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 

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

personalized, safety alerts about your medication

A service launched by quintiles claims to be one of the first to provide post launch drug safety information about drugs directly to any one who is using them.  iGuard is a web-based services that will help you take medication safety without the help of  healthcare professionals.

You can register on the site for free and record all the drugs you are using, along with  general health profile. When the FDA issues advisories and other safety notices for some 20,000 different marketed drugs, or when new research emerges about drugs or drug interactions that may affect them, iGuard members taking those drugs will get an e-mail alert.

The warning system uses a scale of 1 to 5 and is color-coded in a way that was inspired by the U.S. government’s homeland security alerts.

t’s impossible to gauge how many drugs will be given a “1,” which means suitable for widespread use, or a “5,” which iGuard says should be more carefully considered. Lipitor, for the record, gets a “2” rating from iGuard.

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