IBM wants to sweeten chocolate the genomic style

Dont get your imagination run wild, you IBM machine not going to make Chocolates. Mars and IBM are to combine scientific and research resources with the US Department of Agriculture-Agricultural Research Service (USDA-ARS) in an attempt to sequence and analyse the entire cocoa genome.

IBM said in a statement that the combined effort could benefit more than 6.5 million farmers worldwide and help sustain the supply of chocolate

IBM has produced a video promotion of the Cocoa Genome project which is available on YouTube

Does Firefox 3 have better memmory usage compared to Opera 9.5- !

Since its record setting release day a lot has been written about Firfox3. And many said it has better memmory usage. Firefox 3 engineer Pavlov says Fiefox 3 has better memmory utilization, and I have looked at every blog and website that talked about how Fiefox 3 is better is terms of memmory use.

So I am surprised to see that in my office PC( IBM, Machine with Pentium 4 and 1GB RAM, WinXP)  opening google home page using an ultra high speed Corporate internet connection in opera 9.5 and Firefox 3.  Firefox raking in more memmory compared to Opera. I’m a big fan of Firefox because it’s so easy to customize, and have been using it for many years. and use it even in the office despite most of our internal applications not working on it, ofcourse I use a lot customizations.

Some How the final release uses more memmory compared to Opera and freezes more often while opening more than 10 or pages. Ofcourse I was not using any extensions while testing Firefox 3 vs Opera9.5

And acording to CNET also opera takes less memmory compared to Firefox 3

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 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

Semantic search startup Hakia June 19 made its Syndication Web Services APIs available to search engine marketing or publishing businesses and others that want to provide their users with better ways of finding information. The XML search option and feed syndication search servicces are certinaly good

Hakia is offering 30,000 free (and advertising-free) searches per day to early adopters until the partners’ quota is filled.

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 first product May 12, a search engine focused on finding articles on Wikipedia. And there is roumor that Microsoft will acquire Powerset Semantic Search engine very soon for nothing less but USD 100M

May be because Yahoo is already offering Semantic webs earch using through its SearchMonkey platform

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

Genetic testing impacts life insurance policies

The Association of British Insurers (ABI) has suspended the use of predictive genetic testing until the year 2014. allowing consumers to continue taking out cover without disclosing the adverse results of tests to predict a predisposition to cancer or heart disease.

Does that mean they will discriminate us later

Did they never heard of Genetic Information Nondiscrimination Act (GINA) the rule signed by US prsident with the intention of that will protect Americans against discrimination based on their genetic information when it comes to health insurance and employment.

Stephen Haddrill, the ABI’s Director General, said:

“The moratorium on the use of predictive genetic test results works well for consumers. It means people can insure themselves and their families, even if they have had an adverse result from a predictive genetic test. The moratorium has proved effective since its introduction in 2001 and can now continue

The moratorium was established in 2001 and covers policies worth up to £500,000 for life insurance, £300,000 for critical illness insurance and £30,000 a year for income protection insurance. The extension leaves consumers free to apply for cover up to these levels without advising an insurance company of the adverse results of any predictive genetic test they have taken.

According to the ABI, around 3% of policies sold in the UK are above these limits and in these cases, insurers can request predictive genetic tests but only if the tests are approved by an independent Government committee.

So far, the only test that has been approved in this way is for Huntington’s disease, for life cover over £500,000.The ABI has updated its consumer guide “Insurance and genetics: what you need to know”, which can be downloaded from its website. It will commence the next review of the moratorium in 2011

Deadline for Personal Genomics Companies

State of New York has issues warning against Personal genomics companies , after they have received many complaints. Now the State of California Department of Helath (CDPH) is trying to keep consumer genetic testing companies from offering their services to the state’s residents and last week sent letters to 13 firms saying they are violating state law. The companies have time till today June 24 to respond to the notice. While New York State warned several companies that genome tests could not be performed on samples from New York residents without formal state approval.

CDPH requirements mandate that

1. Any business offering genetic tests to California residents must be licensed as a clinical laboratory in California
2. The laboratory must have must have a CLIA certificate for laboratory testing
3. All genetic tests must be ordered by a licensed physician

The 3rd part of the requirements mean the end of DIY genetic testing and more headches for companies in coming weeks.

Google-backed 23andMe and Navigenics are also included in the list of companies that received the notice The major companies, including 23andMe, Navigenics, and Decode Genetics have issued statements confirming that theya re using CLIA registered laboraotries for the testing DNA genotyping. 23andMe partners with Illumina, while Navigenics collaborates with Affymetrix.

Steven Murphy compared these companies to napster check out his blog post1 post2 on this subjetcs. He is certainly not likely to be excited to learn that 23andMe has launched a wiki page called 23andWe to recruit its customers to participate in studies trying to shed additional light on genetic predispositions for certain diseases and adverse drug reactions.

23andMe has maintained that it is not selling a medical service but rather giving people access to their genetic information. They company prefers to call its 23andWe study participants “customers” and not “patients,” . Smart move but lets see if CDPH is going to buy that argument.

But today 23andMe shot back to CDPH that they’ll be doing neither cease nor desist. We believe we are in compliance with California law and are continuing to operate in California at this time,” the company said in a statement released to Wired.com

The company has has argued that the testing they provide isn’t a prevention aid, but merely offers “individuals contextual information about their genetic makeup, including ancestry and applicable scientific research.”

No one wants to believe Carl Icahn’s offer of $15 B for Biogen- even when he says he will increase R&d Spending

CNN once referred him as shrewdest investor on the planet. Carl Icahn who is now in the eye of storm for his involvment to throw the board of Yahoo for rejecting bid offer from Microsoft. The Billionaire corporate raider has made a beeline for the Lifescience Industry.

Carl Icahn, embroiled in a proxy battle with Biogen Idec, offered to pay as much as $15 billion last year for the company, the largest maker of drugs for multiple sclerosis. This week his move to throw out the board of Biogen has been rejected by shareholders as they voted in favor of the biotech’s own slate of directors instead of those nominated by activist investor Carl Icahn.

Seems like no one wants to believe him when he says he will pump in more money into R&D. Really?

according to a memo to shareholders filed today with the ( SEC) Securities and Exchange Commission. Icahn wants to boost spending on research and development, improve employee morale, mend relations with partners, and possibly cut expenses outside research,

In the biggest biotechnology deal of 2007, Icahn pushed MedImmune Inc. to sell itself to London-based AstraZeneca Plc for $15.2 billion

Why Pfizer planning a $5B USD counter bid for the largest Indian branded generics

While Invitrogen is making news merging into Applied Biosystems, with its $ 6.7 B USD deal creating the first of its kind of company, that can boast to own and invade every sphere of biological research from wet lab to information systems.

Pfizer is planning to counter bid the $4.6 billion offer by Japan’s Daiichi Sankyo Co Ltd  for the Indian generic drug maker Ranbaxy Laboratories Ltd. Ranbaxy has been a thorn in the big pharma fight against, generics and branded generics. Reason Ranbaxy just got FDA approval–and 180-day exclusivity–to sell a copycat version of Pfizer’s cholesterol lowering drug lipitor beginning in March 2010. Why should  lose all that cholesterol-drug revenue when, with a buyout, it could recapture it?

Raising fears that Indian companies that supply WHO and other World Organizations with cheap medicine will go under the hammer of Big multinationals, prompting hike in prices of drugs for treating  AIDs to cancer, cholestrol , hyper-tension or even antibiotics to fight infections, whose prices are the lowest in the world . Perhaps the era of cheap drugs may be over.

India is the biggest supplier of cheaper versions of essential drugs to the developing world and has a share of nearly 25% in the overall generic space. Domestic generic biggies particularly Ranbaxy and Cipla have been recognized globally, not only for their low-cost medicines, but also of their ability to produce quality medicines.

For instance, Cipla offers a first line AID Medicine which is a combination of three drugs, at a price of $100 per patient per year as against the MNC tag of $10,349, a huge reduction of over 100 times.

Microarrays in Personalized Medicine- $200M-US Aided Personalized Medicine Program

I have written quiet often about this subject and companies that promises solution for personalized medicine. especially the use of genomics information in organ transplant patients and cancer treatment. XDx and Genomic Health are two such companies . XDX has applied microarray, to monitor the immune system, with the help of Gene expression to address the challenge of balancing the risk of acute cellular rejection against the known adverse effects of immunosuppressants; especially inexpression testing for patients with heart transplants. Genomic Health provides individualized genomic profiling of tumor tissue may help improve cancer management.

personalized medicine is still dismissed of by many as the cost are still high, and there are very few trained physicians who can use this extra information for better clinical outcome.

US institutes Biodesign Institute at Arizona State University, Fred Hutchinson Cancer Center Translational Genomics Research Institute (TGen), the Institute for Systems Biology, and the Partnership for Personalized Medicine will help the government of Luxembourg start a three-pronged, $200 million-plus biomedical initiative focused on harnessing genomics technologies to study human health problems.

For those who wants to cry foul that genomic information can lead to discrimination against individuals by insurance companies or others can take solace on GINA . In may 21.2008 President  George Bush has signed into law the Genetic Information Nondiscrimination Act (GINA) that will protect Americans against discrimination based on their genetic information when it comes to health insurance and employment.

The most immediate benefit of GINA is to remove barriers to identifying individuals at high risk for diseases due to genetic mutations before the onset of the disease

Physician digital marketing & sales trends webcast

Taking the Pulse® U.S. — Physicians and Emerging Information Technologies, is a syndicated multi-client physician research study and advisory service focused on understanding technology adoption and integration trends among U.S. practicing physicians. Now in its seventh year, the primary objective of the research study is to track which technologies physicians have adopted, how they are currently using them, and how they plan to use them in the future.

Taking the Pulse® v8.0 was fielded in Q1 2008 among 1,832 practicing U.S. physicians. Covering subjects that ranges from

• General Access and Technology Profile: Practice technology profile, frequency of Internet use, frequency of professional activities online
• Online and Offline Professional Information Sources: Online and offline information sources used, including textbooks, journals, CME, reps, search engines, sites visited, conditions researched
• Detailing and Pharma Services: eDetailing participation and future interest, use and interest in full-service portals, product and corporate site visitation, rep technology usage
• Web 2.0 Technologies: Awareness and use of streaming video, blogs, podcasting and social networking, including use of sites such as Sermo
• Email Use and Opportunity: Email newsletters, email with patients, colleagues, and pharmaceutical, biotech or device companies
• Patient Interaction and Education: Patients bringing information into office, sites recommended to patients, types of patient education sources of interest
• Digital Health Infrastructure: ePrescribing, EMR, Practice Management, Speed of Access
• Mobile Technology Profile: PDA, Mobile Phone, Internet, Mobile Integration, iPods, MP3 players and tablet PCs

The Webinar is on June 5 2008, by Manhattan Research about physician digital marketing & sales trends webcast –register at manhattanresearch.webex.com

Note: as is from manhattanresearch website

Pepsi selling Food containing Genetically Modified Products

Tests commissioned by Greenpeace, shown that Pepsico’s Doritos Corn Chips contains Genetically Modified Mon 863 and NK 603 variety corn ingredients.

Both Mon 863 and NK 603 are Monsanto’s genetically modified corn varieties. Mon 863 has a bacterial gene to give pest tolerance, while NK 603 has a bacterial gene for herbicide tolerance. An Independent analysis last year, done by the Committee for Independent Research and Information On Genetic Engineering and French National Committee For Risk Assessment of GMOs had concluded that both Mon 863 and NK 603 pose serious health impacts.

The find comes from India by Greenpeas after  an independent laboratory in germany conducted Tests on products picked up randomly from a supermarket in New Delhi.

Under existing Indian laws this is illegal practice. Every importer is required to label the products containing any GM content as well as get prior approval from the Genetic Engineering Approval Committee which falls under the environment ministry.

Surprisingly in 2007 United Arba Emirates have confirmed that 40% of the food in the UAE is genetically modified yet is sold to the end users without proper labelling.

While in Europe if an item contains more than 0.9 per cent of GMOs it is required to carry a label.

Its growing concern among many developing countries that import products from US where Monsanto dominates the food chain with its GM seeds. And it is going to create more controversy as Monsanto has aggressive plans in milk production. It already has a product on Bovine somatotropin a natural protein produced in the pituitary glands of all cattle which helps adult cows to produce milk. Monsanto’s version of Bovine somatotropin is a leading dairy animal health product in the United States and many other countries.

Microsoft Rebrands its Healthcare Software and Introduces it to European Markets

Microsoft is now offering its Amalga health-care software in Europe.  now Known as Microsoft Amalga has many components, from PACS solutions, Managing patient care records to tracking research projects and finance department tasks.

Microsoft Amalga  was previously known as Azyxxi which was acquired from General Datomics and  MedStar Health in 2006. This was positioned as a health intelligence Software.

But the New Amalga is more powerful and it bring the synergies of various microsoft acquisitions. It now Has a Hospital Information System (HIS) earlier known as Hospital 2000 “hospital information system for developing and emerging markets acquired from the  Thai developer Global Care Solutions (GCS) in 2007.

Amalga also boast of a Microsoft Amalga RIS/PACS earlier  known as GCS Amalga.

Amalga is being used by eight hospitals in MedStar Health’s network, which covers the Washington, D.C., and Baltimore areas, as well as Johns Hopkins Hospital, among others.

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

Surface plasmon resonance Imaging ushers in label free microarray analysis

Surface plasmon resonance (SPR) reflectivity measurements are surface-sensitive, spectroscopic methods that can be used to characterize the thickness and/or index of refraction of ultrathin organic and biopolymer films at gold, silver  surfaces.

The probes can be proteins, peptides, nucleic acids, sugars, membranes, or any other molecule. GWC Technologies is one such company that offers the services in this field

SPR imaging detects the presence of a biopolymer on a chemically modified gold surface by the change in the local index of refraction that occurs upon adsorption.

Research Papers are on , Uiversity of California, Irvine page   and also at

UC Davis Biophotonics center web page                  

Succeeding at open-source innovation: An interview with Mozilla’s Mitchell Baker and the USD $34 million Indian Government plan for Opensource Drug Development

Benjamin Franklin said “As we enjoy great advantages from the inventions of others we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously.” - Any one listening !

Leaders and veterans in Biotechnology and Health care research industry may not be welcoming open source ideals. But IT industry has set new benchmarks and proved that open source brings in much needed new ideas and innovation. So hear out loud from none other than chairman and former CEO of Mozilla. The article is published for free at the Mckinsey quarterly

Mitchell comments that Mozilla’s real contribution isn’t just the browser but the model of participation.

In 2005 annual report on Association of American Medical Colleges acknowledged that industry, academic and government researchers can and must work together to remove scientific hurdles in drug development.

For hte uninitaited a look at the article published in Nature Magazine in 2006 with help from Pharma major Eli Lilly-Open source R&D and collaborative drug discovery and other related blogs  MnDoci FuturePundit

And don’t think these are just rants of an overenthusiastic researchers, who doesn’t know the dynamics of business, why because Director-General of the Council for Scientific and Industrial Research (CSIR) in, India unveiled a USD $34 million plan for Open Source Drug Discovery. CSIR is one of the world’s largest publicly funded R&D organisations 38 laboratories working on a range of subjects from molecular biology to road research to Himalayan bio-resources. The Council has more than 4,000 scientists working for it at these 38 labs.

The January 18 2008 meeting in NewDelhi in India was organized by Knowledge Commons, Delhi Science Forum, IIT Delhi, Red Hat and Sun on Free and Open Source model of knowledge. The highlight of the event was opensource drug development — make sure you read the Opensource India blog by Venkatesh

CSIR’s chief Sameer K. Brahmachari says, he looks for “taare zameen par” (stars on earth, a reference to one of Bollywood’s latest blockbusters), in large numbers

OSDD has the support of Sun Microsystems Inc. Hewlett-Packard, IIT Delhi, Red Hat and Indian corporate houses like TCG Life Sciences.

Related Topics Video: open source drug discovery for neglected diseases from google tech talks , Articles: The Ecconomist -An open-source shot in the arm

If you still think open source has no place in biotechnology and life science its not likely that you would listen to Alexander Graham Bell

“Great discoveries and improvements invariably involve the cooperation of many minds. I may be given credit for having blazed the trail, but when I look at the subsequent developments I feel the credit is due to others rather than myself.’

Is bioinformatics still a viable career choice or a business model?

If you are on linkedin take a look at the question posted by Jake Chen, Founding Director at Indiana Center for Systems Biology and Personalized Medicine.

One area where bioinformatics havn’t experimented a lot is probably adopting SaaS (software as a service) methodology for growth. Software being developed for scientists is still not that user-friendly. Bioinformatics have evolved; but has it been hijacked by engineers?.

Though bioinformatics companies have lost the sheen, the growing need for data analysis is unmistakable , with more large genome projects being announced everyday.

1996-2002 was a period when bioinformatics was the darling of budding entrepreneurs and scientists the world over. Depending on your point of view the industry is now either passé or futuristic. The only ones that made money were the equipment companies and the those making reagents. Propelling the acquisitions phase that is still going on, transforming most of the erstwhile famous names from pure play bioinformatics to drug discovery/development services companies.

The future is there as a CEO puts it “We’re just at the tip of the iceberg of addressing the real problem — helping scientists understand how to use software to make a discovery,”

surprisingly given below is a quote I found in the website of the Stanford University Center for Molecular and Genetic Medicine , for the class on introduction to bioinformatics for fall-quarter 2007. here is the actual link . I hope am not going to be denied an admission there for posting this. But I agree with it completely, and its time for the industry to take note

“There are a wide variety of companies trying to commercialize bioinformatics. Some of these businesses have been around for many years, but a lot of them are just jumping in with nothing but hype to sell, trying and gain some market share and position themselves as “leaders” in the new area of genomics, hoping to become profitable or get bought out before the venture capital funds dry up”.

Genetics Influence Blood Preassure medication

The study published in Jan. 23 issue of the Journal of the American Medical Association  is a thumps up for those interested towards personalized medicine, a small but important step.

A person’s genetic make-up seems to influence how he or she reacts to certain hypertension medications. The new study focused on the NPPA (atrial natriuretic precursor A) gene, which is involved in forming atrial natriuretic polypeptide, which acts as a diuretic.

n all, 38,462 people with hypertension underwent genotyping [genetic testing] and were randomly assigned to receive a diuretic (chlorthalidone) or one of the following three drugs: a calcium channel blocker (amlodipine); an angiotensin converting enzyme inhibitor (lisinopril); or an alpha-blocker (doxazosin).

people with hypertension and two different NPPA genotypes (known as NPPA G664A and NPPA T2238C) responded differently to different medications.

The 1000 Genomes Project to Study Human Genetic Variation to Support Disease Studies

The 1000 Genomes Project, led by an international research consortium, will
sequence the genomes of at least a thousand people from around the world to create the most detailed and medically useful picture to date of human genetic variation.

The international research consortium draws support from the Wellcome Trust Sanger Institute in Hinxton, England, the Beijing Genomics Institute, Shenzhen (BGI Shenzhen) in China and the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH).

The other participants include from as many as 35 Institutions such as the

Sanger Institute, BGI Shenzhen and National Human Genome Research Institute’s Large-Scale Sequencing Network,  Broad Institute of MIT and Harvard; the Washington University Genome Sequencing Centre at the Washington University School of Medicine in St. Louis; and the Human Genome Sequencing Centre at the Baylor College of Medicine in Houston. European Bioinformatics Institute near Cambridge, UK, and the National Centre for Biotechnology Information in the USA

Using standard DNA sequencing technologies, the effort would likely cost more than £250 million. However, leaders of the 1000 Genomes Project expect the costs to fall to as little as £15 million by the use of new sequencing technologies.

The scale is immense. At 6 trillion DNA bases, the 1000 Genomes Project will generate 60-fold more sequence data over its three-year course than have been deposited into public DNA databases over the past 25 years.

Among the populations whose DNA will be sequenced in the 1000 Genomes Project are: Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Gujarati Indians in Houston; Chinese in metropolitan Denver; people of Mexican ancestry in Los Angeles; and people of African ancestry in the southwestern United States.

 

Missing Evolutionary Link -how RNA progressed to share functions with proteins

Alan Lambowitz, director of The University of Texas at Austin’s Institute for Cellular and Molecular Biology and Senior researcher Paul Paukstelis and his team has found the missing links in evolution of life from the simple to the complex and involvement of RNA.

By crystallizing a fungus the team of researchers were able to visualize the process of moving from RNA to RNA and proteins and then to DNA.

The crystal structure provides a snapshot of how, during evolution, protein molecules came to assist RNA molecules in their biological functions and ultimately assumed roles previously played by RNA quoted by Purdue structural biologist Barbara Golden

The study is published at January edition of Nature

Alternative for Smallpox vaccine

University of California, Irvine researchers  Philip Felgner and Huw Davies with the Department of Medicine found that the modified vaccinia virus Ankara (MVA) produced the same antiviral response in human and animal studies as the current smallpox vaccine Dryvax.

Smallpox was declared eradicated worldwide in 1980; the last naturally occurring case in the world was in Somalia in 1977. and last I heard of it was when I watched the zombie movie I am Legend  last year,

In the study, Researchers applied blood serum samples taken from both humans and animals to microarray chips containing more than 200 vaccinia virus proteins, on which they simultaneously studied how the serum antibodies responded to all the vaccinia proteins

Details are on the UCI website press release