Semantic Search Engine for PubMed- Microsoft Vs Yahoo Vs Google Vs Oracle in Semantic Web Search

Hakia is a semantic web search engine, so what you might think. The difference is hakia targets legal, financial and Medical web searches. Thye have even licensed its technology to a startup company that summarized information for government and pharmaceutical companies

There is more starting from April 2008 using Hakia you can search Pubmed. Adding more than 10 million abstracts from PubMed to their index and setting up a new site dedicated to searching this content at pubmed.hakia.com. The PubMed content will also be visible in search results on the hakia medical search site and via the main hakia search page

For exmaple my query of microarray software Pubmed returned 1646 results and Hakia 15 some times having too much is not good idea, especially when you are looking for specific text.

It doesnt even stop there, the result also showed me Meet Others who asked same query in PubMed Semantic search with the option to even add a post so I found a job for part-time employee to work in a microarray lab. This I think is a great tool especially if more people use it you can use the feature to locate people working on similar topic. Ofcourse you can any of the much known social tools like Linkedin

Still not convinced of the merits take a look at the comparison of the search results on new regulatory problems affecting personal genomics companies, in google and Hakia

You can also generate a custom seach box that can be added to your website much like the custom google search box .

and yes there is competition to Powerset has launched its

May be because Yahoo is already offering Semantic webs earch using

But there is more than what meets the eye. Remember Interestingly in 2007 June Oracle staked its claim to leadership in the enterprise side of the emerging semantic Web space, saying that more than 100 commercial and open-source applications are using its version of the technology. Oracle do offer search called Oracle Secure Enterprise Search. Take a look at the Oracle Semantic Technology Centre

Microsoft can also say to be making up for the loss of TripleHop to Oracle,

There is still more surprises Evri.com a Paul Allen backed semantic search engine has launched a Beta release in June 24.

Other similar service providers includes TextDigger, Radar Networks Peer39.com that offers semantic technology in advertising, Gloofi.com Twine, then there is Spock calling itself a vertical search engine for people, usign top-down semantic search. In that sense we can call Google Maps to be using semantic technology though it cant be called a thorough breed in this field

Entire Genome Sequencing from Single Molecule DNA

Cambridge based Helicos Bioscience announced the publication of a report in Science Magazine demonstrating the first single molecule sequencing of an organism (M13 virus genome) examining more than 280,000 strands of captured DNA.

Helicos’ uses a proprietary form of sequencing-by-synthesis called True Single Molecule Sequencing(tSMS)™. Unlike other methods, the technique builds up the sequence of each strand of DNA one base at a time.

Microarray Blog is on The Science Advisory Board

After a brief hiatus am back to work, Microarray blog is chugging along slowly though I get very less time now a days to write , I have no plans to stop the blog. But reaching out to more people is an issue If I cant post atleast once a week.

Still I am going to take the challenge of writing another blog this time on the The Science Advisory Board website for microarray. Am happy the folks at SAB are using wordpress platform, so no hickups there.

I am going to maintain both the blogs for a while and perhaps spend more time on this blog on other subjects that I am interested in bioinformatics other than microarary such as Pharmacogenomics, Clinical genomics, SaaS in bioinformatics, Opensource and Adoption of technology among biologists to name few.

The new post in microarray is available at http://microarray.scienceboard.net

CombiMatrix Molecular Diagnostics Launches Microarray Test for Detection of Autism Spectrum Disorder

CombiMatrix  has completed the clinical validation of the  BAC array CGH based clinical microarray tests. ATScan is designed to detect known genomic copy-number variations  associated with Autism Spectrum Disorder and this test is now available to physicians and consumers.

Silicon Microarray technology receives award for application product of the year 2007

Parallel Synthesis Technologies’s Silicon Microarray technology has received the Small Times 2007 Best of Small Tech Award for application product of the year. NanoCon International conference

Silicon Microarray technology is a set of micromachined silicon pin tools for printing DNA or protein microarrays.

The identically micromachined printing tools, which can produce microarrays containing up to 50,000 highly uniform spots (about 250 picolitres each) of DNA on a 25x75mm substrate, are substantially less expensive than traditional technologies.

The Staphylococcus aureus microarray Database inching closer to Staph Infection Vaccine

MRSA the very name send shudders to any one working in a hospital setup, the aggressive Methicillin-resistant Staphylococcus aureus (MRSA) , is a bacterium responsible for some difficult-to-treat infections in humans.

The organism is often the cause of community-acquired MRSA (CA-MRSA) or hospital-acquired MRSA (HA-MRSA) depending upon the circumstances of acquiring disease,

University of Southern Mississippi biological science professor Dr. Mohamed Elasri and student Vijayaraj Nagarajan, a doctoral student have developed an online database that holds collected data on genes related to stap.The Staphylococcus aureus microarray meta-database, known as SAMMD

There are more than 400 SAMMD users from 23 countries with numbers increasing daily. As researchers work to find a vaccine for MRSA, Elasri said this program can cut a significant amount of time it takes to find information about staphylococcal genes

microarray-based Clinical diagnostic tests

 Pathwork Diagnostics, and the Virginia Commonwealth University School of Medicine has initiated an investigational study Genomics-Based diagnostic Test to determine a tumor’s origin so that tissue-specific management can begin.

The test uses microarrays from Affymetrix

More news on Pathworks website 

New Microarray technology replacing PCR and speed up HTS

Dr. Richard Gibbs, director of the Baylor College of Medicine Human Genome Sequencing Centre and his researchers along with the help of  NimbleGen Systems the  company recently acquired by Roche Applied Science has developed a new technique that combines gene chip technology with the latest generation of gene sequencing machines to allow fast and accurate sequencing of selected parts of the genome

 The technology, called “sequence capture,” enables fast and accurate enrichment of thousands of selected genomic regions, either contiguous or dispersed, such as segments of chromosomes or all genes or exons uses , The study had uses NimbleChip™ microarrays in preparation for a high-throughput 454 Sequencing™.

The study Direct Selection of Human Genomic Loci by Microarray Hybridization presented on October 10, 2007, at the J. Craig Venter Institute’s Genomes, Medicine, and the Environment (GME) conference, Roche NimbleGen and 454 Life Sciences, working with Dr. Richard , will create a whole-genome human exome (all exons) microarray, with the goal of resequencing the entire human exome faster and cheaper.

Till now researchers relied upon PCR for selection of specific genomic regions for resequencing

Limitations of PCR  meant the length of sequence it can amplify was small, is difficult to scale or multiplex for the enrichment of thousands of fragments, and has limited performance in the repetitive regions typical of complex genomes, such as human.

The sequence capture microarray technology bridges the gap between next-generation DNA sequencing technology and current sample preparation methods by providing an adaptable, massively parallel method for selective enrichment of genomic regions of interest.

The new process is simpler, more accurate and efficient than the multiplex PCR . In one experiment, more than 6,400 exons (the part of the genetic code that carries the instructions for making proteins), were analyzed. Using the old technology this would have taken at least six months.

A new strain of virus named after Washington University

A new strain of virus has been identified by the medical school and named the “WU” virus after Washington University.

The virus, a type known as a polyomavirus, is closely related to two others, JC and BK, which attack the nervous system of HIV patients and cause kidney transplants to fail, respectively.

The virus has been reported in such geographically disparate countries as the United States, Australia, Germany and Korea, according to Gardner.

In fact, the first samples of the then-unknown WU virus came from the University of Queensland in Australia.

The samples were sent to the University because the school has ViroChip, a sophisticated pan-viral DNA microarray. This tool allows scientists to quickly screen viral samples and compare their structure to more than 22,000 known viruses. It was instrumental in distinguishing SARS from known viruses during the 2003 outbreak

David Wang, a University professor who leads the research team, states that the WU virus has unique properties unlike either of the others and he questions if it even is a human pathogen.

The scientific article is published at PLOS Identification of a Novel Polyomavirus from Patients with Acute Respiratory Tract Infections

Transposon insertion site profiling chip (TIP-chip)

Transposon insertion site profiling chip (TIP-chip) was invented by Researchers at the Johns Hopkins’ High Throughput Biology Center. Tip-chip can be used to help identify otherwise elusive disease-causing mutations in the 97 percent of the genome long believed to be “junk.”

TIP-chip (transposable element insertion point) can locate in the genome where so-called jumping genes have landed and disrupted normal gene function. This chip is described n the Proceedings of the National Academy of Sciences. the article titled Eukaryotic Transposable Elements and Genome Evolution Special Feature: Transposon insertion site profiling chip (TIP-chip

The most commonly used gene chips are glass slides that have arrayed on them neat grids of tiny dots containing small sequences of only hand-selected non-junk DNA. TIP-chips contains all DNA sequences. Because each chip can hold thousands of these dots – even a whole genome’s worth of information – scientists in the future may be able to rapidly and efficiently identify, by comparing a DNA sample from a patient with the DNA on the chip, exactly where mutations lie.

Jef Boeke, Ph.D., Sc.D, professor of molecular biology and genetics and director of the HiT (High Throughput Biology Center), who spearheaded both studies at the Institute of Basic Biomedical Sciences at Hopkins, and his team have focused particularly on transposable elements, segments of DNA that hop around from chromosome to chromosome.

These elements can, depending on where they land, wrongly turn on or off nearby genes, interrupt a gene by lodging in the middle of it, or cause chromosomes to break. Transposable elements long have been suspected of playing a role vital to disease-causing mutations in people. Boeke hopes that the TIP-chip eventually can be used to look for such mutations in people.

The new TIP-chip contains evenly sized fragments of the yeast genome arrayed in dots left to right in the same order as they appear on the chromosome. Boeke’s team used the one-celled yeast genome as starting material because, unlike the human genome, which contains hundreds of thousands of transposable elements of which perhaps a few hundred are actively moving around, the yeast genome contains only a few dozen copies.

Like a word-find puzzle, where words are hidden in a jumbled grid of letters, the TIP-chip highlights exactly where along the DNA sequence these elements have landed. By chopping up the DNA, amplifying the DNA next to the transposable elements and then applying these amplified copies to the TIP chip, the researchers were able to map more than 94 percent of the transposable elements to their exact chromosome locations.

double-tiled DNA chip 

Standard chips contain one layer of DNA dots that read from left to right, like the across section of a crossword puzzle. Boeke’s new double-capacity chips hold two layers of dots, a bottom layer that reads across and a top layer that reads down, again using the crossword analogy. So if their experiment lights up a horizontal row of dots, the researchers learn that the data maps to the region of the genome contained in the bottom layer; likewise, if the experiment highlights a vertical row, the data correspond to the top layer.

Says Boeke, “It’s so easy to differentiate the top and bottom layers. Next we’re going to try adding another layer reading diagonally” to triple the amount of genomic information packed onto the tiny chips.

Authors of the TIP-chip and double-tiled DNA chip papers are Sarah Wheelan, a new faculty member in the Department of Oncology, Lisa Scheifele, Francisco Martinez-Murillo, Rafael Irizarry and Boeke, all of Hopkins.

Affymetrix and Illumina in war path again as fresh patent litigation on microarray patents

Illumina and Affymetrix have been in a patent battle since 2004. In its second wave of patent infringement litigation cas against illumina filed in UK, Germany and US, Affymetrix has targeted technology offered by Solexa, the company acquired by Illumina in January 2007, as well as all of Illumina’s BeadArray(TM) products.

The new case is for patents 5,902,723, 6,403,320, 6,420,169, 6,576,42, 7,056,666, 0834575, 0853679, 0799897

Affymetrix previously sued Illumina for patent infringement in 2004 in the United States District Court for the District of Delaware. In March 2007, the jury returned a verdict in favor of Affymetrix.

Affymetrix has developed one of the industry’s strongest patent portfolios, featuring more than 400 patents granted in the U.S. and more than 40 patents granted in Europe.

More details on the case is available at Affymetrix Investor Website

Things have improved for Affymetrix this year, The company has aposted Q3 profits with the company’s revenues for the quarter increasing 12 per cent to $94.9m compared with $84.7m during the same period last year.

The results of these lawsuits could dramatically change the face of the DNA microarray market that has seen such growth due to the application of genetic information to drug discovery and ‘personalised medicine’.

 

Online Drug Discovery Database Launch

Assay Depot is claiming to become an on-demand” drug discovery services. The company is has launched Internet marketplace for the pharmaceutical services industry. By acting as a single point of contact between drug researchers and research service providers, the Assay Depot dramatically improves the efficiency of drug discovery research and, ultimately, helps deliver better and safer drugs to market. By bringing the true benefits of outsourcing to the pharmaceutical industry

The San Diego company has raised $ 1.8M of funding from private finanical firms. CEO Kevin Lustig has also been the Co-Founder and Research Direcotr at Kalypsys

Microsoft Research, HIV, SPAM – MS anti-spam techniques help research HIV vaccines

Ever heard of the Teiresias algorithm, for spam detection developed by Chung-Kwei at IBM – the algorithm was developed in the bioinformatics group of IBM to detect patterns in DNA

This algorithm is tested for SPAM detection- discussed in my  my earlier bioinformatics post

So you may be wodering whats thats got to do with this post, OK I am coming to it- 

Microsoft is helping  David Heckerman a Physician with a PhD in computers with spam-blocking team at Microsoft Research, to find drugs for HIV, by learning from how Anti SPAM softwares works

An e-mail featuring “Viagra,” for example, was a good bet to be spam–but things got complicated in a hurry.

if spammers saw that “Viagra” messages were getting zapped, they switched to V1agra, or Vi agra. It was almost as if spam, like a living thing, were mutating

This parallel between spam and biology got the attention of David Heckerman

Bill Gates, the company chairman “got really excited,” Heckerman says. Well versed on HIV from his philanthropy work, Gates lined up Heckerman with AIDS researchers at Massachusetts General Hospital, the University of Washington, and elsewhere.

Since then, the 50-year-old Heckerman and two colleagues have created their own biology niche at Microsoft, where they build HIV-detecting software. These are research tools to spot infected cells and correlate the viral mutations with the individual’s genetic profile. Heckerman’s team runs mountains of data through enormous clusters of 320 computers, operating in parallel. Thanks to smarter algorithms and more powerful machines, they’re sifting through the data 480 times faster than a year ago. In June, the team released its first batch of tools for free on the Internet.

watch the video to learn more about the work

Microsoft Research, Indian Institute of Science Collaborate

Microsoft Research announced a sponsored research and collaboration agreement with the Indian Institute of Science (IISc) in Bangalore, India, to accelerate the scientific discovery process by increasing computational power in scientific and engineering research. This is the first agreement Microsoft Research has signed in India as part of a global effort to collaborate with leading institutions around advanced computing for science and engineering. Under this agreement, Microsoft Research has committed to providing funding and research expertise to assist with major projects around life sciences research and advanced high-performance computing platforms based on Microsoft Windows Compute Cluster Server 2003 for scientific applications, such as modeling of the Indian Ocean in the coming two to three years.

Professor Nagasuma Chandra, on the faculty of the Bioinformatics Centre at IISc, will be the principal investigator collaborating with Microsoft Research India for the biological data mapping project. The goal of the project is to create research tools for integration of various biological data, leading to greater understanding of biological systems as well as facilitating ready applications in many stages of drug and vaccine discovery.

Prof. R. Govindarajan of Supercomputer Education and Research Centre at IISc will lead the second project on high-performance applications using commodity clusters.

Gene Logic sells in genomics division

It hardly a week I have wrote about acquisition and mergers , it seems the rain is noit going to stop any time soon, the latest one , to give away the home plate is Genelogic agreeing to sell its genomics division to India HQ Ocimum Biosolutions subject to the authorization of the transaction at a special meeting of shareholders of Gene Logic.

This is a transforming event of significant strategic proportion,” said Charles L. Dimmler, III, President and Chief Executive Officer of Gene Logic.

Genelogic bought its preclinical division from TherImmune, a Gaithersburg company, in April 2003 for $51 million which was sold to Bridge Pharmaceuticals for $15 Million,

Gene Logic Inc said it agreed to sell its Genomics assets to Ocimum Biosolutions Ltd for $10 million in cash. Under the terms of the Ocimum sale agreement, Gene Logic retains full rights in perpetuity to utilize the existing information data bases of its former Genomics business as key elements in building its emerging drug repositioning and development business. Furthermore, the Company will retain specified assets related to molecular diagnostics and will continue to explore strategic alternatives for these assets

The sale is part of the Genelogic new strategy to focus on to build drug repositioning and development business which was decided last year.

Ocium will assume certain liabilities associated with the Genomics assets and business and will pay Gene Logic $7 million at closing and $3 million payable in a promissory note due 18 months from closing.

The purchase includes Gene Logic’s Knowledge Products business including the The BioExpress® System a continually growing genomic database of gene expression data and associated clinical information from over 18,000 human and animal tissues and cell line samples. ToxExpress® a toxicogenomics reference database.

Ocimum will continue to operate the business out of the current state-of-the-art laboratory facility of Gene Logic in Gaithersburg, Maryland.

Mergers Acquisitions Consolidation-Microarray Industry bubble in making- The days are numbered

Bioinformatics promise has already had its brush with plenty of resistance, not it seems the time for microarray industry with consolidation and acqusitions and megers announced almost every week. The slow adoption and too many fragmented with disparate standards has made the industry a victim of its own success.

the new kid on the block to unload its microarray and genomics business include Nanogen with its plans to unload its loss making microarray business, While the most of the biotech IPO featured in the market in the last 6 month in US have failed to generate expected results.

But pharmaceutical firms are racing to buy up biotech firms Roche has acquired 454 Life science,and Nimblegen and now Bristol-Myers Squibb is buying Adnexus Therapeutics for $430 million. Wyeth has bought Haptogen Ltd, which emerged from Aberdeen University five years ago, pharmaceutical firm Wyeth is the fourth largest biotechnology company in the world. PerkinElmer is planning to buy the cord blood banking firm Viacell Inc

On the the report of Bradstreet Israel warning on Sunday that majority of Israel’s publicly-traded biotechnology companies will be forced to halt their research and development activities in as little as two-and-a-half years if they do not alter their business strategies immediately, research company Dun & In many cases, biotech companies are not doing sales, but only conducting research programs,” said Reuven Kuvent, director-general of D&B Israel. “They don’t focus enough on raising capital or attracting investor things they must do if they intend to continue to be operational over the next few years.”

While Asian genomics and biotech companies like Biocon which recently sold its enzu=yem business to NovoZyme and Strand Genomics which was selected as TECHNOLOGY PIONEERS 2007 by World Ecconomic Forum and smaller startups like Ocimum Biosolutions which are now pumping vast amount of funds into acquiring genomics business across US and Europe are waiting inthe wings to take off . Still there are others racing to create the cheapest microarray and sequencing methods only time will tell theeir fate,

Oracle Openworld 2007- Personalized Genomics session

Its the time -Personalized Genomics

Advances in genetic information and laboratory technologies mean new ways to diagnose disease and determine patient risk. The wealth of genetic information makes it harder to provide meaningful information. During Oracle OpenWorld 2007 Oracle is presenting how laboratory information systems principles and Oracle customer relationship management and enterprise resource planning applications weave together, using Oracle Fusion Middleware to create a unique platform for translational medicine.


Click here to register now.

Oracle OpenWorld

Experience Innovation. November 11-15, 2007, San Francisco, Moscone Center.

As the Life Sciences industry continues to grow and change, Oracle is there to help you learn, adapt, and succeed.

Please join us this fall in San Francisco as we address some of the biggest challenges facing the Life Sciences industry and how Oracle is prepared to meet those challenges.

Session highlights include:

  • Product Lifecycle Management—At this session, learn how Oracle’s Agile product lifecycle management solutions for Life Sciences improve new product introduction cycle times, reduce direct material and operating costs, and enable cost-effective compliance.
  • A Cure for Clinical Trials: From Data Capture to Submission—Approximately 80,000 clinical trials are being conducted in the United States at any given time. More than half of them are behind schedule by one to six months. Clinical trial sponsors hope to reduce this and other costly delays through the use of IT. Hear how the latest enhancements in Oracle’s industry-leading Life Sciences applications are streamlining the process of data capture, management, analysis, and reporting.
  • Enabling Personalized Medicine in Research and Development—The sequencing of the human genome is yielding exciting new tools to help physicians tailor treatments to individuals and their diseases. This powerful new capability, called personalized medicine, holds great potential to improve patient health. Learn how Oracle’s technology is enabling personalized medicine and improving efficiencies and outcomes in clinical development.

Click here for a full list of Life Sciences sessions.

Registration is now open for the most exciting technology and business conference of the year.
Registration fees go up soon So don’t wait—act now to save $900.

Click here to register now. To receive your special discount, select a registration category and enter keyword: ORF at the bottom of step 2 of the registration process.

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Copyright © 2007, Oracle Corporation and/or its affiliates. All rights reserved.  

Scholarly publishers throws out Microsoft

After PLOS nature its the turn of microsoft, Life science researchers are in no mood to relent to industry’s interests.

Microsoft’s latest Word release has caused chaos in scholarly publishing circles. Submit a paper to, the journal Nature in Word 2007, and you will face the following warning:

We currently cannot accept files saved in Microsoft Office 2007 formats. Equations and special characters cannot be edited and are incompatible with Nature’s own editing and typesetting programs.’

And it’s not just Nature. Try Science, The Lancet and pretty much any ‘mathematics-intensive’ journal in the world and you will hit the same problem

Science and Nature will no longer accept manuscripts written in Microsoft’s Office 2007 suite. because the latest version of Word is no longer compatible with Mathematical Markup Language (MathML), the de facto standard for writing equations in text documents, according to recent notices posted on the Web sites of both Science and Nature journals. In Office 2007, Microsoft’s own Office MathML (OMML) is used for equations.

And it doesnt end there Microsoft and Sun and open world society are up in arms against each other on adoption of Open Source Document Format. Microsoft supports OOXML and Sun supports ODF (Open Document Format alliance)  which also is enjoying widespread support from academia and corporates like Oracle, IBM, Red Hat, Sun Microsystems, Google

India’s  21-member technical committee decided that India will vote a ‘no’ against Microsoft’s Open Office Extensible Mark Up Language (OOXML) standard at the International Standards Organisation (ISO) in Geneva on September 2.

Laying with the Lions

The following article is one of the best I just came across which talkes about advantages of better collaboration in pharma companies.

 

The study and articles are on Act Magazine website

 

DNA test results in three days, or Money Back

IDENTIGENE Becomes First DNA Testing Lab to Promise Fast Results with a Money-Back Guarantee . The company now Now Offers the Industry’s First Money-Back Guarantee, together with a Three-Day Turnaround on Results

the website says IDENTIGENE is the only DNA testing lab with a money-back guarantee

 

 

 

 

 

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