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Open Science Picking up momentum Now on it is only looking forward Subbiah Arunachalam Distinguished Fellow Centre for Internet and Society, Bangalore.

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Presentation on theme: "Open Science Picking up momentum Now on it is only looking forward Subbiah Arunachalam Distinguished Fellow Centre for Internet and Society, Bangalore."— Presentation transcript:

1 Open Science Picking up momentum Now on it is only looking forward Subbiah Arunachalam Distinguished Fellow Centre for Internet and Society, Bangalore 1 ICFOSS, Thiruvananthapuram 19 December 2014

2 2 This is not an original research paper. My own perception of open content and open access, why they are needed and what their advantages are have been shaped by conversations with many individuals and collaborators around the world. I have borrowed freely from the writings of many others and my own.

3 ICFOSS, Thiruvananthapuram 19 December Philosophy of Open Science

4 ICFOSS, Thiruvananthapuram 19 December This is the well recognized martyr for India’s freedom – Bhagat Singh (1907 – 1931)

5 ICFOSS, Thiruvananthapuram 19 December This is the first martyr for the cause of open knowledge. A boy prodigy and a whiz kid, he lost his life in an unequal fight with an unreasonable US prosecutor. Aaron Swartz 8 Nov 1986 – 11 Mar 2013

6 ICFOSS, Thiruvananthapuram 19 December Aaron did more than almost anyone to make the Internet a thriving ecosystem for open knowledge, and to keep it that way. His contributions were numerous, and some of them were indispensable. When asked in late 2010 for help in stopping Combating Online Infringement and Counterfeits Act (COICA), the predecessor to the Stop Online Piracy Act (SOPA) and Protect IP Act (PIPA) Internet blacklist bills, he founded an organization called Demand Progress, which mobilized over a million online activists and proved to be an invaluable ally in winning that campaign.

7 ICFOSS, Thiruvananthapuram 19 December Some people think that Aaron Swartz went against the law by downloading copyright material. I want them to know that Mahatma Gandhi often resorted to civil disobedience, which in the eyes of the prevailing laws was a violation of law. But his cause, like the cause Swartz wanted to uphold, trumped the prevailing laws. The world glorifies Gandhi but our laws punish Swartz. Unfair.

8 ICFOSS, Thiruvananthapuram 19 December This is the school kid who at the age of 15 invented a test for some cancers, whose breakthrough would have never come about were it not for free access to online journals – what Internet guru Aaron Swartz was promoting before his death.

9 ICFOSS, Thiruvananthapuram 19 December Jack Andraka created a novel paper sensor that detects pancreatic, ovarian, and lung cancer in 5 minutes for as little as 3 cents. He conducted his research at Johns Hopkins University and won many awards and honours. Jack later on worked with a team of teens (Gen Z) on the Qualcomm Foundation Tricorder X Prize and speaks about open access, STEM education, and universal Internet availability. He has won awards at multiple national and international math competitions.

10 ICFOSS, Thiruvananthapuram 19 December “Poor and rich people pay taxes for the research that goes into these journals. Only those wealthy enough to pay for subscriptions or go to universities can reap the fruits of their funding... It reinforces fundamental social inequalities.” - Swartz's best friend and colleague in many of his battles for free and open Internet access Ben Wikler. “Aaron would want all the Jack Andrakas to carry this torch forward now (…) He'd also say, don't accept the lie that the world has to be the way it is now,” Wikler says.

11 ICFOSS, Thiruvananthapuram 19 December Today our institutions and librarians are taking away taxpayers’ money and paying it to journal publishers. The leading publishers report profit margins of % even when the economy is reeling under recession and most industries are struggling to survive. We are giving away money that can be used for research. Robin Hood, the legendary outlaw, was known for "robbing from the rich and giving to the poor.“

12 ICFOSS, Thiruvananthapuram 19 December Prof. Elinor (Lin) Ostrom, the first woman Nobel Prize winner in Economics, worked on ‘natural resources commons’ throughout her life. She said the commons approach alone can sustain the world. There is another kind of commons, the ‘knowledge commons.’ And it is only through free and unhindered access and sharing we can ensure democratization of knowledge and its rapid growth. This is the basic idea of open science.

13 ICFOSS, Thiruvananthapuram 19 December What is ‘open’ in the context of science? OPEN = Digital content or data that is free to use, reuse and re-distribute without technical or legal restrictions What are Digital or Knowledge Commons? “Information and knowledge resources that are collectively created and owned or shared between or among a community and that is (generally freely) available to third parties. Thus, they are oriented to favour use and reuse, rather than to exchange as a commodity."

14 ICFOSS, Thiruvananthapuram 19 December "Open science is the idea that scientific knowledge of all kinds should be openly shared as early as is practical in the discovery process". – Michael Nielsen It is science carried out and communicated in a manner which allows others to contribute, collaborate and add to the research effort, with all kinds of data, results and protocols made freely available at different stages of the research process.

15 ICFOSS, Thiruvananthapuram 19 December Open Science is underpinned by the following broad principles: ·Transparency in experimental methodology, observation, and collection of data [Open methods] · Public availability and reusability of scientific data. [Open data] · Public accessibility and transparency of scientific communication. [Open access]. · Using web-based tools to facilitate scientific collaboration.

16 ICFOSS, Thiruvananthapuram 19 December “The European Commission is now moving beyond open access towards the more inclusive area of open science. Elements of open science will gradually feed into the shaping of a policy for Responsible Research and Innovation and will contribute to the realisation of the European Research Area and the Innovation Union, the two flagship initiatives for research and innovation.” But there are challenges to be addressed issues raised by intellectual property rights data analytics (also known as Text and Data Mining), alternative metrics, research e-infrastructure, and inter-institutional, inter-disciplinary and international collaboration among all actors in research and innovation.

17 ICFOSS, Thiruvananthapuram 19 December Unequal contribution and participation in science. Territory size shows the proportion of all scientific papers published in 2001 written by authors living there. The distribution of science in 2001

18 ICFOSS, Thiruvananthapuram 19 December If this trend continues, soon the whole continent of Africa will disappear from this map and India and Latin America will become thinner and famished. If science were to be a truly global enterprise, knowledge should flow freely and unhindered. That is why all of us should adopt open science.

19 ICFOSS, Thiruvananthapuram 19 December One member of the larger set of Open Science is Citizen Science. The idea here is: Why use one brain when you can use 7 billion? 1.The public can find new hypotheses and ‘think outside the box’ 2. Using citizens’ computing power 3. Using citizens’ brain power 4. Citizens can collect data 5. Citizens can help evaluate data

20 ICFOSS, Thiruvananthapuram 19 December Citizen Science, some examples Polymath The SkyNet Galaxy Zoo Moon Mappers Foldit EyeWire Genographic Project eBird OSDD

21 ICFOSS, Thiruvananthapuram 19 December Galaxy Zoo is perhaps the most famous example of citizen science, with over 200,000 volunteers classifying galaxy images taken from a robotic telescope. Citizens have always played an important role in astronomy but now anyone can contribute without buying expensive equipment. We humans are needed to describe the images but the task is too large for a researcher or group of researchers to take on. Thus far over 150 million galaxies have been classified by volunteer astronomers (zooites) and a few have gone on to make really neat discoveries.

22 ICFOSS, Thiruvananthapuram 19 December Foldit is an online puzzle video game about protein folding. Developed by the University of Washington's Center for Game Science in collaboration with the UW Department of Biochemistry, the objective of the game is to fold the structure of selected proteins as well as possible, using tools provided within the game. The highest scoring solutions are analysed by researchers, who determine whether or not there is a native structural configuration that can be applied to the relevant proteins. Scientists can then use such solutions to solve "real-world" problems, by targeting and eradicating diseases, and creating biological innovations.

23 ICFOSS, Thiruvananthapuram 19 December Open Source Drug Discovery (OSDD) is an Indian initiative with global partnership. It provides a global platform where the best minds can collaborate to discover novel therapies for neglected tropical diseases like Tuberculosis, Malaria, Leishmaniasis etc. It brings together informaticians, wet lab scientists, contract research organizations, clinicians, hospitals and others. Many undergraduate students have taken part.

24 ICFOSS, Thiruvananthapuram 19 December A major component of Open Science is data. A great example of open data is GenBank, the set of 40 databases maintained by NCBI. It contains publicly available nucleotide sequences for more than 280,000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large- scale sequencing projects. As of mid-December 2014 traditional GenBank database had data on 184 billion bases and 179 million sequences, and Whole-Genome Shotgun database (WGS) 848 billion bases and 200 million sequences.

25 ICFOSS, Thiruvananthapuram 19 December

26 ICFOSS, Thiruvananthapuram 19 December P&G, the first major corporation to think of open innovation, launched the Connect+Develop program more than 10 years ago and has developed more than 2,000 global partnerships, delivered dozens of new products, accelerated innovation development and increased productivity, both for P&G and its partners. The C+D website receives about 20 submissions every weekday – or more than 4,000 a year – from all over the world.

27 ICFOSS, Thiruvananthapuram 19 December What does open innovation mean to pharma companies? Pharmaceutical R&D is under pressure to counter rising operational costs, depleted pipelines and impending patent expiries. These challenges can be met in the long term only by increasing R&D productivity. Advances have been made through Computer Aided Drug Design, high-throughput techniques, and the ‘Omics’ revolution. But, what is the next step?

28 ICFOSS, Thiruvananthapuram 19 December Radical new ways of working and a culture of external collaboration are key elements in turning around pharmaceutical R&D productivity and bringing new medicines to patients faster and with more control on costs.

29 ICFOSS, Thiruvananthapuram 19 December AstraZeneca adopted open innovation in order to develop treatments for Alzheimer’s, cancer, and diabetes. They decided to collaborate and share knowledge and resources with other scientists and organisations rather than work in isolation. The AstraZeneca Open Innovation platform provides a robust but simple process for linking their expertise, experience, resources, and technology with those of external experts and to explore prospective partnerships that accelerate the advancement of medical science and breakthrough therapies for patients

30 ICFOSS, Thiruvananthapuram 19 December On June 20, 2013, thirteen Champions of Change were honored at the White House for their extraordinary leadership in "open science." From left to right: First row: Jack Andraka, David Altshuler, Rebecca Moore, Kathy Giusti, Jeremiah P. Ostriker, Eric Kansa, Paul Ginsparg and David J. Lipman. Second row: Drew Endy, Atul Butte, John Quackenbush, William Noel, and Stephen Friend. Champions of Change

31 ICFOSS, Thiruvananthapuram 19 December David J. Lipman In his 25 years as the founding director of the National Center for Biotechnology Information Lipman has had a tremendous impact on the amount of biomedical data and health information that are publicly and easily available. His contributions include setting up GenBank and PubMed Central.

32 ICFOSS, Thiruvananthapuram 19 December John Quackenbush is Professor of Biostatistics and Computational Biology at the Dana-Farber Cancer Institute. He designed tools to handle the vast quantities of data on human health and disease. He founded GenoSpace, a company that develops advanced software tools for collecting, interpreting, and sharing clinical and genomic data to further biomedical research and facilitate personalized medicine. GenoSpace has created software portals that engage patients as partners in defeating multiple myeloma.

33 ICFOSS, Thiruvananthapuram 19 December Paul Ginsparg Theoretical physicist Paul Ginsparg created an open access system in 1991 for physicists to share their cutting-edge results. Called arXiv.org, it serves as the primary daily information feed for global communities of researchers in physics, mathematics, computer science, and related fields. Today, arXiv.org provides access to more than 997,000 documents and supports hundreds of millions of full-text downloads per year. Modelled after arXiv, many subject-oriented repositories were set up: e.g. The NASA Astrophysics Data System (ADS).

34 ICFOSS, Thiruvananthapuram 19 December To conclude We need to introspect. We can no longer delay throwing open science and scholarship, our research publications and data, our educational course ware and our libraries. If organizations and our leaders are unwilling and indifferent, the scientists and citizens should lead the way. In the US, before John Holdren came up with his OSTP memo, more than 60, 000 people had signed a “We the people” petition on the White House website.

35 ICFOSS, Thiruvananthapuram 19 December We should persuade students and other citizens (taxpayers whose money supports most research) to join the movement. We should write to our Parliamentarians to enact laws to mandate open access to publicly-funded research. And, however indifferent they may be, we should keep trying to impress upon the vast majority of our scientists to place the full texts of all their research publications and their data in open access repositories.

36 ICFOSS, Thiruvananthapuram 19 December Prof. Timothy Gowers of Cambridge University, a Fields medalist with interests spanning several areas of mathematics, is a very busy man. And yet he devotes considerable time to fight injustice in the scholarly communication space. He mounted the ‘Boycott Elsevier’ movement. More than 14,000 researchers have lent support. Not many Indian scientists have shown any inclination to see a just order in this space. He also founded the famous citizen science project Polymath which has attracted a whole range of people – from university dons to office goers – to collectively solve difficult mathematical problems.

37 ICFOSS, Thiruvananthapuram 19 December We would like many Indian scientists to follow the example of Prof. Gowers and not only perform world class science but also champion open science. Thank you.


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