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.’

George Bush Sings Glory to Open Source

The truth behind the new bill signed into law by President Bush on 26 December 2007, which states that the findings of NIH-funded research must be made freely available to the public within one year of publication.

But all is not Hunky dory , as more obvious once you go through the complete text of the LAW as published in Government website

And it clearly states that copyright law takes precedence over deposition into PubMed Central.

What does that mean, when you publish a research paper it usually belongs to the University or the institution that funded the project. ie if you did sign a copyright transfer agreement with your publisher or sponsor of your funding he can deny the article being published in open source website or journal.

The only surprise is that in future based on the new Law the Director of NIH can prevent publication by grant recipients in journals that don’t allow publications of articles into PubMed Central. Aha now thats not good news for scientists and many are not going to welcome it either

But how many would care NIH is not the lone sponsor of grants, and yes certainly none from healthcare/pharma companies would allow their articles be published at open source journals. that questions how helpful the law would become

But certainly Many Many thanks and Happy New Year to  SPARC and the Alliance for Taxpayer Access  for making the first step, and it sure is a big one

There is certainly going to evoke multiple responses from everyone, wired magazine says its bad news for the science publishing industry, who’ve rallied against initiatives such as PRISM, and other open source websites such as PLOS, to preserve the right of journal publishers to charge for access to federally-funded findings. that means they will find their ways

Am certainly one of those not so politically obsessed persons, and I dont know that many politically savvy lab rats. may be few of those working in stem cell research, cloning or any other controversial topics might be. but I am beginning to like Dubya more. Not a bad a move for someone more associated bad grammar

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 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

 

OneOncology’s online sales with reverse auctions in Cancer Medications

A new cancer-drug distribution system that aims to cut drug costs for community oncology practices around the country is being launched by OneOncology Inc., of Orlando, Fla., which started its Web-based system

In a challenge to the status quo of the drug-distribution business, OneOncology plans to conduct periodic online “reverse auctions.” Wholesale-drug distributors would bid on the opportunity to fill product orders pooled from hundreds of community oncology clinics around the country. OneOncology thinks this will give smaller clinics access to lower prices than they get now, according to Chief Executive
Steven Kirchof. Under the current system, small practices typically have longstanding relationships with distributors.
“It threatens the existing status quo for companies like Oncology Supply,” said Kirchof, a former executive with International Business Machines Corp.’s ( IBM) healthcare unit. “I believe that most of the distributors will come and play, and probably play very aggressively.”

Microsoft accelerates free access to journals

Information technology company Microsoft will give technical assistance to enhance access to online research for scientists, thats when most of the publishers of scientific journals are fighting against Open Access journals. Take a look at the blog  on the subject by  Greg at nodalpoint

Announced at a meeting in Washington in July Representatives from the World Health Organization, the Food and Agriculture Organization, the UN Environmental Programme, and leading science and technology publishers, together with representatives from Cornell and Yale Universities met to officially extend their free access to peer-reviewed journals for many developing world scientists to 2015, in line with the UN’s Millennium Development Goals.

Microsoft will provide new software called the Intelligent Application Gateway 2007 (formally Whale) that will meet increased demand for access to heavily trafficked portals and perform at the standards of today’s most heavily trafficked websites. The system will also enhance security through authentication of users when they log on.

The website that benefit includes open access websites such as   HINARI  Cochrane Library   AGORA and Online Access to Research in the Environment (OARE),  

Collaborative Drug Discovery

Collaborative Drug Discovery Releases Next Generation Database for Both Private Collaborations and Public Open Access

Collaborative Drug Discovery enables scientists to archive, mine, and collaborate to more effectively develop new drug candidates for commercial and humanitarian markets.

 The technology enables novel community-based research efforts that become more and more useful as additional participants contribute data. Publicly available data sets currently in the system include the FDA orphan and approved drugs and small molecule drug discovery data dating back over half a century. These data sets pertain to a diverse group of neglected diseases, including malaria, tuberculosis, African Sleeping Sickness, Chagas Disease and Leishmania.

New horizons ahead

Its been two years since I have been with Ocimum Biosolutions ,the India HQ company serving bioinformatics and microarray market in US with office in Indianapolis and another lab in netherlands, I have been working in the business development of the company’s microarray arm in US which was acquired from MWG biotech, we had tasted success,

I have been busy lately as I have resigned from the company now that explains the absence of any new posts for few weeks now. Ocimum is one of the unique bioinformatics oraganization to make its mark in this industry, because unlike many new companies .  it was started by people with no biological background but has been selected as one of fastest growing life science company in India and Asia many times by Deloitte ranking and many other independent agencies. apart from winning awards from government and even a funding fro world bank. So what makes them so sucessful

Ocimum offers services in bioinformatics oligo microarray and R&D but its the presence of its labs near to its customers and the company’s software development division housed at Hyderabad India that makes the difference. Coupled with India’s cost efficiency, it has many advantages

Bioinformatics industry is going through a face of consolidation, marketed in India in its infancy as a glamorous field to work many who jumped into the fray has burned their hands. and industry analysis in 2000 predicted the industry to become a 100 billion worth by 2004, yet even in 2007, majority of the biologists are yet to warm upto the industry in a way predicted by the software pundits

Research and Markets (http://www.researchandmarkets.com/reports/c59429) has announced the addition of “Biomed Outsourcing Report: An Overview of the Life Sciences and Outsourcing Landscape in India: Spotlight on Bangalore” to their offering.

How Many Scientists Does it Take To Fix a Gene?

The headline of the article that appeared in a news paper was interesting, I thought I will use the same headline to right about it.

The original text of the article can be read at cityonHillPress

While reading the article I also came thougth its worth to have a look at the book Building Biotechnology  written by  Yali Friedman who serves on the science advisory board of Chakra Biotech and the editorial advisory boards of the Biotechnology Journal and Open Biotechnology Journal.

 Yali also publishes a blog at BiotechBlog.com

From science to business

It takes upto to 15 years and multimillion  dollar investments  to patent and market one successful drug for pharmaceutical and biotech industry. Trying to make the sure that the scientists receive the best R&D support possible companies have looked at outsourcing and insourcing and everything else.

And the new boy in the buzz world is “crowdsourcing” claiming businesses a way to tap into a larger, global community of scientists and R&D exeutives.

Crowdsourcing is a business model in which a company or institution takes a job traditionally performed by a designated agent (usually an employee) and outsources it to an undefined, generally large group of people in the form of an open call over the Internet. The work is compensated with little or no pay in most cases. However, in a few examples the labor is well-compensated .

Did that made sense it sounds like open source in biotech fields. but hold on your horses, it not that straight forward, remember Nature has published an article about open source in drug discover industry some time back, there is big list of things that makes it a difficult project.

But there is one company that has pulled it off successfully set up by drug giant Eli Lilly in 2001, for its projects Innocentive is one such crowdsourcer, So far, chemicals and life sciences have been the main users of crowdsourcers, offering rewards of up to $1m if they are successful. There are other places , such as Nine Sigma and Yet2.com and Scienteur, offer similar models.

Another firm Procter & Gamble P&G also works with Nine Sigma , YourEncore andYet2.com and Innocentive

Boeing , Dow Chemical , Eli Lilly and Procter & Gamble , Solvay are number of companies that have benefited fro this model ,

IT industry has grown to this level because people were willing to share data and collaborate , ofcourse there is much difference between IT and biological industry . But will scientists from life science industry would do it- So far the answer is No- may in future they might be more open to such needs

Read Related studies Further at
The Value of Openness in Scientific Problem Solving

Can open-source R&D reinvigorate drug research a nature Review

Previous Blogs

Open source in Biotechnology

Online data Sharing for scientists – Will they accept it

Data sharing policies at 10 journals- blog of the week

Heather Piwowar  blogging at ReseacrhRemix made a post on Data sharing policies at 10 selected journals.  general science (Nature and Science), medicine (JAMA and NEJM), oncology (JCO and Cancer), genetics (Human Molecular Genetics and PLoS Computational Biology), and bioinformatics (Bioinformatics and BMC Bioinformatics). she has published a spreadsheet comparing the results at http://spreadsheets.google.com/pub?key=pdheCmaT42j62B-a7sx0BRA

Open source and Biology Are we there yet?

one of the lines I heard in past was that scientists had shunned wikis, tagging, and social networks that may be true to some extent .Even the mighty nature network which is read by thousands had a hard time attracting scientists and making sure that they keep the blog at pace. Blogging may be too early in the scene coupled with many other issues that bog the idea such as identity authneticity of the information and content et al. But what is causing the lethargy towards open access and peer review database and websites.

Beginning from March 2007 Nature Biotechnology is recommending that raw data from proteomics and molecular-interaction experiments be deposited in a public database before manuscript submission. There are many articles about the power of citation from open access database and peer reviewd articles. Still the number of top research papers appearing in these websites does seem to support the enthusiasm shared by everyone.

I came across a very good blog about how the Open access amplify a whole university’s research impact chek out the blog by Peter Suber The Open access News blog    The research Informatio network team blog from UK also publishes some of the best work in this subject chek RIN blog

Search Engine for Life science Data

NextBio is a web-based scientific data search engine that offers instant access, search and collaboration across a vast repository of life sciences information

i-Kode to take control of your scientific mail and email.

 Practicallly I use the Foward feature of GMAIL to send my mails to the my corporate email address this I can make sure that no has my Id but also When I leave the company I still get to have acess to all the newsletters i received and I can even forward it to the new email address if need to

but I still thought or writing about www.i-kode.com as its a new service and has a lot features too and obviosly its freee and you can even win price too, UMM sound too good ha

you can select from a list available scientific newsletters and search for new one or add your own new

The i-kode.com™ service lets you take control of your scientific mail and emails journals and online magazines in one place.

    Get the mail you want

  • Don’t get the mail you don’t want
  • Add yourself to mail lists
  • Remove yourself from mail lists
  • Find Vendors of key products and services
  • Manage your contact with Academic Societies and Journals
  • When you move, update them all in less than a minute

You can read an article about i-kode.com and see what other scientists think of our service here or you can read our latest press release.

Latest! Online File Storage and Spam-free Secure Email Inbox.

You can store files online in your own secure Document Store or receive Spam-free Email without interference from spam filters.

And ofcourse Rewards when you refer colleagues

Read an article on OBBEC magazine http://www.obbec.com/lscbio/

Moleculare Frontiers Intiative for researchers of future

Molecular Frontiers is a global effort to promote the understanding and appreciation of molecular science in society

THe initiative offers an arena for budding biologists and life science researchers of the future. Wish them all the best. Some of the interesting aspects are

Catalytic Forum

think tank to discuss and analyze current scientific developments with researchers from all over the world.

MoleClues

A web site where young people are invited to explore the realm of molecular science.

 

Online Data sharing for scientists

Brent Edwards director of the Starkey Hearing Research Center in Berkeley, California, who blogs on innovation in science is writing his blog about an article on Nature magazine on online data sharing. Brent comments about the potential of new online data sharing sites such as Swivel and IBM’s Many Eyes . Accoding to the Nature reprt some scientists are already using these new tools to share sequence and microarray data. The potential value from scientists openly sharing their data is huge, possibly akin to the value provided by open-source software development.

Once data are uploaded to these sites (which are still being tested), people can reanalyse the numbers, mix them with other data and visualize them in different ways. Swivel focuses on letting users combine data sets, with some basic ways to present the results such as scatter graphs and bar charts. Many Eyes allows users to generate more complicated graphs such as network diagrams, which depict nodes and connections within networks, and treemaps, which display data as groups of nested rectangles

Despite the availability of many software solutions at the dispoal of scientists many of them still write their own code for bioinformatics and statistical analysis, perhaps the next frontier that might help the comunity could be the development of Firefox like software, that offers some basic functions free of cost, additional function can be bought or acquired free of cost as add ons form researchers, such a move would benefit researchers and students alike,

There are sure many more data sharing website like http://www.gotomyfiles.com, http://www.xdrive.com, http://www.ibackup.com, but these are more of a data storage sites, and these does not offer the level of document collaboration features required by a life science researcher

Then there is few other sites like microsofts foldershare and others that offer features such as remote PC access gotomyPC VNC and webex are a few exmaple of this stable. some of these also allows to by pass even a firewall such as foldershare and can pose serious security risks to data and pc if handled improperly

Yahoo answers- Interact with the President of India

Thats not really a big surprise considering he himself is a scientist, Dr. Abdul Kalam Azad the President of India who is also the commander in chief of the Army,Navy and Airforce of India, and is key force for India’s nuclear and Space power and technology uses, yahoo answer so that he can listen and hear from his people, so what about our scientist ! especially in life sciencs and academicians. Recently I had posted about the similar attempts by US presidentail hopeful’s sudden rush to web2.0. and how youtube is helping the science

Dr. Kalam’s His thought provoking question,  has garnered over 28000 answers in just 30 days. wow thats a response rate you could never expect in any other online forum asking for soutions to a scientific question or problem

chekout more visit his profile at http://in.answers.yahoo.com/my/profile?show=1e6b7ca835ee0cc4185b0ab950476c08aa
Some leading Indian figures like Sri Sri Ravishankar, Kiran Bedi, and Leander Paes have posted answers to Dr. Kalam’s question

less than 10% of people build content in an online community — in this case answer questions. The popular thumb-rule for online participation is 1% visitors would be hard-core contributors, 10% mild contributors, and 90% would be beneficiaries

By 2006 end, Yahoo! Answers had gained over 60 million unique users on a monthly basis

http://answers.yahoo.com/question/index?qid=20070112135510AAD7SB8

Indian company gets 6.5 million USD IFC funding to promote contract research in bioinformatics and genetics industry

Hyderabad, November 15, 2006 – Ocimum Biosolutions today announced that International Finance Corporation (IFC), the private sector arm of the World Bank Group, will invest USD 6.5 million of equity, for a minority stake, and debt in the Company. Funds raised from this transaction will be used for financing both organic as well as inorganic growth of the Company.

Says Ms. Anuradha Acharya, Founder & CEO of Ocimum Biosolutions, “We are very happy to have IFC as our partner for growth. These are exciting times for Ocimum and to have IFC as an investor in the company brings a lot of confidence in our clients and partners.”

Iyad Malas, IFC’s Director for South Asia, said, “IFC’s support to Ocimum will provide the company its much needed growth capital to establish an internationally competitive contract research outsourcing company and promote the discovery of new drugs at lower costs. We will also help institute improved corporate governance standards.”

This is Ocimum’s first round of fund raising from private equity investors. The Company is contemplating another round of fund raising in the next 18-24 months.

Recently, Ocimum acquired a Europe based oligo manufacturer. The Company is also scouting for more targets in the European market.

Avendus Advisors was the sole financial advisor to Ocimum for the deal. Commenting on the transaction, Shiraz Bugwadia, A.V.P., Avendus Advisors “Ocimum is one of the few Indian players within the BioIT and micro arrays space to have scaled up successfully over the last couple of years. Ocimum has also been successful at using the inorganic route to scale rapidly by acquiring niche good quality companies in Europe such as MWG Biotech’s division and now a Netherlands based oligos manufacturer.”

About Ocimum Biosolutions:

Ocimum Biosolutions is a life sciences R&D enabling company with three main focus areas, BioIT, Microarrays and Contract research services. The US operations of the Company focuses on custom contract research services in the molecular biology area while the Indian operations provide BioIT services and leverage on India’s low cost advantage in IT space. The Company enjoys a strong brand image in the market and has worked with some of the best research organizations in the world like IIT Kharagpur, National Research Council of Canada, Agriculture and Agri Foods, NIH, Dow Agro Sciences, etc.

Ocimum has adopted an inorganic strategy to ramp up the business fast and has demonstrated its capability to execute this strategy in the past. As a part of its strategy, Ocimum acquired a division of MWG Biotech, Germany in 2005. The Company has received a host of awards and recognitions. The Company has recently received the IT Innovation award by NASSCOM, presented by H.E. the President of India. Also, Red Herring magazine picked Ocimum as one of the eight companies to watch in India and was a winner of Red Herring’s Asia 100. Deloitte ranked the Company as Fastest growing life sciences company in India.

For more information, please visit: www.ocimumbio.com.

About International Finance Corporation:

The International Finance Corporation, the private sector arm of the World Bank Group, is the largest multilateral provider of financing for private enterprise in developing countries. IFC finances private sector investments, mobilizes capital in international financial markets, facilitates trade, helps clients improve social and environmental sustainability, and provides technical assistance and advice to businesses and governments. From its founding in 1956 through FY06, IFC has committed more than $56 billion of its own funds for private sector investments in the developing world and mobilized an additional $25 billion in syndications for 3,531 companies in 140 developing countries. With the support of funding from donors, it has also provided more than $1 billion in technical assistance and advisory services.

For more information, please visit www.ifc.org.

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