open science
cpikas | January 16, 2010John Hogenesch, Assistant Professor of Pharmacology - Penn School of Med
gene-at-a-time is giving way to genome wide - larger datasets, collaborative research
last year more added to genebank than all previous years combined (wow!) - exceeds Moore's law.
Academia responds by buying storage and clusters - but you need great IT staff - and it's really hard to get and keep them (they go to industry), heating & cooling, depreciation, usage/provisioning (under/over utilized). Larger inter-institutional grids - access is tightly regulated, they are very complex to program in/for
Cloud computing…
pontiff | January 13, 2010Missed this over the break: a facebook note about the future of funding of the arXiv. The post points to two documents of interest, the first a statement about support:...We intend to establish a collaborative business model that will engage the institutions that benefit most from arXiv -- academic institutions, research centers and government labs -- by asking them for voluntary contributions.
and also a handy dandy FAQ about the changes.
clock | December 18, 2009Two years ago, at the 2008 Science Blogging Conference, Dave Munger introduced to the world a new concept and a new wesbite to support that concept - ResearchBlogging.org. What is that all about?
Well, as the media is cuttting science out of the newsroom and the science reporting is falling onto institutional press information officers and science bloggers, more and more people are looking for scientific information on science blogs, especially as the expertise of the blogger is likely to provide a more accurate assessment of a freshly published study than the mainstream media can usually do…
clock | December 18, 2009The December 2009 edition of the Journal of Science Communication is now online with some intriguing articles - all Open Access so you can download all the PDFs and read:
Control societies and the crisis of science journalism:
In a brief text written in 1990, Gilles Deleuze took his friend Michel Foucault's work as a starting point and spoke of new forces at work in society. The great systems masterfully described by Foucault as being related to "discipline" (family, factory, psychiatric hospital, prison, school), were all going through a crisis. On the other hand, the reforms advocated by…
clock | December 18, 2009As many of you, my readers, are interested in Open Access publishing and have given it quite some thought over time, I think you are the right kind of people to contribute to this in a thoughtful and persuasive manner. Please do it.
From everyONE blog:
The White House Office of Science and Technology Policy has invited comment on broadening public access to publicly funded research and they want to hear from you. Please post your contributions to this blog.
Their Request for Information (RFI) lasts for just 30 days and expires on 7 January 2010, so we'd like to encourage you to get involved…
clock | December 16, 2009
I know there is a nice subset of my readers who can read Serbian language. If you are one of those, you may be interested in the last issue of 'Pancevacko Citaliste'. Along with several interesting articles about science publishing and librarianship, there is also an interview with me by Ana Ivkovic, librarian at the Oncology Institute in Belgrade. The journal is Open Access, so you can download and read the PDF here.
cpikas | November 28, 2009With well known and respected open science projects coming out of chemistry as well as cool tools like pubchem and emolecules... it seems a bit unfair of me to ask if chemists are grinches. But there has been and there continues to be a lot of study of data/information/knowledge sharing in chemistry - or, really, the lack thereof. In general, pre-prints are not passed around or self-archived, there is very little data sharing (there are counter examples in crystallography), and details are withheld from conference presentations or the conference slides are not made available (Milo used to…
dgmacarthur | November 18, 2009European Genetics and Anthropology has a neat little tutorial that may be of interest for genetic hobbyists: it provides instructions on how to run the program STRUCTURE on your own genetic data generated by a personal genomics company such as 23andMe or deCODEme.
STRUCTURE is an extremely popular tool among researchers working in population genetics, which allows you to generate plots showing estimates of the proportion of an individual's genome belonging to different population clusters.
The tutorial on the blog shows you how to run your analysis using a subset of just 125 markers…
clock | October 22, 2009It's barely been a day since PLoS ONE published the article Discovery of the Largest Orbweaving Spider Species: The Evolution of Gigantism in Nephila when a video appeared on YouTube mashing up images and text from the press release:
Of course, as this is Open Access, nobody needs to worry about copyright and stuff....though a direct link to the paper would have been nice (or, considering the infamous YouTube commenters, perhaps better not!).
See the related blog post as well.
clock | October 22, 2009Open Access Week is in full swing and there is a lot of blogging about its various events in many countries.
OA week was marked in Serbia this year as well. As you may remember, I went to Belgrade twice in the past two years - in 2008 and 2009 and gave a total of four lectures, one brief TV interview, four long radio interviews and a print interview. I am now writing a paper about Open Access for one of their journals as well.
This effort has paid off.
I have remarked before how difficult it is to make changes in smaller countries - the scientific community is small, everyone knows everybody…
clock | October 19, 2009
This week - 19th-23rd October 2009 - is the Open Access week around the world - fitting nicely with the 5th birthday of PLoS Medicine. And when I say 'around the world' I really mean it. Just check out all the global events happening this week.
The OA Week is co-organized by Open Access Directory, PLoS, SPARC, Students for Free Culture, eIFL (Electronic Information for Libraries) and OASIS.
Many countries are participating this year, including some with numerous events all around the country. See, for example, all the events in Germany (there are 67 events in that country alone!),…
cpikas | October 13, 2009This was in an earlier EOS (pdf, not available online for institutional subscribers so I found this by flipping through the print!) - number 32 of this year from 11 August. They're trying what Nature tried and dropped and what EGU has been fairly successful with in Atmospheric Chemistry and Physics - although neither gathered/s many comments.
They're trying it for just a year and only for a few journals:
G-cubed
Global Biogeochemical Cycles (?)
JGR-Earth Surface
JGR-Planets
Radio Science
It's completely voluntary.Registration is required to comment. The formal reviews will be posted (may be…
clock | October 7, 2009Press release (in Swedish - translation from the Swedish by Ingegerd Rabow):
The Swedish Research Council requires free access to research results.
In order to receive research grants the Research council requires now that researchers publish their material freely accessible to all.
The general public and other researchers shall have free access to all material financed by public funding,
The thought behind the so called Open Access is that everybody shall have free and unlimited access to scientifically refereed articles, The Research Council has now decided, that researchers who are…
clock | September 18, 2009If you are a regular reader of this blog, you are certainly aware that PLoS has started making article-level metrics available for all articles.
Today, we added one of the most important sets of such metrics - the number of times the article was downloaded. Each article now has a new tab on the top, titled "Metrics". If you click on it, you will be able to see the numbers of HTML, XML and PDF downloads, a graph of downloads over time and a link to overall statistics for the field, the journal, and PLoS as a whole.
Mark Patterson explains (also here and here), what it all means:
We believe…
clock | September 10, 2009On Speaking of Medicine:
PLoS Medicine turns 5 years old on October 19th, 2009. To highlight the crucial importance of open access in medical publishing we're holding a competition to find the best medical paper published under an open-access license anywhere (not just in PLoS) since our launch.
Vote for your choice from the 6 competing papers, detailed below -- nominated and then shortlisted by our editorial board. Winners will be announced during Open-Access week (19-23rd October 2009). If you're interested in how we came up with this shortlist of top-quality open-access medicine papers,…
clock | September 8, 2009
Dinosaur fossils have been dug out for a couple of centuries now. They have been cleaned up and mounted in museums and described in papers and monographs. The way this is all done has evolved over time - the early techniques were pretty crude compared to what palaeontologists do today. One of the important techniques is actually quite simple: making measurements of bones. And yes, many such bones have been measured and the measurements reported in the literature. And that literature is scattered all over the place in many different formats in many different journals. Nobody has put all the…
clock | August 29, 2009Leo Laporte and Kirsten Sanford (aka Dr.Kiki) interviewed (on Twit.tv) Jason Hoyt from Mendeley and Peter Binfield from PLoS ONE about Open Access, Science 2.0 and new ways of doing and publishing science on the Web. Well worth your time watching!