Saturday, May 10, 2008

References and Bibliography research

I am still toying with various research tools. Today, I compiled a little list of references for the marine midges Pontomyia spp. Using JabRef I was able to compile a well-formated bibliography in about an hour and a half, with over 40 references. I think it will be faster once I figure out how to do it all automatically. This was clearly a victory, however.


Google Scholar offers the preference of using bibtex citation export mode. A friend mentioned he's been struggling with bibliography formats. Perhaps a little introduction?


BibTeX is a database format for bibliographic citation for use with the TeX and LaTeX typesetting tools. TeX is a fullblown typesetting language based on Donald Knuth's extensive study of "meat space" typesetting techniques of real printers/typesettings. LaTeX is the macro package, easier to use than TeX. I use LaTeX. These systems are remarkable for hundreds of reasons that I cannot go into at this point. Among them is the handling of references, cross-references, and bibliographic citations. BibTeX is the method for the database. A typical citation is as follows:


@ARTICLE{ruxton2008cea,
author = {Ruxton, G.D. and Humphries, S.},
title = {{Can ecological and evolutionary arguments solve the riddle of the
missing marine insects?}},
journal = {Marine Ecology},
year = {2008},
volume = {29},
pages = {72--75},
number = {1},
publisher = {Blackwell Synergy}
}

I found a great JabRef improvement. Two actually. One of them is Jab2HTML, that enables an export handler that outputs excessively beautiful html from a bibtex file or the entries one has selected. The big thing is the html has links to googlescholar. Secondly, this guy has now put together the means to incorporate the googlescholar links on the summary view of jabref itself, without outputting html:

- http://keijisaito.info/arc/biblio/en_jabref_bibtex.htm

His explanations are for Windoze, but they work ok if you change to Unix directory format, and define your own directories when that comes up. I installed both Jab2HTML and the Pref-* file. I like the Pref- changes alot.

Bibliography Formats


I do almost all text output formated via LaTeX markup. I have found emacs org-mode very, very useful in a number of ways. Org-mode outlines are eventually exportable as LaTeX source, and it works well. If I do this in org mode--- "/Pontomyia pacifica/"---the LaTeX output will be italic, and *xxx* would output xxx in bold. _hello_ would render hello as underlined. This and other matters, including the easy table editor, are really useful. I admit I've spent way too much time learning how to use it, but it's starting to make sense. Todo lists, notes, whatever, preliminary notes. I should be typing this letter in org-mode, one good reason to use Gnus for email (it's way too hard for reading mail with many tags, but easy to compose) and with the emacs-based w3m browser, I can cut and paste text between email and www and whatever I'm writing. I can compose long email messages in org-mode. I understand some people blog from org-mode. You aren't going to want to know about this, I guess, but another reason for me to stay focused on Emacs.

BibTeX gives you a bibliographic database. Emacs is a good way to edit bibtex (*.bib) files, but JabRef and kbibtex and cb2Bib all are essentials to the way I work so far. Zotero I did use today, but I'm not up to speed with bibliography use. I am using it for making notes, like google notes on steroids, but then I can have automatically generated bibtex entries for the source pages for these notes.

I just put together a bibliography in an hour and a half this morning on Pontomyia spp. marine midges. I'll try to attach the html output. What I think is amazing is the speed and relatively clean output. Note the links to google and google scholar.

When one is writing a report---say I am writing a report or proposal for working on Pontomyia. I refer to the *bib file. I'll try to attach that too. Boring.

Two years ago, one wouldn't have found an open specification file format used so widely, for example with Google Scholar using it to export bibliography citations.

I can refer to pontomyia.bib in my proposal and then cite a particular article by Cheng\cite{cheng1978mmp}. If I am publishing an article in Science, I invoke the science citation style, and both the citation ([1] for example) and the formatting of the text in the bibliography will be taken care of by LaTeX/BibTeX. I know it's possible to output a fully formated annotated bibliography by including annotations or notes fields in the bibtex database entries. LaTeX/BibTeX will only print those references in the database that are cited in the article, and one can do all kinds of specific formatting, like including page numbers in teh citation \cite[39-40]{cheng1978mpp}.

LaTeX, by the way will automatically do a crosseferenced bibliography, for example, and correct the page numbers each time the document is processed. Indexing and glossaries the same.

Friday, May 2, 2008

More Notes and References Software

These are somewhat heavyweight, and for the most part are beyond my modest needs and ability.

TiddlyWiki


NeuroScholar
(Demo)


RRiki


RefBase

Tide graph experiment: seeking a colorblind friendly palette

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