Tag 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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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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Enhanced ScienceDirect Goes Live

- Lisa Green

Remember my blog post NextBio Elsevier Partnership telling you that Elsevier was going to use NextBio technology to enhance ScienceDirect? Well, the updated version of ScienceDirect went live yesterday and now you can see the enhancements for yourself!

ScienceDirect users who are logged into their account will now see a box titled “Relevant Terms extracted from this Article” beneath the familiar “Article Toolbox” box.
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The Four Musketeers

- Hope Leman

As I try to grasp the revolution in scientific and medial research that Science 2.0 and Medicine 2.0 are effecting I often find that I am literally being rendered sleepless by trying to keep up on the writings of the leading thinkers on the subject such as Cameron Neylon, Jean-Claude Bradley, Michael Nielsen and the new kid on the block, Steve Koch.

It is quite daunting to try to keep up with the many fascinating things they have to say and the many links they provide to their colleagues in the field such as Bill Hooker and Rich Apodaca (How I wish that the latter two would add “Follow me on Twitter” buttons to their blogs. They have fascinating things to say and I find that the best way by far to keep up with thinkers and doers is via Twitter. RSS is so 2006.)
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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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FriendFeed and Twitter

- Hope Leman

It is 5:10 a.m. I am working on a netbook in a hotel room in San Francisco. I am attending the Web 2.0 Expo and covering it for the blog AltSearchEngines. While I am attending that event, I have been invited to a dinner sponsored by Microsoft Live Search. Yesterday I attended sessions about Web site monitoring and about how to build online social communities.

All of these activities tie into the world of Science 2.0 and Open Science. For example, the presenter on the online social communities asked what we would leave disappointed about if it were not addressed. I immediately shouted out, “FriendFeed!” because the Science 2.0 and Life Scientists rooms of FriendFeed are fascinating venues for those of us interested in how science is being conducted in the age of Web 2.0.
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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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