Evie Browne's blog

Bioinformatics in China

Evie Browne — Fri, 25 Apr 2008 07:10:03 -0700

Today marks the publication of a new article in PLoS Computational Biology’s regional perspective series, this time focusing on the development of bioinformatics in China. We are pleased to be able to publish forward-thinking articles of this type, which examine scientific publishing and research in non-Western countries, and have so far published articles on Mexico , Brazil, Cuba, Argentina, and Costa Rica. The bioinformatics and computational biology market is particularly booming in China and India, and PLoS Computational Biology especially is seeing a large increase in submissions from these countries. In these early months of 2008 alone, we have had almost a dozen research articles submitted from China, and the same amount from India and Switzerland. Our highest submitting country remains the USA, followed shortly by the UK, Germany, Japan, and Israel. We’re also pleased to note we have reflected this geographical spread in our Editorial Board, with editors from all of the above mentioned countries.

The article, Bioinformatics in China, explores both the history of and the current projects in computational biology in China, including the Chinese element of the HapMap Consortium and Human Proteome Organisation, and new tools such as the Splice Variants Analysis Platform (SVAP). We also recently published a very high-profile article by authors from Peking University, “Genes and (Common) Pathways Underlying Drug Addiction”, which received coverage in The Economist, Reuters and The China Post. We are proud to be able to bring research from all over the world to the attention of international media, and invite you to comment on any of these articles with your personal experiences of living or working in these countries.

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Computational Biology in Developing Countries

Evie Browne — Tue, 4 Dec 2007 05:05:56 -0800

Last Friday marked the publication of the next installment in PLoS Computational Biology's 'Developing Computational Biology' series, a set of perspectives written by authors in developing countries regarding the state of computational sciences in their nations. Friday's is particularly interesting, as it explores the situation in Cuba. We had some concerns at first whether we could even publish a piece from Cuba, seeing as American editing of Cuban work had been previously considered an activity punishable by imprisonment. Luckily, however, a lawsuit had been filed against the Treasury Department’s Office of Foreign Assets Control (“OFAC”) in 2001, which caused OFAC to reverse this policy and allow Americans to “engage in all the activities that are necessary and incident to publishing works from authors in Iran, Cuba and Sudan without the need to apply for a government license except in very limited circumstances”.

Our perspective explores the current situation of scientific research in Cuba, which is strongly affected by the trade embargo (which the UN recently once again called to lift), as scientists have to import all of their equipment from Europe or Central and South America. Computational biology can alleviate this problem somewhat, as the reliance on computational power and human resources rather than expensive wet lab supplies can provide an opportunity for young researchers to learn and progress.

We are very proud of this series of perspectives; other articles have focused on Brazil and Mexico, and ones to come include Argentina, China and Thailand.

Please have a read of the perspective on Cuba and let us know your experiences of the sciences in developing countries.

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Next generation publishing at Harvard

Evie Browne — Thu, 15 Nov 2007 02:52:15 -0800

On Friday last week, I was lucky enough to happen to be in Boston at the same time as an event titled Publishing in the New Millennium at which PLoS founder Harold Varmus and PLoS ONE Community Manager Bora Zivkovic were speaking. It was a free event organized by Harvard graduate students and aimed at both faculty, students and interested parties.

The lecture hall packed out to hear Harold speak about Open Access, PubMed Central, the NIH, and PLoS, but all eyes and ears were firmly centred on the standoff between his ideas and those of Emilie Marcus, Editor of Cell. Emilie took part in a panel discussion which focused mainly on the financial pros and cons of publishing Open Access and the danger of an ‘author pays’ model leading to ‘vanity publishing’ – the idea that paying for publication can compromise editorial standards. Of course, here at PLoS, the editors do not see the financial disclosure information of authors, and thus it can have no effect on their editorial integrity. It is nonetheless an interesting question, and one which also led Stuart Shieber of Harvard to ask the question – if all journals did go Open Access, would new barriers to publication be created in the form of higher-quality journals charging higher publication fees?

The second forum focused on ‘Science 2.0’ and the semantic web – which John Wilbanks of Science Commons thinks is now a very real and imminent possibility. The web currently does not function that well for science, and the next big leap is taking place in projects like JoVE, Creative Commons, PLoS ONE, and SciVee. Both Nature Precedings and PLoS ONE encourage commenting on articles and interaction between scientific peers, but this can have varying results – Hilary Spencer stated the uptake of commenting on Precedings has not been great, though there is plenty of other activity, while PLoS ONE has had well over 1000 pieces of post-publication commentary. The interactivity of video sites like JoVE and SciVee show the ability of the web to be used for science in ways other than traditional publishing, allowing experiments to be visually demonstrated and authors to present their work in other forms than text. Eventually, will the concept of ‘a paper’ become redundant as we progress towards publishing all data, methods, peer comments and interactive experiments in one package online?

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