3G Doctor

I am working on the topic (software as a service) SaaS applications in Medical and Healthcare field, so the next few months my focus there.

So this week I like to post about 3GDoctor.com a service that allows you to video consult with General Medical Council registered Doctors using a 3G Video Mobile. When you register as a patient with 3G Doctor you can also use it to create, store and manage your Personal Health Record which can be referred to by your Doctor during video consultations. Yummy now that feels like the next google acqusition target.

Mediserve is another company that is now planning to came up with SaaS model of their applications.

And of course have to talk about Microsoft , even though I work for Oracle andicrosoft is competition.

Digipede is developing on microsofts .net plafrom to help anyone providing SaaS on the Microsoft platform. And they claim to have a bioinformatics company testing their application to develop bioinformatics application in SaaS model And it lok like that customer is The Friedrich Miescher Institute (FMI) as a part of the Novartis Research Foundation, details of the case study on Digipede website

And yes I ahve written about  GeneBio earlier their claims to have PhenyxOnline as the first commercial platform in the proteomics field offered in a SaaS model    

Also came across this intersting post by Paweł Szczęsny.  Thinking about RaaS: Research-as-a-Service

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

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

UK Government-backed sociology study using Genetics raises privacy concerns

The Uk government backed UK Household Longitudinal Study to use genetics analysis of British citizens (previous post on UK BioBank) to assess impact of Genetics and lifestyle in health and medical treatment and how it affects people’s social and economic status over time, is turning into controversy. The expansion of the program to cover “nature versus nurture” questions through genetic and medical testing has raised fears among civil liberties campaigners.

More than 100,000 people, including children as young as 10, will be asked to provide saliva tests and DNA samples in a new annual survey of the lives, behaviour and beliefs of people in the United Kingdom.

I thought of how we are going to look at privacy concerns at such government backed studies, Take a look at the blog by Deepak Singh Your personal health: The internet and privacy

Even though participation is voluntary The plan has been denounced by civil rights campaigners. ‘I would not let my DNA details be taken in this way,’ said Richard Clayton, the barrister representing the rights group Liberty in its fight to prevent police from keeping DNA samples of suspects later cleared of wrongdoing as quoted on The Observer

Details of the study is available at the University Essex website of UK Household Longitudinal Study

Searching Through DNA – Impact of new genetics technologies in American Life

One of the reader had posted a question about my earlier post on genetics of Transplant Organ Rejection so this post is a part answer to her comment, I choose the title american way of life as my first post in 2008 is not mine but an interesting article from Newyork Times

A good article about what can we expect from genomics in clinical decision making and therapeutics

DNA-based security solutions to Prevent fraud and theft

Applied DNA Solutions is NewYork company that offers DNA-based security solutions to Prevent fraud and theft

Applied DNA Sciences’ technology has been utilized to successfully mark nearly 1 billion items including DVDs and CDs, fine art, prestige wine, luxury and personal care goods botanical DNA encryption, embedment and authentication solutions that can help protect companies, governments and consumers from counterfeiting, fraud, piracy, product diversion, identity theft, and unauthorized intrusion into physical locations and databases.

ADNAS uses DNA segments from one or more botanical sources, rearrange them into unique encrypted sequences, and then implement one or more layers of anti-counterfeit techniques

MIT team discovers new DNA modification in bacteria acting as DNA Bookmark

Researchers from MIT have discovered that bacterial genes, known as the dnd gene cluster, gives bacteria the ability to employ DNA modification by adding sulfur to the sugar-phosphate DNA backbone as a phosphorothioate,

The same method used in laboratories worldwide to modify synthetic oligonucleotide.Why would bacteria conserve this system which requires five enzymes, each with different co-factors?”

Peter Dedon says the modification system might serve as either protection against foreign (unmodified) DNA, or as a “bookmark” to assist with transcription or replication of DNA.

Record songs onto a Bacteria- yes Researchers from Pacific Northwest National Laboratory can claim to use bacteria as an ipod storage device

Researchers Store children’s song It’s a Small World on bacteria and recovered it from the 100th Generation

Researchers from Pacific Northwest National Laboratory used artificial DNA sequences to encode portions of the text of the children’s song It’s a Small World, added the sequences to bacteria DNA, allowed the bacteria to multiply, then extracted the message part of a DNA strand and retrieved the encoded information, Bliss ha just the kind of solution I need to store all my digital music when my ipod gets full.

Well may be not so easy since there are some potential problems the memory capacity would be huge because each bacteria in a colony could encode different information; it is very difficult to select a single bacteria from a colony, well that cant good, But I like the concept pretty futuristic

These DNA messages, each about 150 bases long, were inserted into bacteria such as E. coliDeinococcus radiodurans. Because DNA is passed down through generations of living organisms, information stored this way should survive for as long as the line of organisms survives, said Pak Wong, a chief scientist at the Pacific Northwest National Laboratory. DNA is made up of four bases attached to a sugar-phosphate backbone. Different sequences of the four bases can represent digital information

Considering that a milliliter of liquid can contain up to 10 billion bacteria, the potential capacity of bacterial-based DNA memory is enormous

The researchers let the bacteria propagate for 100 generations, then retrieved the encoded information by extracting the message part of the DNA strand from the youngest generation and reading it via polymerase chain reaction, a laboratory procedure that took about two hours and involved a series of heating and cooling cycles.

The researchers used seven different bacteria to store and retrieve seven DNA fragments that ranged from 57 to 99 base pairs long and encoded text from the children’s song

The study was published in 2003

So Thats how Humans Evolved! – Now we can begin to answer the big question

Which of the thousands of long stretches of repeated DNA in the human genome came first? And which are the duplicates the question have been answered by a team of scientists from University of Washington School of Medicine and University of California, San Diego.The research published by Evan Eichler from the University of Washington School of Medicine provide the first evolutionary history of the duplications in the human genome that are partly responsible for both disease and recent genetic innovations.

Evan Eichler has analyzed segmental duplications in the human genome and have successfully pinpointed the ancestral origin of each and identified the newly named core duplicon.

The study presents a comprehensive global analysis of the evolution of segmental duplications in the human enome. The authors identify the origin of ancestral duplication loci, regions of clustered duplicons, and evidence upporting a punctuated model of evolution.

This work marks a significant step toward a better understanding of what genomic changes paved the way for modern humans, when these duplications occurred and what the associated costs are – in terms of susceptibility to disease-causing genetic mutations.

Apart from the above study  the recently completed (check previous blogs) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences the study helps to explain the evolutionary origins of human DNA and the role played by transposons

Genomes can duplicate long stretches of DNA from one chromosome and insert the duplication in another area of the genome. The resulting segments of DNA are called segmental duplications.  They are important because they hold evolutionary secrets

Finding answers to questions such as, Which set came first? What changes were innovated, when and why? What was sacrificed when an innovation took effect? What is the connection between disease and innovations within segmental duplications?, are important because researchers can then design specific medical treatments and can lead to ket discoveries in  Pharmacogenomics research

Download the Research Article

Final week to register for 2007 Emerging Technology Awards

Final week to register for 2007 Emerging Technology Awards

Join the Silicon Valley/San Jose Business Journal as we honor the companies on the forefront of technology and celebrate those who are leading the way in innovation and entrepreneurship at the 2007 Emerging Technology Awards.

Reserve your spot now! Registration deadline is Friday, October 26, 2007. To register please click the registration link below or email sjevents@bizjournals.com. For more information, call 408-299-1871.

Individual tickets $95 or purchase Premium VIP tickets for 10 with reserved priority seating and company signage at the row for $950.

Winners will be announced in the following categories:

  • 1. Biotechnology
  • 2. Collaboration
  • 3. Entertainment
  • 4. Green/Clean Technology
  • 5. Medical Devices
  • 6. Mobile Technology
  • 7. Resource Management
  • 8. Search
  • 9. Security
  • 10. Social Networking
  • 11. Internet Telephony
  • 12. Wireless & Networking
  • 13. Judge’s Award 
  • 14. And a special Vision Award for individual venture capitalists who have championed emerging technology.

Registration & Wine Reception 5:30pm
Awards Ceremony 6:00-7:00pm
Networking Reception with heavy hors d’oeuvres, wine and dessert 7:00-8:00pm.

Event Sponsors:

When? Thursday, November 1, 2007, 17:30:00
Where? Computer History Museum 1401 N. Shoreline Blvd., Mountain View, CA 94043
Click here to register online

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,

Microsoft launches Personal Healthcare Intiative -conversation with Peter Neupert VP of Microsoft’s Health Solutions Group about HealthVault

After Google announced the personal genomics and healthcare library intitaitves it is now the turn of Microsoft offering free personal health records on the Web

Microsoft announced HealthVault, an online platform where personal electronic health records can be stored.

The company’s consumer health offering includes a personal health record, as well as Internet search tailored for health queries, under the name Microsoft HealthVault www.healthvault.com

The organizations that have signed up for HealthVault projects with Microsoft include the American Heart Association, Johnson & Johnson LifeScan, NewYork-Presbyterian Hospital, the Mayo Clinic and MedStar Health,

Take a look at the  conversation with Peter Neupert VP of Microsoft’s Health Solutions Group about HealthVault  from the Channel9 MSDN

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

 

Toxicogenomics can change face of clinical trials

“Genomics is only the start. Proteomics has been around for years and metabonomics is an up and coming important technology, both of which are complimentary to genomics. But still I think that genomics will be the most successful and most predictive of all these technologies.” Dr Phil Hewitt  Head of Toxicogenomics at Merck.

Meanwhile Gene Logic Provides the FDA with Access to Toxicogenomics Data and Analysis Systems for Reviewing Voluntary Genomic Data Submissions, and Iconix Released On-Line Version of World’s Largest Toxicogenomic Reference Database ,

Growing like IT companies- can Biotech do the magic

Information technologies have significantly contributed to the evolution of work over the last fifty years. At first, IT was primarily applied to automate back office, highly repetitive and fairly standardized tasks, such as financial transactions, payroll, and inventory management.

Customer self-service was arguably the commercial killer-app of the Web in the ’90s. Now giving way to SOA and web collaboration technology, and the SaaS

So where does that put the pharma and biotech industry, we are not so famous for collaboration within the industry. The blatant patent wars and the triumphs to outdo the competitor by developing better and blockbuster drugs have certainly not contributed much to the developemnt of Drug industry in ways that supported the end users/customers. Infact the majority of the big inventions in the last 25 years were borne out of intelligent observations rather than from technological marvels, most of them were the bi product or came across as a lightning discovery during some other research projects.

That role is changing atleast now IT is looked upon and using it to drive business innovation. The involvement is present at every department, from Collaborative drug designing, Online Data sharing, ERP, CRM, use of enterprise systems in clinical research and post launch studies and Business intelligence

Better adoption of IT can dramatically improve the efficiency of and drive business innovation  even using internet to speedup clinical research

Its interesting to learn about Conformia a company that claims to do so by Product performance and life cycle managemnet software for pharmaceutical product development industry and people seem to take attention -SAP an Enterprise application provider has mae investment in joint collaboration with conformia

Perhaps it time we see some major investment and IT helping Pharma companies in post product launch studies, to this date pharma companies do not have enough access to pefroamce data of the drugs present in the market , since hopsitlas and GPs will not like to part with data. Perhaps cost effective IT services might help in avoiding vioxx like incidents by giving pharma companies access to patient data,

Such improvements can only cement the future of genomics /personnal medicine such as samller steps are taken in this direction such as the  Large-Scale Medical Sequencing Clinical Research 

%d bloggers like this: