Category Archives: Open Science

Final Scifoo Wrap-up

Posted on August 10, 2007 by | 2 comments

As I predicted, bloggers have waited a day or two before they wrote much of substance abour Scifoo. First, you don’t want to miss out on any cool conversations by blogging instead. Second, the experience is so intense, one needs to cool down, process and digest everything. Before I write my own thoughts, here are some links to places where you can see what others are doing:
The campers are joining the Science Foo Camp Facebook group (honor system – only campers are supposed to join, but it is open) and exchanging links, pictures and information.
There is an official aggregator where you can see the recent posts by bloggers who attended scifoo.
More and more people are loading their pictures on Flickr.
You can see blog posts and pictures on Technorati (watch out for the dates – the 06 and 07 pics are mixed up together).
There is a Nature aggregator as well (appears to be the cleanest of them all), or you may choose to use Connotea instead.
Or you can use Google Blogsearch to find the recent posts about the meeting. They are all worth reading (I’ll highlight a few posts below).
Patrick is collecting a list of books mentioned at Scifoo.
Finally, people are posting ideas about potential future projects on Scifoo Prototypes, set up by Nikita of JoVE.
My previous posts about it are here:
Taking over the Silicon Valley
Science Foo Camp – Friday
Science Foo Camp – Saturday morning
Science Foo Camp – Saturday afternoon
Science Foo Camp – Sunday
Home
A question for Scifoo campers
That out of the way, follow me under the fold if you want to hear my angle on the story….
—————————

Continue reading →

2 Comments

Posted in Blogging, Framing Science, Open Science, Personal, PLoS

Is research information as important as medications for Third World countries?

Posted on August 8, 2007 by | 1 comment

Gavin has an interesting take on it:

I’ve long believed that there are parallels between the global campaign for open access to the biomedical literature and the campaign for access to essential medicines.
For a start, both information and medicines can promote health and save lives. Indeed the late James Grant, former executive director of Unicef, argued that, “the most urgent task before us is to get medical and health knowledge to those most in need of that knowledge. Of the approximately 50 million people who were dying each year in the late 1980s, fully two thirds could have been saved through the application of that knowledge.” Part of the moral case for disseminating the results of health research universally stems from the urgent need to deliver information to health workers in low and middle income settings.

Read the whole thing….

1 Comment

Posted in Open Science

Last day in San Francisco

Posted on August 3, 2007 by | 1 comment

A month has passed.
It was a steep learning curve, but I think I have climbed high enough on it to be confident that I’ll be fine on my own back in Chapel Hill. Being a part of the PLoS team is such an exhillarating experience – there is so much energy and optimism around the office, everybody from CEO to the newest intern living, breathing and dreaming Open Access 24/7.
Not to bore you about the job any more – you will be hearing about PLoS over and over again here – let me, for now, just show you some pictures (under the fold) from the farewell party last night at Jupiter in downtown Berkeley, where some of us spent about six hours drinking last night…
Who was there?
Four of us Sciencebloggers: Alex Palazzo and his lovely wife, Josh Rosenau (and his parents) who has just arrived, after driving all the way from Kansas, to take on his new job at NCSE, Chris Hoofnagle and myself.
There were several of my new PLoS colleagues: Russell Uman, Barbara Cohen, Hemai Parthasarathy, Liza Gross, Gavin Yamay and, briefly, Peter Jerram with whom I had a great lunch conversation earlier in the day.
Then, some other local bloggers, scientists, friends, fans and scifoo campers: Chris Patil who is very funny, especially after a few beers (and his command of the Croatian language is getting good!!), old blog friend of mine Alvaro Fernandez and his summer intern Andreas Engvig (an MD/ PhD in Cog Neuroscience from Norway), Josh Staiger who is an old blogging friend from his days in Chapel Hill (before Google stole him from IBM), Meg Stalcup, currently in her fourth graduate program (which makes her so interdisciplinary, one’s head hurts, so of course she is invited to Science Foo Camp), Attila Csordas who is editing his Dissertation on his blog, Curtis Pickering of JeffsBench, Bosco Ho, a postdoc in Dave Agard’s lab at UCSF, and…heck, after all the beer, I am not sure I got all the names so add yourself in the comments if you were there and I omitted you from the list.
It was so much fun to see all these people get to know each other and make friends…

Continue reading →

1 Comment

Posted in Blogging, Fun, Open Science, Personal, PLoS

Open Access news

Posted on July 31, 2007 by | Comments Off on Open Access news

The Demise of Old-Fashioned Scholarly Journals? (I love the photo on the top of the article!)
Thoughts about the sea of information
Open Science like the start of Apple?
Nonsense, and pernicious nonsense at that.
Reading Journals Can Seriously Damage Your Wallet
Hybrid journals and the transition to OA
Oxford open access experiments
Oxford: Traditional Publisher Illustrates Leadership in Transition to Open Access
Transitioning to open access series
Course check: A conversation with three open access publishers about the challenges of sustainability

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Posted in Open Science

Science 2.0 Conferencing

Posted on July 28, 2007 by | Comments Off on Science 2.0 Conferencing

Why do conferences all tend to happen at the same time, hogging a couple of weekends per year, with vast chasms of free time in-between?
So, next weekend, there is going to be a lot of science content, including a science blogging session at YearlyKos. You’ll be able to meet Tara, Chris, Sean, Ed, Karmen and Lindsay there, among many others.
At the exactly the same time, Alex, PZ and I (and many others who have not made their participation public yet) will be at Science Foo Camp, down at Google campus in Montain View (no link as the site is not open for public yet). That was not an easy choice to make.
Then, nothing happens for months….
In late October, though, there are several overlapping events. Fortunately, they are not completely 100% overlapping, so I will be able to go to the last two days of the ASIS&T meeting to participate in a Science 2.0 session, after I am done with my Science 2.0 session at ConvergeSouth. I may even be able to squeeze in a day at The 2007 Microsoft eScience Workshop at RENCI in between the two.
Then nothing happens for months…
In January, I hope to see you at the Science Blogging Conference – I have still not heard about any overlaps between it an other meetings, and I hope it stays that way.

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Posted in Blogging, Open Science

Mind Mashup: A Video Contest to Showcase Student Views on Information Sharing

Posted on July 25, 2007 by | Comments Off on Mind Mashup: A Video Contest to Showcase Student Views on Information Sharing

SPARC just announced the Mind Mashup: A Video Contest:

SPARC (the Scholarly Publishing and Academic Resources Coalition) today announced the launch of the first annual SPARC Discovery Awards, a contest to promote the open exchange of information. Mind Mashup, the theme of the 2007 contest, calls on entrants to illustrate in a short video the importance of sharing ideas and information of all kinds. Mashup is an expression referring to a song, video, Web site or software application that combines content from more than one source.
Consistent with SPARC’s mission as an international alliance of academic and research libraries promoting the benefits of information sharing, the contest encourages new voices to join the public discussion of information policy in the Internet age. Designed for adoption as a college or high school class assignment, the SPARC Discovery Awards are open to anyone over the age of 15.
Contestants are asked to submit videos of two minutes or less that imaginatively show the benefits of bringing down barriers to the open exchange of information. Submissions will be judged by a panel that includes:
• Aaron Delwiche, Assistant Professor in the Department of Communication at Trinity University in San Antonio, Texas
• José-Marie Griffiths, Professor & Dean at the School of Information and Library Science, University of North Carolina at Chapel Hill
• Rick Johnson, communications consultant and founding director of SPARC
• Heather Joseph, Executive Director of SPARC
• Karen Rustad, president of Free Culture 5C and a senior at Scripps College majoring in media studies
• Jimmy Wales, founder of Wikipedia
• Peter Wintonick, award-winning documentary filmmaker and principal of Necessary Illusions Productions Inc.
“I’m very proud to be judging this contest,” said Karen Rustad. “When it comes to debates over Internet information policy, students are usually subjects for study or an object for concern. I can’t wait to see what my contemporaries have to say about mashup culture and open access to information once they’re given the mike — or, rather, the camera.”
The contest takes as its inspiration a quote from George Bernard Shaw: “If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas.”
Submissions must be received by December 2, 2007. Winners – including a first-place winner and two runners up – will be announced in January 2008. The winner will receive $1,000 and a “Sparky Award.” The runners up will each receive $500. Winning entries will be publicly screened at the American Library Association Midwinter Conference in January 2008 in Philadelphia and will be prominently featured in SPARC’s international advocacy and campus education activities.

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Posted in Blogging, Education, Open Science, Science Education

Facebook News and (my) Views

Posted on July 22, 2007 by | 2 comments

Let’s start with some Essential Facebook Readings of the day:
The Facebook Juggernaut…bitch!
Where are Facebook’s Early Adopters Going?
Hmmm, Facebook: a new kind of press release
All your widgets are belong to Facebook
Why We’re Like a Million Monkeys on Treadmills
Facebook: the new data black hole
What would get me (and others) to shut up about Facebook?
Why I Dropped Scoble and Seceded from the Hunt for Newer Shinier Things
My predictions for the near future, and I’ll explain them below:
1) In a Clash Of Titans, Google turns iGoogle into something better than Facebook. Facebook is crushed into oblivion.
2) In a Clash Of Titans, Facebook adds everything that is currently still missing in a frenzied flurry of activity and becomes the ‘It’ thing. Google is crushed into oblivion.
3) Google buys Facebook for a gazillion dollars and incorporates it into its arsenal.
4) Facebook resists sale now and, two years later, buy Google for a gazillion dollars and incorporates it into its arsenal.
5) I am totally wrong.
Why am I making such outrageous statements?
Because, most of the people pontificating on Facebook are techies. They love to try new things – the New Shiny Objects. They are, thus, a tiny minority. 99.9% of the people do not operate that way. They want to have One Thing.
This is a time of frantic experimentation, with apparently a new communication gizmo or ‘killer app’ appearing every day. It’s confusing. It’s too much. In a Darwinian struggle, all of those will die and one most liked by the general public will win. It may not be the best one (remember – VHS beat out Betamax), but it will be the one that most people are most comfortable with. Both Google and Facebook are now getting too close to that ideal to allow any newcomer to threaten them. They are the VHS and Betamax of the Web. Either they will fuse (in a friendly or unfriendly way), or one will beat the other. This world is too small for both of them.
What do most people want? What is that One Thing?
This means that anyone, anytime, anywhere can get on any computer, or game console, or pick up a cell phone and, with a single ID and password, access one’s own homepage. That homepage will look either like iGoogle or like Facebook homepage. The default will be just fine, so your Web-innocent sister-in-law will find it useful and easy to use, but it will be very easy to modify to meet everyone’s own needs and wants.
And there, all in one place, is everything you need and want: your Gmail, hotmail, yahoo mail, aol mail, AIM, local time, local weather, latest news from CNN, BBC, NPR and NYT, the cat photo of the day, your twitter, your Wall, a feed that shows what your friends are up to, your Skype or phone, portal to your island on Second Life, your blog, an RSS feed for news, an RSS feed for your favourite blogs, your RSS feed for latest Open Acces scientific papers with your keywords in them, your daily sudoku, your calendar and To Do list, your photo album, your podcast collection, your video collection, your music collection, your book library list, your Google Search, Google Blogsearch, Google Scholar, Google News, …. and all of that in one place, with a single ID and a single password, completely mobile.
Everything in one place – this is something that kids and grandmothers of techies are really looking for, and now techies themselves need to realize this simple little fact. Sooner or later, there will be no more New Shiny Objects to chase, as there will be only One Thing that everyone in the world is using. Like a phone. Or TV. Ubiquitous. Simple. Standardized. Foolproof.
And Vernor Vinge will be proven right once again.

2 Comments

Posted in Blogging, Open Science, Society

Science Blogging at Duke

Posted on July 22, 2007 by | Comments Off on Science Blogging at Duke

Duke University, after years of being behind the curve, is now striving mightily to establish itself as a leader in online science communication. As a recent news article shows, the school is activelly encouraging its students to keep blogs and make podcasts.
I have already mentioned Sarah Wallace and her blog about genomics research in Chernobyl.
Nicholas Experience is a blogging/podcasting group working on environmental science (OK, Sheril is their most famous blogger, but she did it herself, without being prompted by the Nicholas Institute).
At the Howard Hughes Precollege Program Summer 2007, 15 local high school students blog about doing research in the life sciences at Duke University.
Finally, 30 undergrads are writing fascinating stuff about their research experiences, each on a separate blog, with the central place (with a complete blogroll on the right sidebar that I urge you to explore) being the Student Research at Duke blog.
Much of that activity can be traced back to an old blogger meetup and, now that Anton Zuiker is starting to work on their health/science/medicine communications this week, Duke really has a chance to become cutting edge.

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Posted in Blogging, North Carolina, Open Science, Science Education, Science Reporting

Great News!

Posted on July 20, 2007 by | 2 comments

HOUSE BACKS TAXPAYER-FUNDED RESEARCH ACCESS
Final Appropriations Bill Mandates Free Access to NIH Research Findings
Washington, D.C. – July 20, 2007 – In what advocates hailed as a major advance for scientific communication, the U.S. House of Representatives yesterday approved a measure directing the National Institutes of Health (NIH) to provide free public online access to agency-funded research findings within 12 months of their publication in a peer-reviewed journal. With broad bipartisan support, the House passed the provision as part of the FY2008 Labor, HHS, and Education Appropriations Bill.
“The House has affirmed the principle that broad sharing of publicly funded research findings on the Internet is an essential component of our nation’s investment in science,” said Heather Joseph, Executive Director of SPARC (the Scholarly Publishing and Academic Resources Coalition), and a leader of the Alliance for Taxpayer Access (ATA). “This action paves the way for all scientists and citizens to access, use, and benefit from the results of publicly funded biomedical research.”
“We’re pleased by Congress’s recognition of the fundamental rationale for public access – that better-informed patients, clinicians, and researchers will mean better health outcomes,” said Sharon Terry, President of the Genetic Alliance and an ATA activist. “The time has come to sweep away unnecessary barriers to understanding and treating disease. The Genetic Alliance thanks and congratulates the House of Representatives for taking this vital step.”
The current NIH Public Access Policy, implemented in 2005 as a voluntary measure, has resulted in the deposit of less than 5% of eligible research by individual investigators.
In a recent letter to Congress, 26 Nobel Laureates called for enactment of mandatory NIH public access, noting that, “requiring compliance is not a punitive measure, but rather a simple step to ensure that everyone, including scientists themselves, will reap the benefits that public access can provide. We have seen this amply demonstrated in other innovative efforts within the NIH – most notably with the database that contains the outcome of the Human Genome Project.”
“The coalition of support for the NIH policy is extremely broad,” added Joseph. “This critical step was achieved as a result of the vision and collective effort of patient groups, scientists, researchers, publishers, students, and consumers who registered their support.”
A similar measure has been approved by the Senate Appropriations Committee and will be considered by the full Senate later this summer.

More information will be available shortly on The Alliance for Taxpayer Access website.

2 Comments

Posted in Open Science, Politics

Online Science Discussion

Posted on July 18, 2007 by | 1 comment

Curtis, one of the founders of JeffsBench wrote a very interesting article comparing JeffsBench to PLoS ONE in their roles in fostering online scientific discussions. Register, look around and comment….

1 Comment

Posted in Open Science, PLoS

Nursing PLoS

Posted on July 18, 2007 by | Comments Off on Nursing PLoS

Kim of Emergiblog explains nicely why you should support Open Access publishing:
The Public Library of Science:

You are writing a paper. You need to do some research, so you google your topic.
Ah ha! There it is! The perfect article for your paper. The abstract is right in front of you, but you must go to the actual journal for the full text.
Hmmm…you can access the full text of the article, but you must pay to do it! Anywhere from nine dollars to almost thirty dollars for twenty-four hour access.
“No way”, you say! “I have access to my university’s online library, I’ll just go there and look it up for free!”
Except the journal isn’t in the online database or it has to physically come from another library, and you happen to live two thousand miles away from your “campus”.
Reluctantly, you pay for access to the article. Or not….

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Posted in Open Science, PLoS

Open Science Session in October

Posted on July 17, 2007 by | 2 comments

ASIS&T 2008 meeting – Joining Research and Practice: Social Computing and Information Science will be held in Milwaukee on October 19-24, 2007. The Program is now available online and it is very exciting. Especially this session 😉

2 Comments

Posted in Open Science

Science Envy

Posted on July 15, 2007 by | 3 comments

I missed this by weeks, but Dave asked a set of questions that I was pondering on, but found no time and energy to answer until now.
PZ, Janet, Martin, Chad and RPM responded (I am assuming some people outside SB did as well) and their responses (and their commenters’) are very interesting.

1. What’s your current scientific specialty?

Chronobiology, although I have not seen the inside of the lab for three years now. So, scientific publishing, education and communication – does that count?

2. Were you originally pursuing a different academic course? If so, what was it?

Yes, I went to vet school before I came to the States. Finished 3.5 out of 5 years of it, too.

3. Do you happen to wish you were involved in another scientific field? If so, what one?

It took me a while to respond to this, because it was really hard for me to answer this question. I love my field and would do it all over again. Yet, I also love evo-devo. And animal behavior. And comparative animal physiology. And palaeontology. And neuroscience. And evolutionary theory. And marine biology. And….well, pretty much everything in biology.
If I could go all the way back to early childhood and got to start all over again, no other science is completely out of the question, form math, physics and chemistry, to archaeology and psychology.
I also agree with some of my SciBlings on the Math/CS envy. I was REALLY good at math until I was about 18 or so. Decades of unuse, and now I can do little more than balance my checkbook.
In 1980 or so I had all the opportunities to turn myself into a computer programmer, but I decided that playing games was more fun, so, beyond basic HTML, I now know nothing about computers, code, and anything related and I really feel a big gap in my knowledge and ability to function bacause of this.
Another envy is philosophy – I never had an opportunity to take a single philosophy course, not even in high school, so I am completely self-taught and it shows.
But after all this thinking, I realized someting else – I am really envious of 19th century scientists! They felt no need to specialize. Why have to pick and choose, when you could do everything?
Just look at Darwin! He got to travel the world. He wrote papers, technical monographs, popular science books, a travelogue and memoirs. He did geology, palaeontology, taxonomy, comparative anatomy, natural history, plant physiology, animal behavior. Oh, yes, I heard he also dabbled in theory, so he could subsequently do evolutionary biology as well. And many consider him a philosopher.
Perhaps that is why I am so gung-ho about Science 2.0. I see a possibility that the new technology will give rise to new ways to do, publish and communicate science, forming connections between fields that were difficult or impossible to do in the 20th century, when a separate graduate degree may have been needed for such a thing.

3 Comments

Posted in Academia, Open Science, Personal, Science Practice

Help Save Serbia’s #1 Science Blog

Posted on July 13, 2007 by | Comments Off on Help Save Serbia’s #1 Science Blog

Remember the threat of closing the KOBSON blog?
Well, Danica was a brave warrior for Open Science and published an article about this at a much more prominent place: on Global Voices Online.
While this may not be an immediate positive move for Danica’s own career, it is a good move towards persuading the powers-that-be in Serbia that the way forward is towards more openness, not the opposite.

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Posted in Open Science

Make your data freely available if you want to get cited more

Posted on July 13, 2007 by | Comments Off on Make your data freely available if you want to get cited more

This paper (by Heather Piwowar) is not that new, but it is only now starting to get some traction and I’d like to see more people be aware of it:

Background
Sharing research data provides benefit to the general scientific community, but the benefit is less obvious for the investigator who makes his or her data available.
Principal Findings
We examined the citation history of 85 cancer microarray clinical trial publications with respect to the availability of their data. The 48% of trials with publicly available microarray data received 85% of the aggregate citations. Publicly available data was significantly (p = 0.006) associated with a 69% increase in citations, independently of journal impact factor, date of publication, and author country of origin using linear regression.
Significance
This correlation between publicly available data and increased literature impact may further motivate investigators to share their detailed research data.

65% increase in citation is nothing to scoff about, dont’ you think?

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Posted in Open Science

Call for Action: guaranteed public access to publicly-funded research results

Posted on July 13, 2007 by | 1 comment

In the USA:

Effective this week, both the House and Senate Appropriations Committees have proposed FY08 spending bills that direct the National Institutes of Health (NIH) to change its Public Access Policy so that NIH-funded researchers are required to deposit copies of NIH-funded research into the online archive of the National Library of Medicine.
This is big step toward making the policy a success — we need your help now more than ever.
The bills now go to the full House and the Senate for approval. To help ensure success there, we ask that all supporters contact their Representatives AND Senators with support of the proposed bills by phone or fax as soon as possible. The House is expected to convene on Tuesday, July 17, so we ask that Representatives be contacted no later than MONDAY afternoon.
Contacting your Representatives and Senators:
– ALA Legislative Action Center
– Find your Representative
– Find your Senator

And in Europe:

The German parliament just passed a new copyright law that will hinder the free exchange of scientific information. Thus, European copyright politics become more important to override this German decission in the future.
As in the US we have a movement in Europe for open access to publicly funded research results. The Petition for guaranteed public access to publicly-funded research results has been signed by nearly 26000 individuals and many institutions but of course it needs as many signatures as possible.

1 Comment

Posted in Open Science

Obligatory Readings of the Day – competition vs cooperation in science

Posted on July 12, 2007 by | 1 comment

Four excellent, thought-provoking articles all in some way related to the idea of Open Science. One by Bill Hooker:
Competition in science: too much of a good thing
and three by Janet Stemwedel:
Clarity and obfuscation in scientific papers
Does thinking like a scientist lead to bad science writing?
OpenWetWare

1 Comment

Posted in Academia, Open Science, Science Education, Science Practice

San Francisco – a running commentary

Posted on July 11, 2007 by | 8 comments

OK, so I’ve been here for about a week now. It’s been so far an exciting and overwhelming experience – there is so much to learn! And I am impatient with myself and want to get in the groove right now. I need to learn to slow down a little…
Anyway, I did manage to drop in here at the blog a couple of times and report on meetups with some local bloggers, but here is a little bit more about the week so far…

Continue reading →

8 Comments

Posted in Fun, Open Science, Personal, PLoS, Science Education

Fighting for Open Access in Serbia

Posted on July 9, 2007 by | 1 comment

Vedran Vucic is a Linux afficionado in Serbia. He and his organization have gone all around Serbia, wired up the schools, taught the teachers and students how to use Linux, taught the teachers and students how to use various online educational resources ranging from blogs to ATutor, etc.
Vedran also gives technical support to about 40 Serbian bloggers whose work he also aggregates.
He is now putting a lot of energy into persuading scientists, especially the young, not-yet-entrenched ones, to go online and to promote Open Access. It is an uphill battle, but he is persistent!
You’ll see that he has PLoS as his top link on both of his websites.
Scientists in the developing world are going to be among the biggest beneficiaries of Open Access in the future and I am looking forward to working with Open Access promoters in various countries around the world. With Vedran and Danica, I already have a head-start with Serbia. Where are the others? E-mail me!

1 Comment

Posted in Open Science

Open Access this week

Posted on July 8, 2007 by | 4 comments

First, I’d like to thank Darksyde for placing the discussion of Open Access science publishing on the front page of DailyKos. If you are a registered user there, go ahead and add your 2 cents to the conversation.
Matt at Behavioral Ecology Blog explains RSS, what it is, how it works and how to use it to get science news. Recommended.
Greg Laden is a Linux advocate. While I am not, I understand that, though Open Source and Open Access are not the same thing, they do go hand in hand in a way. Something to think about…
Bjorn Brembs provides me with some useful advice and ideas.
My SciBlings Josh Rosenau and Alex Palazzo discuss scientific publishing, present and future.
Two interesting articles I will study in detail:
Toward a Post – Academic Science Policy: Scientific Communication and the Collapse of the Mertonian Norms by David Kellogg
Using Social Psychology to Motivate Contributions to Online Communities
Finally, thanks to Mike the Mad Biologist, Anton Zuiker, Gus diZerega, Jacqueline of Element List, Stephen Downes and Melissa McEwen for celebrating my first day at work with me.

4 Comments

Posted in Open Science

Obligatory Readings of the Day – Science 2.0

Posted on July 4, 2007 by | 1 comment

Interview with Timo Hannay, Head of Web Publishing, Nature Publishing Group
Scientific Communications in Web 2.0 Context
Publishing Versus Posting: Nature Magazine Turns to a Conversational Content Model

1 Comment

Posted in Open Science

Free Access or Open Access?

Posted on July 3, 2007 by | 3 comments

Buyer beware! Not everything in science publishing that calls itself Open Access actually is so.

3 Comments

Posted in Open Science

Do Serbian scientists need a blog of their own?

Posted on June 29, 2007 by | 5 comments

Not that it costs anything to have one…
Yet, the Konsortium of science libraries in Serbia is seriously contemplating shutting down their KOBSON blog, an invaluable tool in science communication in the region.
Danica, who the regular readers of this blog are quite familiar with as she is the Number One Champion for Open Science and Web 2.0 science in Serbia, has put a lot of effort into building the online infrastructure for Serbian scientific communication, including the KOBSON blog and the KOBSON wiki, as well as teaching and preaching to the local scientific community about the importance of catching up with the world after a decade of isolation and fully embracing the modern communication tools. She was also involved in setting up the Serbian Citation Index, from which I mined a paper that I used to demonstrate how important Open Access is to scientists in developing countries.
There is not much more that Danica alone can do in the present situation to save the KOBSON blog, but perhaps YOU all can help. How? Let’s demonstrate the power of Science 2.0 by direct example! Go to the KOBSON blog and explain the importance of such a tool in the comments of this post. Even better, if you are fluent in one or another variant of the Serbo-Croatian language, post a comment on the Serbian version of the post. Then, post a link and this plea to your own blog as well and ask your readers to do the same.

Update: On the front page of the KOBSON home (not blog) there is “contact” information and an e-mail address:
nainfo@nbs.bg.ac.yu
Be polite and explain why hosting (and pointing to) a blog is essential for 21st century science.
The problem is not just saving the blog where it is on WordPress, but also moving it onto the Library server, or at least linking to it from the homepage so people see it and use it more. Right now, only people “in the know” use it which severely limits its usefulness.
You should also join the ‘Fight for Science Blogs‘ Cause on Facebook and invite all your friends to join it as well (the ’causes’ function is malfunctioning on Facebook right now, so try later if you cannot sign up right now).

5 Comments

Posted in Balkans, Blogging, Open Science

Referees’ Reviews on PLoS-ONE

Posted on June 29, 2007 by | 2 comments

It’s always intriguing to know what the peer-reviewers have thought and written about a particular manuscript. Now, you can find out, at least in some cases, on PLoS-ONE papers. Chris Surridge explains.

2 Comments

Posted in Open Science

Prometeo Network

Posted on June 27, 2007 by | Comments Off on Prometeo Network

Nature News just had an article announcing a new social networking site for physicians and biomedical scientists called Prometeo Network. Another one to check out and add to the ever-growing list of such new sites.

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Posted in Open Science, Science Practice

Nature Precedings

Posted on June 25, 2007 by | 7 comments

A few days ago, Nature launched its newest Web 2.0 baby, the Nature Precedings.
It is very interesting to see the initial responses, questions and possible misunderstandings of the new site, so browse through these posts and attached comments by Pedro Beltrao, Timo Hannay, Peter Suber (and again), Kaitlin Thaney, Jean–Claude Bradley, Guru, Egon Willighagen, Deepak Singh, ChemSpy, Putting Down A Marker, Maxine Clarke, Bryan Vickery, Clarence Fisher, David Weinberger, AJC, Euan Edie, Tim O’Reilly, Dean Giustini, Peta Hopkins, Eric, mrees, Sally Wyman, Michael Jubb, Alex Palazzo, Marie, Corie Lok, Attila Csordas, Ben Vershbow, Kathleen Fitzpatrick, Andrea Gawrylewski, Lukasz Cwiklik, Yeastbeast, Kevin Gamble, Andy Powell, lvowell, John Timmer, Brandon Keim, Omics, Revere and many others. It’s worth your time to read all that (and most of the posts are not very long anyway)!
Just a quick thought (more, much more, is likely to come soon!) for now about a couple of questions:
What is the appropriate content?
First, what kind of stuff should one put on Nature Precedings?
For instance, if I have a poster that I took to a couple of meetings in 1999/2000 and the paper has come out since – is it still interesting?
If I have a poster that I took to a couple of meetings in 2001/2002 which contains unpublished data, but does not contain data collected later which somewhat modify the conclusions, is it dishonest to put it on NP? The same for a PPT file of a talk?
If I have published a study on my blog and it is already time-stamped there (first here, then republished here) does it make sense to put the same stuff on NP?
I have posted unpublished data at the very end of this review post. Is that OK for NP?
Are my ClockTutorials fit for this platform? After all, one of them was cited in the “real” scientific paper.
I have posted hypotheses (often embedded into reviews) on my blog before, e.g., here, here and here. Are they appropriate for NP?
Redundancy
What I mean here is the possibility to have stuff posted at several websites simultaneously, thus ensuring that at least one copy survives the next 1000 years or so. NP is going to automatically store everything at a few separate places, I understand, and some of the stuff will get published in peer-reviewed journals later, and some of the stuff will also get re-posted on blogs.
The University library repositories are pretty empty and include only copies of already published peer-reviewed papers. They are also scattered among many institutions. It is so much better to have everything at one place, under the banner of a respectable brand name. And, since it is under Creative Commons licence, Nature has no copyright over the material.
Open Science organizations tend to see each other as potential collaborators, not competitors (soooo 20th century!).
Publishability (did I just invent a new word?)
A recurring question in the posts/comments linked above: will posting stuff on NP make it more difficult to later publish the same data in a Journal? Yes, if it is a Closed Access journal. No, if it is an Open Access journal (or Nature, which I hope will go full Open Access one day soon). Thus, NP is good for Open Science. Put the preliminary results on NP, get feedback, do some more work, write a manuscript, send it to PLoS-ONE, have it peer-reviewed both before and after publication, and enjoy the visibility (and the increased rate of citations) afterwards.
Science 2.0
I think that people misunderstood where I was going with this post a few days ago. I was not suggesting to use Facebook as a platform for science networking (though outreach can certainly be done there). I was suggesting that we study why Facebook is so attractive (and addictive) and try to replicate it for scientists. Read what danah boyd wrote about it the other day for the first inklings of why Facebook is becoming so interesting to ‘grown-ups’ ever since the outside applications were allowed a few weeks ago (she’s in Berkeley, isn’t she – I have to get to meet her and pick her brains while I am there in July).
In other words, Science 2.0 is scattered all over. I have far too many bookmarks to various sites and I cannot and will not check every one of them every 10 minutes. But if there was ONE SINGLE place to go and get all of the stuff, it would be a site of choice to every scientist on the planet.
Just imagine going online in the morning and having your browser ‘home’ set at a website that combines into one spot PLoS-ONE, Knowble, Nature Precedings, Nature Network, Nature Blogs, Nature Blog Network, Scienceblogs.com, Connotea, Postgenomic, Scintilla, JeffsBench, Erudix, ArXiv.com, JoVE, Lab Action, SciTalks and other stuff like thought experiments, medical hypotheses, biological procedures, Open Notebook Science, etc.? Having one Sci-ID (trademark by me) that works on all those sub-sites and places all of your uses of it in your profile that can be used for your promotion, tenure, employment, etc.? Totally Awesome!!!
Obviously, I have been thinking about these questions for a while now and I may be one of the more optimistic folks out there. Hopefully, with my new job starting in less than two weeks, I’ll be able to turn some of the thinking (fueled by optimism) into action and test it in the real world!

7 Comments

Posted in Open Science, Science Practice

The 2006 Impact Factors are now avaliable

Posted on June 20, 2007 by | 4 comments

The 2006 Thomson Scientific Journal Citation Reports were released today. Mark Patterson reports on the PLoS journals, three of which have made it to the list for the first time, as they are too new, so their ratings are based on just a portion of the time:

The 2006 impact factors have just been released by Thompson ISI. The first two PLoS journals continue to perform very well: 14.1 for PLoS Biology (14.7 in 2006); 13.8 for PLoS Medicine (8.4 in 2006). The PLoS community-run journals also received their first impact factors: 4.9 for PLoS Computational Biology; 7.7 for PLoS Genetics; and 6.0 for PLoS Pathogens. (Note that the latter impact factors are based on only around six months worth of publications in 2005, and are likely to increase next year.)
Although the impact factor is an over-used and abused measure of scientific quality, it is a journal metric that is important for the research community, and so until there are alternatives, PLoS has to pay attention to the impact factor.

PLoS-ONE, if I am correct, should appear in the Report next year.
Also, for my circadian readers, it may be of interest how our flagship journal, Journal of Biological Rhythms fared. Here is from the e-mail from the Editor:

I’m happy to report that JBR’s Impact Factor has increased! JBR’s 2006 Impact Factor is 4.633, compared to 4.367 for 2005. JBR is now ranked 7/64 in the Biology category (compared to last year’s 8/65) and 8/79 in the Physiology category (compared to last year’s 8/75).

Update: Alex has access, so he pulled out a few more ratings for top journals.

4 Comments

Posted in Open Science, Science Reporting

Lessig moves on, to even bigger and more important battles

Posted on June 20, 2007 by | Comments Off on Lessig moves on, to even bigger and more important battles

After 10 years of fighting for open source, net neutrality, free information and open education, Lawrence Lessig has decided to change his career and to seriously attack the problem of corruption in the U.S. politics. It’s not going to be easy, but having Lessig on our side in this battle is a great assett. Read his explanation (though you know I disagree with him on Obama and corruption) as it is very telling and well-written.
Hat-tip: Danica (where you can also see the movie of Lessig giving a speech in which he made the announcement).

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Posted in Blogging, Open Science

SciTalk.com

Posted on June 19, 2007 by | 1 comment

On the heels of this post, I was informed of another Web2.0 site for scientists that just launched – SciTalks collects talks and lectures by scientists on a variety of topics. There are already many clips available on the site, which you can rate, or add some from your own collection. You can find out more about the site here and at the site’s blog.

1 Comment

Posted in Blogging, Open Science

Science 2.0

Posted on June 17, 2007 by | 6 comments

I think I have a profile on Friendster – I don’t know, I haven’t checked since 2003. I have bare-bones profiles on MySpace, LinkedIn and Change.Org and I will get an e-mail if you “friend” me (and will friend you back), but I do not have time to spend on there. I refuse to even look at all the other social networking sites like Twitter – there are only so many hours in the day.
But I am interested in possible ways of making science communication more interactive and more Webby 2.0, beyond just blogs. Pedro, Carl and Phillip have recently written thoughtful posts about this topic as well.
So, I am looking around to see what works. I set up profiles on Knowble and Nature Network. I check out the Sci/Tech section of NewsTrust and the Science tag on DailyKos every now and then. I check, as regularly as I can make myself, what’s new on Connotea, Postgenomic, Scintilla and JeffsBench. And of course I read tons of science blogs.
All of those are interesting experiments in different aspects of Web2.0 and, considering my soon-to-start job, I’ll be tracking all those experiments very closely to see what works and what doesn’t and why.
But my own personal favourite – and I’ll have to figure out why I like it so much – is Facebook. Some of my old NCSU students put me on there as soon as it was launched (only a few have un-friended me since) and I can see as they get jobs, get married, etc., which is quite nice. I set up a profile (yes, you can ‘friend’ me – just say you are my reader) and have been hooked ever since.
Then, I started reading what Fred Stutzman writes on his blog – he is doing a PhD on social networks here at UNC, with a special emphasis on Facebook. I repeated for the NCSU network a study he did in the UNC network.
Then, as an experiment, I started friending hundreds of ex-Yugoslavs all around North America and realized how the youngsters appear to have no animosity towards the “other” ethnics groups: Serbs, Croats, Slovenians, Macedonians, Montenegrins, Bosnians, Kosovo Albanians, etc. – all are friending each other, joining various “Yugo-nostalgic” groups, etc.
When Facebook opened its doors to non-‘edu’ addresses, the first result was dismaying. I suddenly started getting friends requests from various scantily clad women who wanted me to support their modeling agencies, or to vote for them on Maxim or some such stuff. My thought at the time was “Oh my, there goes Facebook, following MySpace into the junk territory…”
So, I deleted several hundreds of “friends” and left only those I knew personally very well, either online or offline. That was also the time when others – more serious types – started discovering the Facebook. Now, you can join fan-club groups of such blogs as Pharyngula, Pandagon (also I Am Amanda Marcotte), Shakesville, Pam’s House Blend, Feministe, Firedoglake and Blue NC, or a broader North Carolina Bloggers group. And you can make friends with those blogs’ owners, contributors, commenters and lurkers.
Since yesterday, you can also join the fan-club group of A Blog Around The Clock. Or you may prefer to join the fans of Scienceblogs.com.
There are many fun groups there, like Sleep… it’s the new sex. But there are also a growing number of science-related groups, e.g., Order of the Science Scouts of Exemplary Repute and Above Average Physique, Prof. Steve Steve is my Hero!, The Skeptics’ Guide to the Universe, STS (Science and Technology in Society) and Charles Darwin Has A Posse.
Some groups are more action-oriented, e.g., Access to Research Now!, I want national wireless Internet!, Net Neutrality, Abolish Abstinence Only Sex Education, Support Stem Cell Research or Stop the U.S.Army from bombing Pinon Canyon dinosaurs.
One can follow the links and links-within-links from group to group, from friend to friend, and find all sorts of stuff. Last year, I made an ‘event’ for the NC Science Blogging Conference and will do so again a little later in the year for the Second conference. I may try to promote the Anthology there, or build a fan-club of PLoS. And with the new ability to add all sorts of applications built outside of Facebook, the possibilities for online connections of scientists are endless. Will there be a Connotea app there soon? Postgenomic? All we need to do is get more scientists to sign up and who knows what may come out of it in the end!
Update: I just noticed that Euan also thought about Facebook in terms of Science 2.0
Related: Bertalan Meskó – 10 Tips for How to Use Web 2.0 in Medicine
Has anyone looked at Erudix yet?
And for the YouTube of science, check JoVE and Lab Action
More on Facebook:
Dave Winer:

When someone lists you as a “friend” on Facebook you get to confirm it. That’s good.
When you click on the “Confirm” button, you get a list of choices that almost never seems to have the right choice. Does that mean you don’t have a relationship with the person? No. It means that the list of possible choices hasn’t been updated since Facebook was opened to people outside the education system.

Dave Winer again:

Everyone is going ga-ga over Facebook, but like the people who hold out on Twitter, I’m not ready to give my life to a service that views me as a college student. My relationships are adult relationships. Okay, I probably won’t even use Facebook when they offer me some realistic choices on labels for the arcs that connect me with people in my network, because what we really need is an architecture that allows anyone to add a tag to an arc, the same way we add tags to pictures on Flickr.

BTW, one does not have to choose from one of the given options, but can invent a new one (perhaps they listened to Dave and fixed this).
Fred Stutzman:

I think my thoughts on how higher ed could use the platform warrant another post. I might even mock up a few ideas. Your ideas and feedback welcome in the thread.

Danica:

I love Facebook and all the apps that are popping up each day. This is not anymore the second, but third life…

Scoble:

Conclusions: if you held a gun to my head and made me choose only one of these services I’d pick Facebook. Especially if I already didn’t have a blog as a platform to communicate with other people.

6 Comments

Posted in Blogging, Open Science

PLoS 500

Posted on June 6, 2007 by | 1 comment

Yesterday, PLoS-ONE celebrated the publication of the 500th paper (and additional 13). Here are some quick stats:

1,411 submissions
513 published paper
360 member editorial board and growing
19 day average acceptance to publication
600+ post publication comments posted

I am assuming that the remaining 898 manuscripts are in various stages of the publication process: rejected, in review, in revision, or in the pipeline to appear on the site any day now.
The very first paper was published on December 20, 2006. The 500th paper is this one “Climate Change Cannot Explain the Upsurge of Tick-Borne Encephalitis in the Baltics”, which is quite an interesting read (and I wonder if global warming denialists will try to misuse it in the near future).
Since I got the job with PLoS-ONE I’ve been asked some questions about it (even though I’m just an egg: I will start working a month from now) which reveal some misunderstandings about this journal. So I looked around the site and I asked some PLoS people trying to find the right answers.
First, the word ONE in its title suggests that this is meant to become the flagship journal in the PLoS stable and a direct competitor to Science and Nature. Sure, but that does not mean that the format and the publishing philosophy is the same as those two journals. ONE refers more to being the first (and so far unique) journal using the 21st century model of publishing, rather than to the ambition to reach the #1 spot on the Citation Index.
The hardcopy journals are limited by the size of their journal – how many papers can appear each week? Being entirely online, PLoS has no such space constraints. So PLoS-ONE does not seek only spectacular papers or revolutionary (thus potentially wrong) papers on topics with potentially wide interest. Everything that is well done and well written and passes the peer-review, no matter how specialized or obscure the field, will be accepted. As Chris Surrige, the managing editor of PLoS-ONE explained to me:

ONE certainly isn’t meant to be Science or Nature. What we wanted with ONE was for it to be ONE place to contain all of science. Supremely broad and deep. We want to publish papers that could have been published in Science or Nature AND papers that would otherwise have been heading for the most specialist of specialist journals. PLoS ONE is supposed not to fit within the current hierachy of journals, it stands outside it as an alternative not to any journal in particular
but to ALL conventional journals.

This also means that papers from all areas of science are welcome (excepting, perhaps, meta-science papers, e.g., in history, sociology and philosophy of science). For now, most of the papers published so far are in the biology/genetics/medicine areas, which is understandable as the researchers in these areas are already familiar with the publishing philosophy of PLoS through its other journals. But PLoS-ONE is trying to expand its scope to all the other disciplines as well and is welcoming the brave, enterprenurial people who are willing to break the ice and submit the first manuscript in their area od study (and hopefully bring in other colleagues as well).
These and many other questions have already been discussed (and surely will be in the future) on the PLoS blog which should be your regular read (dig through the archives as well – there is some good and important stuff there). The instructions for submission of manuscripts are clear and detailed: it is fast and streamlined, but it is most definitely peer-review.
Anyway, my job will not be on the publication end of the process, but on the post-publication end – the post-publication peer-review of sorts. PLoS-ONE allows and encourages scientists and other educated readers to annotate the papers and to post comments/discussions on papers. You can read about those here and try it out in a neutral space (if you are still nervous about annotating/discussing a real paper) here. My goal, among others, will be to bring in more people to the site to discuss papers and to develop ways to make this activity worth people’s time and effort (on top of being fun to do, as we bloggers already know). In this effort, I will occasionally use you – my readers – as my own focus group, asking for your feedback on changes and innovations we will try to implement in the future. Stay tuned. I’ll explain more once I actually start working there.

1 Comment

Posted in Open Science, Science Practice, Science Reporting

Open Notebook Science is more than just Open Access

Posted on June 5, 2007 by | 2 comments

As explained by Jean-Claude Bradley in this excellent interview: The Pursuit of Automation: Open Notebook Science:

The difference between Bradley’s idea and traditional open source projects is the clutter, i.e., all of the data collected from research. In a journal article, what the reader receives is a set of findings, published after peer review, along with the conclusions and basic data used to reach them. Bradley’s project allows the reader to see the process unfold, from hypothesis to conclusion, with all data, experiments and notes that are collected along the way. This inclusiveness allows other researchers to better assess their own ideas, because not only do they have the conclusion and data used to support it, but also they have access to every failed or incomplete subset of data to use in their equations.

2 Comments

Posted in Open Science

Hooray for Open Science

Posted on June 5, 2007 by | 4 comments

Social Science and Humanities bloggers have been doing it for quite a while, but natural scientists have largely been very reluctant to do this. Now, with approval of his PI, Attila Csordas will start posting parts of his Dissertation on his blog. Stem cell research – mmmm, nice! Sure, the actual data may never appear there, but this is a big move forward anyway.
Most useful is the view of Nature that he reprints on his blog on what actually constitutes ‘previously published’ work, i.e., what not to do if you want to have the paper published in their journal. I’d really like to see equivalent statements for some other popular journals as well.
And he also points to a student writing her chemistry Masters Thesis on a wiki.

4 Comments

Posted in Open Science, Science Practice

Danica Needs a New Job!

Posted on June 4, 2007 by | Comments Off on Danica Needs a New Job!

Graduate of the University of Belgrade (Serbia), City University (UK) and UNC-Chapel Hill (USA), with a Masters from University of Belgrade, Danica Radovanovic is currently in Belgrade without a job and she is looking for one either in Serbia, in Western/Northern Europe or in the USA.
Danica is the tireless Serbian pioneer in all things online: blogging, open source, Linux, science blogging, open science, social networking software, online publishing, eZine editing, etc. She is the force behind putting Serbian science online and making it open. She has done research on Internet use in Serbia in comparison to the UK and the USA and has been a tireless advocate for the Internet, open source computing and Open Science, travelling around Serbia and the world talking about it. She is also a cybrarian and has experience working at the Library of Congress.
You can learn more about Danica here and check her LinkedIn CV/Resume (expanded). She will send you the real Resume on demand.
This is your opportunity to snag someone with boundless energy and enthusiasm, coupled with knowledge, skill and experience. Do you or your organization need someone like that?

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Posted in Academia, Balkans, Blogging, Open Science, Personal

It’s Official!

Posted on May 24, 2007 by | 66 comments

Yes. I said I wanted this job. And, in a very new and interesting way, after a fun interview, I got it. Signed and faxed the contract yesterday. Will be in San Francisco for a little while in July, then telecommute afterwards. Can pajamas be deducted as tools one needs for the job? Exciting!

66 Comments

Posted in Blogging, Open Science, Personal

How to find freely-available bio-medical papers?

Posted on May 23, 2007 by | Comments Off on How to find freely-available bio-medical papers?

In three easy steps, hopefully made obsolete by a completely Open Science a few years down the road….but surely useful for now.

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Posted in Open Science

Another role for Open Science

Posted on May 16, 2007 by | 16 comments

When I teach BIO101 I usually give at least one assignment that entails finding a biology-related article, writing a short summary of it and explaining the gist of it to the rest of the class. We did that this Monday and the students picked, as usual, some interesting topics (including some that take us way outside of the scope of the course, e.g., game theory and Evolutionarily Stable Strategies). The sources, as usual, are popular science magazines like American Scientist (the last one that is still of high quality, I’m afraid to say), Scientific American, Discover, Natural History, etc.
One of the students talked about the research on butterflies and beetles by Emlen and Nijhout – if this happened just a week later, she could have used the brand new (and better written) article in Seed Magazine on this topic instead of a 1998 article from Discover.
But this year there was a first! One of the students reported on a paper she found online – where? On PLoS-Biology, of course. This paper about ‘Thermal Stress and Coral Cover as Drivers of Coral Disease Outbreaks’. And she did a good job understanding the paper (with a little help from an MSNBC article about it as well). Remember, this is someone with zero background in biology, being able to understand a true scientific paper, not just a popular science article. I was quite impressed!

16 Comments

Posted in Open Science, Science Education