beginning this past summer the firm began taking steps to reduce its operating and interest expense and reduce its exposure to currency fluctuations. “We expec...

The Google Datasets Project Comes to An End Google will shutter its highly-anticipated scientific data service in January without even officially launching the product, the company said in an e-mail to its beta testers. Once nicknamed Palimpsests, but more recently going by the staid name, Google Research Datasets, the service was going to offer scientists a way to store the massive amounts of data generated in an increasing number of fields. About 30 datasets — mostly tests — had already been uploaded to the site. The dream appears to have fallen prey to belt-tightening at Silicon Valley's most innovative company. "As you know, Google is a company that promotes experimentation with innovative new products and services. At the same time, we have to carefully balance that with ensuring that our resources are used in the most effective possible way to bring maximum value to our users," wrote Robert Tansley of Google on behalf of the Google Research Datasets team to i...

This comes as a tribute to XML on its one decade milestone! As anyone with kids—or a good memory—knows, when you cross the "double digits" birthday threshold, it’s a big deal. This year, XML crossed this threshold on Feb. 10, and this got me thinking about questions that I might ask this 10-year-old in order to gain perspective on its past and future. I know I’m late, but XML is nothing if not flexible. It assured me that even a belated party is better than none, especially if I invited Alexander Falk, founder and CEO of Altova (its flagship product XML Spy is one of our favorites) and a real XML aficionado ( www.xmlaficionado.com ). I began with this: "XML, you’re much more famous than your parent SGML, and your sibling HTML 4.01 was deprecated in favor of an XML standard, XHTML. Techies worldwide have heard about you, and mighty standards battles have been waged about you. However, growing is easy the first 10 years, but soon you’ll have to be able to point to practic...

VisiGen Biotechnologies , a University of Houston gene-sequencing outfit acquired by Invitrogen in October for $20 million, represents the university’s biggest return on a spinout to date, and could eventually become one of its biggest overall tech-transfer wins, the school said last week. As a result of VisiGen’s acquisition, UH, which held an undisclosed equity stake in the startup, will receive nearly $500,000 from the initial installment of the deal. Plans for follow-on installments were not disclosed. An indirect benefit comes from the fact that approximately half of VisiGen’s current employees are UH graduates, the school said. Several of the scientists that founded the company will now continue to research second-generation sequencing techniques in their UH laboratories. Whether this research eventually sparks additional collaborations between VisiGen and the university is now up to Life Technologies, the biotech tool giant that resulted from Invitrogen’s multi-billion-dolla...

Here is a hand picked item, one of my favorites among the recent blogs that came across. This articles reflects and talks about many things which i have appreciated in the recent times and have blogged in the past web 2.0 .... Why should a (bioinformatics) scientist learn web development ? Up to now bioinformatics research with genomics datasets, has been happening like that: you download the data from a website of a big-iron institution ( NCBI , TAIR ), set them up locally, BLAST ‘em, MySQL’em, parse them with Perl script, and do all other sorts of un-imaginable things. Even though bioinformaticians might be un-aware of the term, part of the local processing that happens with the data is a mashup. This term translates to the combination of pieces of data from different sources, something akin to what has been happening on the web (see also Web 2.0 or programmable web ). In no way this is close to the myriad of Web 2.0 mashups that exist out there, created using APIs offered openly...

University of Pune (UoP), on behalf of Department of Biotechnology (DBT), Government of India, will conduct the BioInformatics National Certification (BINC) examination. The objective of this examination is to certify bioinformatics professionals, trained formally as well as self-trained. Eligibility Graduate in Science, Agriculture, Veterinary, Medicine, Pharmacy, Engineering & Technology are eligible to appear in the examination. They need not have any formal training, viz. certificate, diploma or degree in Bioinformatics. Students in final year of Bachelor’s degree are also eligible to apply. Application and syllabus The online application begins on 1 December 2008 and will continue until 16 January 2009. The examination fee is Rs 600 for general category, Rs 450 for reserved category and US$ 100 for foreign students. Please visit the website ( bioinfo.ernet.in/binc ) for detail information. Syllabus consists of four sections: biology, physical and chemical sciences, IT, and bio...

Let us force the international community to persuade Pakistan to declare that their nuclear arsenals are not any more in state’s control and that any time they may fall in the hands of terror outfits camped in POK and also declare regions infested by terrorist training camps as federally uncontrollable regions. PAK has to pay for this.. The babus are answerable! We will not forget...WE NEED ACTION...The email campaign... Mumbai: We Will Not be Divided. Sign the petition 'Rebuild India' Mission - Article Repository

Ridiculed by some, Gaia theory - the idea that all living and non-living components on earth work together to promote life - is gaining support. Earth is a perfect planet for life but, according to Gaia theory, this is no coincidence. From the moment life first appeared on Earth it has worked hard to make Earth a more comfortable place to live. Gaia theory suggests that the Earth and its natural cycles can be thought of like a living organism. When one natural cycle starts to go out of kilter other cycles work to bring it back, continually optimising the conditions for life on Earth. Named after the Greek Earth goddess, Gaia, the theory was developed in the 1960s by scientist Dr James Lovelock. At the time, Lovelock was working for Nasa, looking at methods of detecting life on Mars. The theory came about as a way of explaining why the Earth's atmosphere contains high levels of nitrogen and oxygen. Initially, Gaia theory was ignored, and then later ridiculed by scientists such as Ri...

In a paper called "Metagenome Annotation Using a Distributed Grid of Undergraduate Students" I just love this title! It's nerdy and cute, all at the same time. Says Sandra Porter . The paper describes a class where students from Marseilles University investigate the function of unidentified genes from a Global Ocean Sampling experiment. All the sequences are obtained from the environmental sequence division at the NCBI . French researchers describe their strategy for teaching undergraduate-level bioinformatics using cutting-edge genomic data and a Web-based learning tool. The students then annotated real metagenomic sequences from the Global Ocean Sampling experiment. "In return for their much-needed help sorting out oodles of DNA data, the undergrads gain a practical knowledge of the work involved in doing bioinformatics and metagenomics, and, most importantly of all, they get to experience what it's like to do real research," says Karen James at the Be...

A team of American and French researchers used systems biology to identify gene signatures predicting human immune responses to the yellow fever vaccine, YF-17D. The work appeared in an advanced online publication in Nature Immunology yesterday. Using high-throughput gene expression measurements, multiplex analysis of cytokines and chemokines, and multi-parameter flow cytometry, investigators tested samples taken from more than a dozen individuals in the days and weeks following their yellow fever vaccination. Computational modeling allowed them to come up with signatures predicting CD8+ T-cell and neutralizing antibody responses to YF-17D — insights into vaccine immunogenicity that may inform future vaccine research and development. “The identification of gene signatures that correlate with, and are capable of predicting, the magnitudes of the antigen-specific CD8+ T-cell and neutralizing antibody responses provides the first methodological evidence that vaccine-induced immune r...

The Computational Biology Unit (CBU) has been established to conduct top-level European research in bioinformatics, and to serve functional genomics research in Norway with relevant training and services. CBU is searching for an additional group leader. The group leader will carry out research in the field of computational biology/bioinformat ics and contribute to the overall objectives of CBU. The group leader should have a PhD and post-doctoral experience including a solid publication record in a relevant subject. Candidates will be evaluated with emphasis on their ability to raise external funding and to supervise and carry out research projects. The research profile of the candidate should be within a relevant area for CBU. Candidates with profiles in direction of systems biology will be preferred. The group leader will direct a research group consisting of Ph.D. and post-doctoral scientists. The CBU and its partners currently have bioinformatics research activities in the fields ...

The first effort to sequence a complete cancer genome has underscored the power of second-generation sequencing while further establishing the lack of a “killer software app” in the field. In the study, published this week in Nature , a team of 48 scientists at the Genome Center of Washington University and elsewhere sequenced a female patient’s acute myeloid leukemia genome and compared it to the genome of her biopsied skin as well as reference genomes to uncover 10 cancer-associated mutations — eight of which were previously unknown. The team used two high-throughput sequencing platforms — the Illumina Genome Analyzer and the Roche/454 FLX platform — and software tools such as Maq, Cross_Match, BLAT, and Decision Tree analysis. The team also did its own scripting and algorithm development in the course of the project, Rick Wilson, director of the Genome Sequencing Center at Washington University School of Medicine, said. The AML sequencing team applied several established soft...

Dr. Justin Sanchez discusses technologies that enable direct brain to computer interfacing, Dr. Justin C. Sanchez , Director of the Neuroprosthetics Research Group, Assistant Professor, Department of Pediatrics, Division of Neurology, Department of Neuroscience, Department of Biomedical Engineering, University of Florida. I really had no idea that the technologies that Justin has developed existed other than in science fiction. The possibilities are endless, and could change everything from computing, to flying planes, to simply changing the channel… Do you want to know more? Listen to Dr. Justin Sanchez! Be a part of the XTractor community. XTractor is the first of its kind - Literature alert service , that provides manually curated and annotated sentences for the Keywords of user preference. XTractor maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies and enables customized report generation. With XTractor the sentences are categorized into ...

Be a part of the XTractor community. XTractor is the first of its kind - Literature alert service , that provides manually curated and annotated sentences for the Keywords of user preference. XTractor maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies and enables customized report generation. With XTractor the sentences are categorized into biological significant relationships and it also provides the user with the ability to create his own database for a set of Key terms. Also the user could change the Keywords of preference from time to time, with changing research needs. The categorized sentences could then be tagged and shared across multiple users. Thus XTractor proves to be a platform for getting real-time highly accurate data along with the ability to Share and collaborate. Sign up it's free, and takes less than a minute. Just click here: www.xtractor.in .

Biomedical Data mining happens to be a long-standing problem in scientific research. Scientists are constantly in search of newer and innovative means to mine biomedical data. Be a part of the XTractor community. XTractor is the first of its kind - Literature alert service , that provides manually curated and annotated sentences for the Keywords of user preference. XTractor maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies and enables customized report generation. With XTractor the sentences are categorized into biological significant relationships and it also provides the user with the ability to create his own database for a set of Key terms. Also the user could change the Keywords of preference from time to time, with changing research needs. The categorized sentences could then be tagged and shared across multiple users. Thus XTractor proves to be a platform for getting real-time highly accurate data along with the ability to Share and ...

Ask XTractor - XTractor™ now turns ON its ‘Insta Search’. Get a snapshot of the XTractor data for your desired query using the Insta Search feature. Which are the biological processes involved in Leukemia? What are the drugs associated with Ovarian Neoplasm? What are the diseases modulated by FRAP? Then get a snapshot of the XTractor data from the latest published abstracts on your questions using the 'Insta Search' feature. Be a part of the XTractor community. XTractor is the first of its kind - Literature alert service , that provides manually curated and annotated sentences for the Keywords of user preference. XTractor maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies and enables customized report generation. With XTractor the sentences are categorized into biological significant relationships and it also provides the user with the ability to create his own database for a set of Key terms. Also the user could change the Keywords...

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 ...

US FDA , NIH , NCI , MD Anderson , Harvard Medical School , Novartis , Wyeth , AstraZeneca , Vertex , P&G , JNJ many more subscribe to XTractor. “XTractor™ is an intelligence that works so unconscious even for the users to perceive. It is fascinating as to how quickly XTractor transforms the most complex scientific facts into structured knowledge almost instantaneously by bringing about cross entity relationships across abstracts thereby aiding in quicker decision making through the Drug Discovery process” Bangalore, India, October 12, 2008 --( PR.com )-- Indian Life Sciences Informatics Company, Molecular Connections announced today, that its XTractor™ - The first of its kind scientific literature alert service launched in July ‘08 has built a user base of over 900 users form more than 150 premier organizations. XTractor™ has been widely accepted and received well in the scientific fraternity both the academia and the industry across the globe. Be a part of the XTractor commun...

I am off to HGM 2008 HUGO 's 13th Human Genome Meeting Hyderabad, India Sat 27- Tue 30 Sep 2008 Hope to meet many of you there and BioSaga will be back in action form October Be a part of the XTractor community. XTractor is the first of its kind - Literature alert service , that provides manually curated and annotated sentences for the Keywords of user preference. XTractor maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies and enables customized report generation. With XTractor the sentences are categorized into biological significant relationships and it also provides the user with the ability to create his own database for a set of Key terms. Also the user could change the Keywords of preference from time to time, with changing research needs. The categorized sentences could then be tagged and shared across multiple users. Thus XTractor proves to be a platform for getting real-time highly accurate data along with the ability...

Blogging about curation in the past several issues have been discussed but here is something very critical. To thrive, the field that links biologists and their data urgently needs structure, recognition and support. Biocuration , the activity of organizing, representing and making biological information accessible to both humans and computers, has become an essential part of biological discovery and biomedical research. But curation increasingly lags behind data generation in funding, development and recognition. Three urgent actions to advance this key field. First, authors, journals and curators should immediately begin to work together to facilitate the exchange of data between journal publications and databases. Second, in the next five years, curators, researchers and university administrations should develop an accepted recognition structure to facilitate community-based curation efforts . Third, curators, researchers, academic institutions and funding agencies should, in the ...

Well it so exiting to watch how man makes his future ... The future, always so clear..., had become like a black highway at night. We were in uncharted territory now, making up history as we went along. The future is not set, because we control what happens through the choices we make . The GATTACA era is not far off. 23andMe has dramatically slashed the price for its service and expanded its offerings to include a lineage tracing service through a partnership with Ancestry.com. In a statement today said that by cutting the price for its genotyping service from $999 to $399 it is “democratizing personal genetics and expanding the opportunity for more people to benefit from the genetic revolution.” The company said advances made to Illumina’s genotyping technology , specifically the introduction of the HumanHap550-Quad+ BeadChip , made the price cut possible. Illumina is the provider of genotyping tools for 23andMe’s services. 23andMe also said that beyond the new ancestry ser...

Social networking is the latest buzz on the internet. You’ve heard about it, but what does it mean to you as a scientist? Well for one thing, it means that networking has never been easier. Here are six of the best social networking sites for scientists that are designed to help you make and maintain your professional contacts. 1. SciLink is a souped-up networking site that actually knows who a lot of your contacts will be before you even sign up. Uniquely, SciLink mines literature databases to build a network of professional relationships that you can slot into (and of course expand further) when you sign up. You can also find jobs, discussion, news etc on the site. 2. MyNetResearch is a powerful website for finding collaborators for your project. You set up your own account/profile and build a network of contacts as with the other social networks but MyNetResearch is designed to help you find people who work in the areas you are interested in (or interested in expanding into) and ...