Day: January 9, 2009

Bibliographies for the 21st century, why Zotero rules!

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.

via PLoS Computational Biology: Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web

zoteroInteresting look at how to manage scientific information. I use zotero these days. Zotero is a firefox addon that works within the browser, hence is platform independent. It is incredibly powerful, automatically imports meta data from a lot of journal sites, links to microsoft word and openoffice for “cite as you write” and bibliographic generation behaviour, stores pdfs, word docs, excel files, etc as attachments to your citations so if you have a little calculation routine you got from a paper, you can put that in an excel spreadsheet and always have it linked to the paper.

You can synchronize the database to the cloud. And, if you have access to a server with webdav, you can synchronize your attachments as well (i have not tried this yet).

Best of all, it is free and open source.

Anyway, the days of ridiculously expensive and arcane tools like endnote are over.

Autism epidemic not caused by shifts in diagnoses; environmental factors likely

California’s sevenfold increase in autism cannot be explained by changes in doctors’ diagnoses and most likely is due to environmental exposures, University of California scientists reported. The scientists who authored the new study advocate a nationwide shift in autism research to focus on an array of potential factors in the environment that babies and fetuses are exposed to, including pesticides, viruses and chemicals in household products.

Autism epidemic not caused by shifts in diagnoses; environmental factors likely — Environmental Health News

One of the most common arguments you will see about a lot of mental health diagnoses is that doctors have changed their diagnostic practices significantly. While there is evidence of this occurring in diagnoses of childhood depression, anxiety, or even bipolar disorder due to the millions of dollars involved in medication and the attendant corruption, autism is different.

This population study used 17 year data in California and concluded that diagnostic changes were only responsible for a 2 fold increase, not the seven fold increase seen. The rest is unexplained, and the authors attribute it to a confluence of environmental and genetic factors.

And no, for the last time, VACCINES DO NOT CAUSE AUTISM!