open science

As part of his Gene Week celebration over at Forbes, Matthew Herper has a provocative post titled "Why you can't have your $1000 genome". In this post I'll explain why, while Herper's pessimism is absolutely justified for genomes produced in a medical setting, I'm confident that I'll be obtaining my own near-$1000 genome in the not-too-distant future. Matt's underlying argument is that while sequencing costs will continue to drop, obtaining a complete genome sequence that is sufficiently accurate for medical interpretation will require additional expenses (increased sequence coverage to…

As part of his Gene Week celebration over at Forbes, Matthew Herper has a provocative post titled "Why you can't have your $1000 genome". In this post I'll explain why, while Herper's pessimism is absolutely justified for genomes produced in a medical setting, I'm confident that I'll be obtaining my own near-$1000 genome in the not-too-distant future. Matt's underlying argument is that while sequencing costs will continue to drop, obtaining a complete genome sequence that is sufficiently accurate for medical interpretation will require additional expenses (increased sequence coverage to…

Late last week I stumbled across a press release with an attention-grabbing headline ("The Causes of Common Diseases are Not Genetic Concludes a New Analysis") linking to a lengthy blog post at the Bioscience Resource Project, a website devoted to food and agriculture. The post, written by two plant geneticists, plays a tune that will be familiar to anyone who has encountered the rhetoric of GeneWatch UK: basically, modern genomics is pure hype perpetuated by scientists seeking grant money and corporations seeking to absolve themselves of responsibility for environmental disasters.  The…

A reminder to anyone who reads my other blog Genomes Unzipped that we have a reader survey underway there now, which includes some questions about genetic testing experiences and attitudes towards genetics. We're closing the survey to responses this weekend, so if you're an Unzipped reader but haven't had a chance to fill in the survey, please do so now.

Update 30/11/10: 23andMe has extended their 80% discount until Christmas, without a need for a discount code. Personal genomics company 23andMe has made some fairly major announcements this week: a brand new chip, a new product strategy (including a monthly subscription fee), and yet another discount push. What do these changes mean for existing and new customers? The new chip 23andMe's new v3 chip is a substantial improvement over the v2 chip that most current customers were run on (the v2 was introduced back in September 2008). Firstly, the v3 chip includes nearly double the number of…

Back in June I launched a new blog, Genomes Unzipped, together with a group of colleagues and friends with expertise in various areas of genetics. At the time I made a rather cryptic comment about "planning much bigger things for the site over the next few months". Today I announced what I meant by that: from today, all of the 12 members of Genomes Unzipped - including my wife and I - will be releasing their own results from a variety of genetic tests, online, for anyone to access. Initially those results consist of data from one company (23andMe) for all 12 members; deCODEme for one…

Back in June I launched a new blog, Genomes Unzipped, together with a group of colleagues and friends with expertise in various areas of genetics. At the time I made a rather cryptic comment about "planning much bigger things for the site over the next few months". Today I announced what I meant by that: from today, all of the 12 members of Genomes Unzipped - including my wife and I - will be releasing their own results from a variety of genetic tests, online, for anyone to access. Initially those results consist of data from one company (23andMe) for all 12 members; deCODEme for one…

Brian Lehrer was kind enough to invite me onto his show the other day along with Kathleen Fitzpatrick of MediaCommons and Katherine Rowe, guest editor of the ground-breaking openly peer reviewed issue of Shakespeare Quarterly, to discuss digital scholarship, peer review, and open science. Our segment begins at 42:00.

Our friend Victoria Stodden is the lead author on a paper published today in Computing in Science and Engineering summarizing the recommendations of a roundtable we participated in at Yale on data (and code) sharing in (computational) science. Seed's Joy Moore is an additional author on the paper. To adhere to the scientific method in the face of the transformations arising from changes in technology and the Internet, we must be able to reproduce computational results. Reproducibility will let each generation of scientists build on the previous generations' achievements.... Reproducible…

From the New York Times: Now some humanities scholars have begun to challenge the monopoly that peer review has on admission to career-making journals and, as a consequence, to the charmed circle of tenured academe. They argue that in an era of digital media there is a better way to assess the quality of work. Instead of relying on a few experts selected by leading publications, they advocate using the Internet to expose scholarly thinking to the swift collective judgment of a much broader interested audience. Will be interesting to follow the Shakespeare Quarterly experiment...

From the New York Times The key to the Alzheimer's project was an agreement as ambitious as its goal: not just to raise money, not just to do research on a vast scale, but also to share all the data, making every single finding public immediately, available to anyone with a computer anywhere in the world. No one would own the data. No one could submit patent applications, though private companies would ultimately profit from any drugs or imaging tests developed as a result of the effort.

I just read that MIT's ground-breaking OpenCourseWare initiative passed the 2,000-course mark this month. That's a lot of free lectures, course notes, and videos from some of the best scientific minds of the planet... First announced in 2001, MIT OpenCourseWare (OCW) is an ambitious effort to share MIT's education resources freely and openly on the web to improve formal and informal learning worldwide. ... Since the site was launched in 2002, OCW materials have been visited on the MIT site or partner translation sites 98 million times by an estimated 70 million visitors from around the world.

Last week, my SciBling Jason Goldman interviewed me for his blog. The questions were not so much about blogging, journalism, Open Access and PLoS (except a little bit at the end) but more about science - how I got into it, what are my grad school experiences, what I think about doing research on animals, and such stuff. Jason posted the interview here, on his blog, on Friday, and he also let me repost it here on my blog as well, under the fold: Here at Thoughtful Animal headquarters, we're starting a new series of seven-question interviews with people who are doing or have done animal…

I have a few conferences coming up and I thought I'd share my schedule just in case any of you out there in sciencelibrarianblogland will also be attending. I'll list them in order, along with whatever I'll be presenting. BookCamp Toronto, May 15, Toronto 9:30: eBooks in Education and Academia -- the glacial revolution John Dupuis (York University) Evan Leibovitch (York University) Description: Despite growing public acceptance of eBooks, two areas in which they could offer the most benefit -- education and academia -- are far behind the eBook mainstream. This session will discuss issues…

One difference between reading Open Laboratory anthologies and reading the original posts included in them is that the printed versions are slightly edited and polished. Another difference is that the Prefaces and Introductions can be found only in the books. They have never been placed online. But now that four books are out and we are halfway through collecting entries for the fifth one, when only the 2009 book is still selling, I think it is perfectly OK to place Prefaces and Introductions that I wrote myself online. I wrote Prefaces for the 2006, 2007 and 2008 book, as well as the…

US seeks to make science free for all by Declan Butler: The push to open up scientific knowledge to all looks set to go into overdrive. Over the past decade, the accessibility offered by the Internet has transformed science publishing. Several efforts have already tried to harness the web's power to make research papers available for free. Now two parallel efforts from the US government could see almost all federally funded research made available in free, publicly accessible repositories..... Read the whole thing....

I received an email a couple of weeks ago from Daniel Cromer of the Hrenya Research Group located in the Department of Chemical and Biological Engineering at the University of Colorado at Boulder. His group was interested in expanding their online presence and had stumbled up the presentation I'd given a couple of years ago on Academic Blogging: Promoting your Research on the Web. He asked me if I could explore those same ideas in a short presentation to the group. That was Monday. Sadly, I wasn't able to actually go to Colorado for the presentation -- it was all online using the…

You may be aware that, as of recently, one of my tasks at work is to monitor media coverage of PLoS ONE articles. This is necessary for our own archives and monthly/annual reports, but also so I could highlight some of the best media coverage on the everyONE blog for everyone to see. As PLoS ONE publishes a large number of articles every week, we presume that many of you would appreciate getting your attention drawn to that subset of articles that the media found most interesting. So, for example, as I missed last week due to my trip to AAAS, I posted a two-week summary of media coverage this…

In San Diego this week. Check it out. I'll be there - see my session. If you will be there, let me know. Let's have coffee or lunch, etc. My session is on 21st in the morning, and there is a lot of social stuff I agreed to on the 19th in the afternoon and evening, and of course I want to see a lot of other sessions, but I am generally flexible. Just ping me over e-mail or Twitter or phone (if you have my number) or post a comment here.

Aves 3D is a 'three dimensional database of avian skeletal morphology' and it is awesome! This is an NSF-funded project led by Leon Claessens, Scott Edwards and Abby Drake. What they are doing is making surface scans of various bones of different bird species and placing the 3D scans on the website for everyone to see and use. With simple use of the mouse or arrow buttons, one can move, zoom and rotate each image any way one wants. The collection is growing steadily and already contains some very interesting bones from a number of species, both extinct and extant. You can see examples of…