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Posts Tagged ‘Open access’


Reporter:  Aviva Lev-Ari, PhD, RN

Call for Open-Access Publishing in Genomics

January 14, 2013

SAN DIEGO (GenomeWeb News) – Open-access datasets, software, and bioinformatics strategies have become more or less de rigueur in genomics research.

But the field may also be poised to change the way other sorts of information from scientific studies is conveyed to other researchers and to the broader public, according to open-access proponent Michael Eisen, a computational and evolutionary biology researcher at the University of California, Berkeley.

Eisen, a Public Library of Science co-founder, spoke during the morning plenary session here at the International Plant and Animal Genome Conference.

In his presentation, he argued that the inability to freely and unreservedly access the full text of all genome studies performed to date may have led to missed opportunities for the field.

Using the bacteriophage phiX174 genome sequence as an example, he proposed that the general thinking in the genomics field has developed in ways that promote open-access to sequence data and related software. But, he said, the same type of access is not necessarily available for those interested in delving into the details and rationale behind genomics studies, since the corresponding papers may not be accessible in an open-access format.

The UK Medical Research Council Laboratory of Molecular Biology‘s Frederick Sanger and colleagues described the phiX174 sequence in 1977, in a publication that’s generally considered to be the first genome paper. The sequence data presented in that study is now freely available, Eisen explained, in part owing to the advent of sequence databases such as the European Molecular Biology Laboratory Nucleotide Sequence database or the National Center for Biotechnology Information’s sequence database, GenBank.

During the past decade or more, funding agency requirements and pressure from within the genomics community have contributed to the widespread adoption of these and other public genomics resources and repositories.

As these databases have grown and become accepted within the genomics community, Eisen argued that they have spurred the development of computational methods for analyzing genome sequences and datasets that may not have existed otherwise. “Imagine where we would be had we not made the fortunate decision to liberate genome sequences,” he said.

But analogous strategies for combing through text from genomics studies in their entirety have not developed in the same manner, according to Eisen, who noted that the text of the phiX174 genome paper remains behind a pay wall.

“We’ve allowed [journal access] and [data access] to follow very different fates,” said Eisen, who says there are ways to use the information housed within the scientific literature more easily and productively.

He urged attendees to consider publishing their own work in open-access publications. Beyond that, though, Eisen also noted that the community is well positioned to influence the ways in which research information is disseminated, since genomics data increasingly serves as a resource for other spheres of research.

 

 

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SAME SCIENTIFIC IMPACT: Scientific Publishing – Open Journals vs. Subscription-based


Reporters: Aviva Lev-Ari, PhD, RN & Pnina G. Abir-Am, PhD

Drastic change in academic education by design: FREE ACCESS to knowledge — Program edX – the  Harvard+MIT collaboration on Online education!! 
FREE ACCESS to Scientific Journals will be the next step. Research to support that by a study carried by Bjork, B. C., and D. Solomon. 2012. Open access versus subscription journals: a comparison of scientific impact. BMC Medicine. 10(1):73+. 
“Following step will be to demonstrated that Scientific Websites like http://pharmaceuticalintelligence.com have SAME Scientific impact as Open Journals!!
“We are well positioned to demonstrate that” said Aviva Lev-Ari, PhD, RN, Director & Founder of Leaders in Pharmaceutical Business Intelligence and the 2/2012 launcher of the initiative called  http://pharmaceuticalintelligence.com  To trace her contributions to Research Methodology, 1976-2005, go to  https://sites.google.com/site/avivasopusmagnum/aviva-s-home-page
The merit of Scientific Website is manifold:
  • Time from Lab/Desk to Publication on the Internet and Search engines is reduced to seconds
  • comments by other scientists are equally valuable to peer review
  • collaboration with other scientist around the globe is fostered on WWW
  • the platform is of collaborative authoring, we have 60 categories of research in one site
  • interdisciplinary work can be published in one site the over arching domain in our case is Life Sciences, Pharmaceutical and Healthcare
In May 2012 MIT and Harvard are collaborating on distribution of course material of all classes on the Internet – a Program called EdX
In the Press Release“EdX represents a unique opportunity to improve education on our own campuses through online learning, while simultaneously creating a bold new educational path for millions of learners worldwide,” MIT President Susan Hockfield said.

Harvard President Drew Faust said, “edX gives Harvard and MIT an unprecedented opportunity to dramatically extend our collective reach by conducting groundbreaking research into effective education and by extending online access to quality higher education.”

“Harvard and MIT will use these new technologies and the research they will make possible to lead the direction of online learning in a way that benefits our students, our peers, and people across the nation and the globe,” Faust continued.

Princeton, Stanford, Michigan and the University of Pennsylvania announced that they would offer free Web-based courses through a for-profit company called Coursera that was founded by two Stanford computer science professors. One of those professors, Andrew Ng, taught a free online course in machine learning this past fall with an enrollment of more than 100,000 students.

There’s also Udacity, co-founded by a former Stanford professor, andKhan Academy, which boasts 3,100 free educational videos across a variety of subjects.

MIT and Harvard said that they hope to eventually partner with other universities to expand the offerings on the edX platform.

Results of the BMC Medicine study are reported, below and they are:  Open Access, But Same Impact
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BioTechniques

http://www.biotechniques.com/news/Open-Access-But-Same-Impact/biotechniques-333012.html#.UA2SsRxueMU 

Open Access, But Same Impact

07/19/2012

Jesse Jenkins
By comparing two-year impact factors for journals, researchers found that open access and subscription-based journals have about the same scientific impact.
Open access (OA) journals are approaching the same scientific impact and quality as traditional subscription journals, according to a new study. In a study published in BMC Medicine on July 17 (1), researchers surveyed the impact factors, the average number of citations per paper published in a journal during the two preceding years, of OA and traditional subscription journals.

By comparing two-year impact factors for journals from the four countries that publish the most scientific literature, researchers have found that OA journals have about the same scientific impact as their subscription-based counterparts. Source: BMC Medicine.

At first, the study’s authors—Bo-Christer Björk from the Hanken School of Economics in Helsinki, Finland, and David Solomon from the College of Human Medicine at Michigan State University—found that there was a 30% higher average citation rate for subscription journals. But after controlling for journal discipline, location of publisher, and age of publication, their results showed that OA and subscription journals had nearly identical scientific impact.

“The newer open access published within the last 10 years, particularly those journals funded by article processing fees, had basically the same impact as subscription journals within the same category,” said Solomon. “I think that that is the key finding.”

The initial higher citation rate for subscription journals was the result of a higher percentage of older OA journals from countries that are not major publishing countries. “A lot of them are from South America or other developing countries, and they tend to have lower impact factors,” said Solomon. “When you compare apples to apples and start looking within subgroups, particularly journals launched after 2000 in biomedicine for example, the differences fall away.”

However, the authors identified a sector of low quality, OA publishers that are looking to capitalize on the article processing charge model rather than contribute to the advancement of science. Solomon said that this could partly be to blame for negative perceptions about the integrity of OA publishing as a whole and its impact on the peer review system. But most researchers are aware of these low-quality publishers and prefer to publish in more reputable OA journals.

In the end, Bjork and Solomon are hopeful that the study’s findings may help dispel some of the misconceptions in the debate over OA publishing. “Open access journals still have the reputation of being second class in the minds of some people. So, we think that this is important because this is objective data verifying that at least the open access journals published in the last 10 years by professional publishers are on par with subscription journals.”

References

  1. Bjork, B. C., and D. Solomon. 2012. Open access versus subscription journals: a comparison of scientific impact. BMC Medicine. 10(1):73+.

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