Doing Science in the Open

Published on Jun 14, 2012 by OIIOxford

"Michael Nielsen (author and an advocate of open science) discusses open science at a seminar given at the Oxford Internet Institute, University of Oxford.

Michael begins his talk by describing the Polymath Project, an ongoing experiment in "massively collaborative" mathematical problem solving. By combining the best ideas of many minds from all over the world through the use of online tools, the Polymath Project has made breakthroughs on important mathematical problems.

But this is much more than just solving a few mathematical problems. Rather, this project suggests that online tools can be used to transform the way we humans work together to make scientific discoveries. Online tools can be used to amplify our collective intelligence, in much the same way as for millenia physical tools have been used to amplify our strength. This has the potential to accelerate scientific discovery across all disciplines.

However, there is a major catch. Scientists have for the most part been extremely conservative in how they use the net, often using it for little more than email and passive web browsing. Projects like Polymath are the exception not the rule. Michael will discuss why this conservatism is so common, why it is so damaging, and how we can move to a more open scientific culture".

PLoS Moves Up (yet) Another Gear

As of today, it has now been announced >> (in writing) << in the public domain that this year, PLoS ONE, is "soon to become the world's largest (STM - Ed) journal"

In part, here's the word on the webz from PLoS:-

"We need to move because we've simply outgrown our existing location. With the rapid growth of PLoS ONE (soon to become the word's largest journal) and the increasing volume of articles sent to PLoS following the NIH mandate (with hopefully more to come if the Federal Research Public Access Act becomes law), we need to get ready to expand even more".

As a layperson who is totally supportive of Open Science related issues, this is a most welcome development on many levels.

Open Science Contact List

(Image c/o Judy Breck - Flickr)


Back in March, I decided to place into the public domain a working document with contact details for many of the key folks I've connected with in the Open Access Community since late 2006.

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Last weekend on FriendFeed, I came across the following video:-



Following my conversation yesterday with Josh Sommer, Executive Director of the Chordoma Foundation, it would be really useful to work on a similar document but this time, one containing contact details for people who are directly/indirectly affiliated and/or associated in Open Science. As matters stand, (correct me if I'm wrong), I do not think that such a list already exists. If it does, then I will happily scrap this project.

Unlike the previous list, rather than doing this on my own, it would seem much more appropriate to start this myself and then crowd source. As such, I've set up a new Google Doc in the public domain to which anyone can view/edit:-


Open Science Contact List


With my Patient Advocacy hat on, I am mainly thinking about the Life Sciences, but sense that this should also be extended to other areas such as Citizen Sciences.

I would be most grateful for your assistance in helping build a working document/resource which I hope will be of use to many many people/organizations across the world.

Thank you,

Graham

Making the Web Work for Science

'Making the Web Work for Science July 28th 2009. A panel discussion on bringing digital tools to the world of science with panelists Stephen Friend, Jimmy Wales and John Wilbanks moderated by Tim O'Reilly'.

Making the Web Work for Science - Full from Jordan Mendelson on Vimeo.

Click here to the original source to view individual Chapters.

Major H/T to Lisa Green for putting this one together.



Summary

Digital technologies have greatly enhanced our ability to communicate and share information, but the scientific community remains largely untouched by these advances.

Why doesn't the web work for science the way it works for culture and for commerce? What will it take to make science digital?

Join the Commonwealth Club of California for a fascinating discussion on the movement to bring digital methods to the world of science.



BIO


Stephen Friend - Dr. Friend is currently a Senior Vice President at Merck & Co., Inc. where he has had scientific leadership of Merck's Basic Cancer Research efforts since September 2002. In 2005, he led the Advanced Technologies and Oncology groups to firmly establish molecular profiling activities throughout Merck's laboratories around the world, as well as to coordinate oncology programs from Basic Research through phase IIA clinical trials. Prior to joining Merck, Dr. Friend was recruited by Dr. Leland Hartwell to join the Fred Hutchinson Cancer Research Center's Seattle Project, an advanced institute for drug discovery. While there Drs. Friend and Hartwell developed a method for examining large patterns of genes that led them to co-found Rosetta Inpharmatics in 2001. Dr. Friend has also held faculty positions at Harvard Medical School from 1987 to 1995 and at Massachusetts General Hospital from 1990 to 1995. He received his B.A. in philosophy, his Ph.D. in biochemistry and his M.D. from Indiana University.

Tim O'Reilly - Tim O'Reilly is the founder and CEO of O'Reilly Media, Inc., thought by many to be the best computer book publisher in the world. O'Reilly Media also publishes online through the O'Reilly Network and hosts conferences on technology topics, including the O'Reilly Open Source Convention, the O'Reilly Emerging Technology Conference, and the Web 2.0 Conference. O'Reilly's blog, the O'Reilly Radar "watches the alpha geeks" to determine emerging technology trends, and serves as a platform for advocacy about issues of importance to the technical community. O'Reilly is on the boards of MySQL, CollabNet, Safari Books Online, Wesabe, and ValuesOfN, and is a partner in O'Reilly AlphaTech Ventures.

Jimmy Wales - Jimmy Donal "Jimbo" Wales (born August 7, 1966 in Huntsville, Alabama) is the founder, board member and Chairman Emeritus of the Board of Trustees of the Wikimedia Foundation, a non-profit corporation that operates the Wikipedia project, and several other wiki projects, including Wiktionary and Wikinews. He is also the co-founder, along with Angela Beesley, of the for-profit company Wikia, Inc.

John Wilbanks - As VP of Science, John Wilbanks runs the Science Commons project at Creative Commons. He came to Creative Commons from a Fellowship at the World Wide Web Consortium in Semantic Web for Life Sciences. Previously, he founded and led to acquisition Incellico, a bioinformatics company that built semantic graph networks for use in pharmaceutical research & development. Previously, John was the first Assistant Director at the Berkman Center for Internet and Society at Harvard Law School and also worked in US politics as a legislative aide to U.S. Representative Fortney (Pete) Stark. John holds a Bachelor of Arts in Philosophy from Tulane University and studied modern letters at the Universite de Paris IV (La Sorbonne). He is a research affiliate at the MIT Computer Science and Artificial Intelligence Laboratory in the project on Mathematics and Computation. John also serves on the Advisory Boards of the U.S. National Library of Medicine's PubMed Central, the Open Knowledge Foundation, the Open Knowledge Definition, and the International Advisory Board of the Prix Ars Electronica's Digital Communities awards. He also serves on the Board of Directors of the Fedora Commons digital repository organization.

TED Fellowships - Open Science

"And then it struck me...." A line from a film currently under construction that I'm not allowed to say much about, at the moment.

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Like many many others, McDawg is a massive fan of TED. Previous McBlawg TED related posts here. Indeed, TED came into the discussion two weeks ago at CISB'09 and McDawg was most surprised to learn that Henry Gee was unaware of TED. He has been primed about it now.

McDawg wasn't aware of TED Fellows Program until yesterday. Also see The story,How it works and Applying to be a Fellow.

Cue this related thread over at FriendFeed started by Bill Hooker.

I have to say I completely agree with this comment from Bill:-

Yaroslav -- I was indeed thinking of Jean-Claude, Cameron and a growing number of others who are actually *doing* Open Science. The TED people seem pretty forward-looking so I don't think it's necessary to have already changed the world, just made a good start on that project. A TED talk would certainly put ONS on a LOT of peoples' radar, which is where collaborations come from, which is the secret to ONS success...

ONS = Open Notebook Science.



Cameron Neylon and Jean-Claude Bradley

McDawg has had the priviledge of meeting them both in person. Cue this post from Cameron:- The Open Science Endurance Event - Team JC-C

From the comments in the FriendFeed thread, Cameron has kind of ruled himself out but nominated Jean-Claude. I second that nomination.

I would dearly love something like ONS/OS to be platformed at a prestigious event like TED and would encourage someone like Jean-Claude to seriously consider applying to become a TED Fellow. Alternatively, anyone can nominate an individual by email:-

"Note: If you would like to nominate another individual (rather than apply), please email your nomination to fellows@ted.com. Include your and the nominee's contact information (phone, address and email). Please tell us why you'd like to nominate him or her. Also list any pertinent websites that might give us more information about the nominee".

++UPDATE++ Having alerted Peter Suber to the above (pers. communication), he has given this his full approval.

Pacific Symposium on Biocomputing (PSB), Hawai'i, January 2009.

Complete coverage here.

Closing thoughts from Cameron Neylon.....

Why Glycobiology? Here's why

Ever since McDawg was introduced to the field of Glycobiology early 2003, he's remained firmly hooked.

I spotted an excellent new article today via Google News from Science Daily.

In my chosen role as a Patient Advocate, this stimulated me to post something of substance on one of the Forum's that I frequent from time to time. The one in question is 'closed' to non-Forum users since those who are registered, are mostly patients/carers and data/personal information is free for all to see. It's called, PatientsLikeMe. PLM for short.

I've been part of PLM's ALS/MND community for nearly two years now.

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After that introduction, whilst I've not posted anything on that particular Forum for a while, follows a copy of my most recent comment, uploaded today.

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Earlier on today, I spotted something rather important so I wish to bring this up on PLM. This is most probably worthy of a thread of it's own, however, I've chosen to post it on this thread after giving this some thought.

This to me is the most recent further evidence of the importance of Glycobiology as a research field and the wide implications this has when studying diseases both objectively and subjectively.

Rather than starting a new thread however, I thought it was not a bad idea to continue to post items related to Glycobiology under the same roof as it were - hence, why I chose here.

Before I get to the reason for posting this entry, I wish to continue the theme of updating progress (re. my research) generally as per previous posts on this thread.

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I can report the following:-

a) Last Saturday, Professor Peter Murray-Rust and I met in person for the first time and got stuck into writing our Manuscript "Access to Published Medicine: A Universal Right" Thankfully, our paths met at this Conference and as was publicly announced in the wrap up session by Peter, the stage was set for writing. Up till then, we had made some progress online, but in the end, it required a physical meet up to get things moving along.

Here we are chatting during a Manuscript writing 'tea break':-


(the Prof is the bearded one)

b) I continue to make progress on points b) and c) above. A few other co-authors (undergrad to PhD to Professor) from various countries have joined those who have already agreed to write up the next two chapters of this set of Manuscripts. One is namely ALS/MND orientated, the other, a more general review of protein misfolding diseases and published/unpublished data/research. All of my/our research is destined for Open Access Journals.

c) I'm particularly attracted to the ethos of Open Science. Discussing and sharing thoughts/ideas/data about new research ahead of publication in a peer reviewed journal - very much what we do here at PLM !! There's a great new feature article about this entitled "Era of scientific secrecy nears its end" over at MSNBC which is well worth a read. Moreover, having at last met (also last weekend) the key scientists who are leading the way, this drew it home to me that this can be done, and is being done.

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So, without further ado, here is:- "Do 68 Molecules Hold The Key To Understanding Disease?" from Science Daily 4th Sept 2008. I have previously had contact with both Prof Jamey Marth and Prof Ajit Varki who are world leaders in the field of Glycobiology.


"Like the periodic table of elements, first published in 1869 by Russian chemist Dmitri Mendeleev, is to chemistry, Marth’s visual metaphor offers a new framework for biologists."