Traditionally, at the end of the year Science and Nature come up with kind of top science breakthroughs of 2008. These two lists correspond to the two different approaches. Science magazine judges pure scientific meaning, while Nature also count broader impacts like news, and future implications. Personally, I share Nature’s view on the most important scientific discoveries, as they have broader influence not only on science but also on life in general.

Broad impact means more corresponding hedlines and larger traffic to the news sources. The Large Hadron Collider (LHC) is definately top celebrity of the year! This is clearly visible just by looking onto Google Trends graph in comparison with whole stem cell research (Science magazine breakthrough), Nobel prizes and Paris Hilton :) Continue reading →

22nd December, 2008 No Comments

It’s easy to find the latest in scientific publications by going to a search engine, such as Web of Knowledge or PubMed, that specializes in the relevant literature. But, if you’re looking for something in general you’re likely to turn to a search engine. These usually will return a Wikipedia page within the top 10 hits. In increasing numbers, scientists are reasoning that, if people are going to look at the Wikipedia page anyway, the scientific community should probably ensure that the information there is good. In the latest manifestation of this trend, a RNA biology journal that specializes in RNA research is requiring any authors that submit a specific type of paper also prepare an additional document for peer review: a Wikipedia page summarizing the paper!

The first examples of this program in action are already online. The journal is hosting an open access paper that describes a family of RNA molecules found in nematode worms; a corresponding Wikipedia page is already in place.

19th December, 2008 No Comments

Are you still struggling to organize your article collection manually? The recent PLoS Computational Biology article reviews several next generation web bibliographic tools and compare them. Authors emphasize several issues with current tools and possible ways how to overcome them. Do you use any mentioned desktop or web–based tools? Why?

Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.

Duncan Hull, Steve R. Pettifer, Douglas B. Kell (2008). Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web PLoS Computational Biology, 4 (10) DOI: 10.1371/journal.pcbi.1000204

21st November, 2008 No Comments

In recent years, scientific publishing has changed profoundly as the Internet simplified access to the scientific journals that once required a trip to a university library. That ease of access has caused many to question why commercial publishers are able to dictate the terms by which publicly funded research is made available to the public that paid for it. Open access proponents won a big victory when Congress voted to compel the National Institutes of Health to set a policy of hosting copies of the text of all publications produced by research it funds, a policy that has taken effect this year. Now, it appears that the publishing industry may be trying to get Congress to introduce legislation that will reverse its earlier decision under the guise of strengthening copyright protections.
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17th September, 2008 No Comments

Our work on AIMD simulation of CL-20 thermal decomposition just get published in the J. Phys. Chem. B!

CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane or HNIW) is a high-energy nitramine explosive. To improve atomistic understanding of the thermal decomposition of CL-20 gas and solid phases, we performed a series of ab initio molecular dynamics simulations. We found that during unimolecular decomposition, unlike other nitramines (e.g., RDX, HMX), CL-20 has only one distinct initial reaction channel—homolysis of the N—NO₂ bond. We did not observe any HONO elimination reaction during unimolecular decomposition, whereas the ring-breaking reaction was followed by NO₂ fission. Therefore, in spite of limited sampling, that provides a mostly qualitative picture, we proposed here a scheme of unimolecular decomposition of CL-20. The averaged product population over all trajectories was estimated at four HCN, two to four NO₂, two to four NO, one CO, and one OH molecule per one CL-20 molecule. Our simulations provide a detailed description of the chemical processes in the initial stages of thermal decomposition of condensed CL-20, allowing elucidation of key features of such processes as composition of primary reaction products, reaction timing, and Arrhenius behavior of the system. The primary reactions leading to NO₂, NO, N₂O, and N₂ occur at very early stages. We also estimated potential activation barriers for the formation of NO₂, which essentially determines overall decomposition kinetics and effective rate constants for NO₂ and N₂. The calculated solid-phase decomposition pathways correlate with available condensed-phase experimental data.

Isayev, O., Gorb, L., Qasim, M., Leszczynski, J. (2008). Ab Initio Molecular Dynamics Study on the Initial Chemical Events in Nitramines: Thermal Decomposition of CL-20. Journal of Physical Chemistry B, 112(35), 11005-11013. DOI: 10.1021/jp804765m

28th August, 2008 No Comments