Integrating NGS data into clinical practice
Category Archives: Open Science
Crowdsourcing solutions for life
From the lab to scientific publishing to clinical solutions, the Open Access movement is changing the way science advances
(Guest post by Joseph Jackson)
The 2nd Open Science Summit is the weekend of October 22-23, 2011 at the Computer History Museum in Mountain View, just before the 2011 Open Access (OA) week, which runs October 24th-28th. Open Science evokes different associations for different people, depending on which part of the scientific process they most regularly engage with. One critical component focuses on access to scientific literature. The OA movement has made great strides in the last ten years with the creation and maturation of journals and publishers like PLoS and Biomed Central.
But the most critical shifts toward Open Science arguably are happening in the life sciences. The technological revolution underway in next generation sequencing is enabling, but also requiring bold new collaborative approaches to manage increasing complexity and accelerate the translation of scientific discoveries into desperately needed therapies.
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Science meets Web
Using the internet for open science
A few days ago, PLoS hosted a talk by Michael Nielsen at their San Francisco offices. Nielsen, author of the book “Reinventing discovery”, due late this year from Princeton Press, is a strong-voiced proponent of the need for a change in the way we share data.
The Polymath project, his opening story, is one of the best examples of how and why open science works. Tim Gowers, a Fields medalist, posted a famous mathematical problem on his blog, an open invitation to anyone interested to try their hand at solving it. For the first 70 hours, nothing happened. Then a math professor left a comment, quickly followed by a high school teacher, another Fields medalist and so on. In the span of 37 days, over 800 comments collectively solved the problem. How many conferences and scientific papers, peer reviews boards and editorial revisions would it have taken to even get these diverse minds thinking together in the same space? Nielsen describes it as the difference between “driving and pushing your car”.
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Q & A with Sepandar Kamvar
“In biology, the ability to create information has increased tremendously, faster than the traditional journal system gives the ability to propagate, review, endorse, and remix.”
The Web is an information source to most of us. But it’s also a dynamic, interactive medium, fluid as much in its substance as in its focus. In some ways, the same could be said of scientific data and the trajectory of research, especially in bioinformatics and genomics. As a constantly growing information repository and source, genomic data is constantly re-interpreted to increase our understanding of disease risks, pharmacogenomics, personalized medicine, and much more.
Sepandar Kamvar is no stranger to large amounts of confusing data. After all, he co-authored the book “We Feel Fine: An Almanac of Human Emotion”. Previous head of personalization at Google and currently on the technical advisory board of organizations as diverse as Etsy and NextBio, the assistant professor of Computational and Mathematical Engineering at Stanford University spoke with NextBio about the future of scientific information exchange.
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Data Sharing
If you ask scientists “Why do science?”many of the answers will be along the lines of “In order to advance human knowledge.” But if the goal of science is to contribute to the sum of human knowledge, why don’t scientists place more emphasis on sharing data? Wouldn’t the most efficient path to advancing knowledge be to pool our information and work together? Scientist may have idealistic intentions and magnanimous motivations, but the fact remains, they do not share well.
So why don’t scientist share data well? Nature recently addressed this question in a special issue dedicated to data sharing that is available free of charge online.
Data sharing is an incredibly important issue and I am very happy to see it being addressed by such a respected and widely-read publication. With modern, high-throughput techniques bringing us into an age of data-driven science it may be more important now than ever before. But sharing data has always been central to science, it takes many minds and many perspectives to extract the full value of knowledge from data. As Cambridge professor and Rufus Pollock says : “The best thing to do with your data will be thought of by someone else.” (Voices from the future of science: Rufus Pollock of the Open Knowledge Foundation)
Nature’s special data sharing issue contains:
An editorial titled Data’s shameful neglect
A feature by Bryn Nelson called Data sharing: Empty archives
Two collaboratively written opinion pieces
Prepublication data sharing
Post-publication sharing of data and tools
Any one of them provides a thought-provoking read. Taken together they make a thorough statement on where we are now and where we need to get to in order to take full advantage of the massive amount of experimental data being generated.
by Lisa Green
If you ask scientists “Why do science?”many of the answers will be along the lines of “In order to advance human knowledge.” But if the goal of science is to contribute to the sum of human knowledge, why don’t scientists place more emphasis on sharing data? Wouldn’t the most efficient path to advancing knowledge be to pool our information and work together? Scientist may have idealistic intentions and magnanimous motivations, but the fact remains, they do not share well.
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Opening Science
– Steve Koch
Thank you, Lisa, for inviting me to post a blog here! In thinking about what to write, I noticed two previous entries on this blog: the first was one by Lisa discussing Francis Collins possibly being the next director of the NIH. Francis Collins was the leader of the wildly successful, amazingly collaborative human genome project—an awesome project that demonstrates the huge accomplishments that can come from scientists openly collaborating. Dr. Collins was the principle investigator of the first lab I joined at the very beginning of my academic research career. He is one of my science heroes, and I am really hoping that he becomes the next director of the NIH. With Collins at the helm, I have great confidence that the NIH will be a strong leader in funding and promoting Open Science and Science 2.0 innovations. The second post that caught my eye was by Jean-Claude Bradley discussing the possible necessity of science blogging. Jean-Claude is a huge proponent of Open Science and a leader in Open Notebook Science. Reading these posts made me wonder whether readers of the NextBio would like to know, “what is open science?”
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Is the Human Ego good for Science?
- Jean-Claude Bradley
I have just finished reading the fascinating book “The Emperor of Scent” by Chandler Burr. It starts off describing the world of perfume with a focus on Luca Turin, a man with the unusual talent of being able to review perfumes with great eloquence, conjuring up beautiful metaphors of experiencing their scent.
The book then takes an unexpected turn into the description of Turin’s theory about the mechanism of olfaction. There is some truly interesting science there, such as Turin’s discovery of a binding site for NADPH and another for zinc on a protein thought to mediate smell. This supports his hypothesis that the protein functions as an electron tunneling spectroscope detecting differences in vibrational modes. Further evidence is provided by comparing the different smells of deuterated molecules like acetophenone and the similarity of the stench of boranes with thiols, which share similar IR spectral bands. This idea is at odds with the conventional view that molecular shape is responsible for the activity of odorants. (For a summary of Turin’s theory I would suggest watching his recent TED talk “The Science of Scent” and his Wikipedia entry).
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The Future of the Web
- Lisa Green
Recently, I watched Sir Timothy Berners-Lee’s TED talk The next Web of open, linked data . Berners-Lee is the inventor of the World Wide Web and the talk is extremely thought-provoking.
Today’s internet is something we frequently take for granted – as if we have always had the power to access a trillion hyperlinked documents. But listening to Berners-Lee makes you consider the time before the web was born. In the 1980s, Tim Berners-Lee was frustrated by the difficulty in unlocking the enormous potential of his lab’s data, methods, devices and protocols. He sought a way to easily share documents and link information and eventually came up with the idea of using the internet to link hypertext documents.
A Global Perspective On The Open Access Effect
- Lisa Green
I am quite interested in the debate regarding Open Access (OA) to scientific publications. Accordingly, this week my attention was drawn to a one-page article in Science by University of Chicago researchers James Evans and Jacob Reimer titled Open Access and Global Participation in Science.
The question of how OA influences science is a popular one. In the last decade, many studies have addressed the question: are OA papers more widely disseminated, read and cited? Evans and Reimer take a new perspective and ask how the influence varies by per capita gross national income (GNI).
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Finding Common Ground – An Evening With Creative Commons
-Lisa Green
Last night Creative Commons held a salon in San Francisco with short talks given by several members of the Creative Commons team including John Wilbanks from Science Commons.
John is an excellent speaker whose enthusiasm reveals his passion for improving science. He gave a thought-provoking talk about creating a network effect in science similar to the effect that drove the evolution of ARPANET into the Internet we know today.
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