Today is the 200^th anniver­sary of the birth of Charles Dar­win, one of science’s most revered fig­ures. Spe­cial events mark­ing the occa­sion are planned through­out the world espe­cially in Eng­land where he was born on this date (Feb­ru­ary 12^th) in 1809. This year’s also the 150^th anniver­sary of the pub­li­ca­tion of the famed naturalist’s most impor­tant work, On the Ori­gin of Species by Means of Nat­ural Selec­tion, a book that rev­o­lu­tion­ized the sci­ence of biol­ogy, and despite enor­mous amounts of evi­dence in its favor remains con­tro­ver­sial to this day.

Darwin’s works have played a key role in advanc­ing sci­en­tific thought in such fields as biol­ogy, genet­ics, bio­chem­istry, and pale­on­tol­ogy (just to name a few!). The life and works of Dar­win have been deemed so impor­tant by sci­en­tists from around the world that hun­dreds of muse­ums, orga­ni­za­tions, and sci­en­tific soci­eties have decided to cel­e­brate his birth­day and his research. Here are some of the notable events planned in cel­e­bra­tion of Dar­win, his life, and his con­tri­bu­tions to the field of sci­ence.
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12th February, 2009 Comments Off

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 Comments Off

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 Comments Off

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 Comments Off

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 Comments Off