That store is ripe for a hooligan to change the P to a B.

Ever since I struggled to write a paper for a physics lab class and my friend introduced it me I have been a fan of LaTeX. Since that moment I have written everything that needed any sort of typesetting in TexShop for OS X.

Recently I needed to organize several papers for their references, I conveniently found in installation of BibDesk. This was a wonderful find. BibDesk was able to create my BibTeX file for my references as well as organize all of the PDFs for papers. With it I am able to now start a centralized organization for academic papers, something that will hopefully help me in the long run.

Furthermore it has helped me write my papers. I was able to load in a dozen papers related to my topic (Ganymede) and systematically read through the papers adding more information to my paper. The simple addition of a read checkbox to BibDesk makes the whole thing just work perfectly.

Of course after talking to a Windows using roommate about this I was only able to recommend LaTeX and BibTeX and not any neat front ends.

Oh, it’s very useful not to have sixty million copies of your bibliograph file floating around.  To avoid that and to put all your LaTeX style files in one place (that is not the same place as the document itself):

# The empty component at the end means that the
# system-defined locations will be included.
export TEXINPUTS=.:..::~/system/tex/inputs:
export BIBINPUTS=.:..:

De fa uns dies he passat a organitzar la bibliografia amb Mendeley. Es tracta d’un programa de gestió de bibliografia gratuït que manté una base de dades d’articles acadèmics (incloent els PDFs) i que permet importar i exportar, entre altres formats, BibTeX. Té dues parts: d’una banda, un programa instal·lat localment a l’ordinador, Mendeley Desktop, amb la llista de referències i els PDFs; de l’altra, una llibreria on-line amb la mateixa llista de referències sincronitzada (i amb un límit d’espai per PDFs).

Però Mendeley no és només això: la versió web del programa és també una xarxa social on pots mantenir un perfil amb el teu currículum i articles publicats, contactar amb altre gent amb interessos de recerca similars i compartir col·leccions d’articles, per exemple amb els companys del teu grup de recerca. Tot amb un estil similar al de last.fm, i és que alguns dels creadors de Mendeley provenen d’aquesta xarxa musical.

Altres característiques útils de Mendeley són anotar PDFs en la versió local, renombrar els articles amb un nom més agradable que l’usual que obtens al descarregar-te’l (d’una manera molt semblant a com l’iTunes organitza la música), plugins per incloure referències per als que utilitzen Word o OpenOffice i importar articles directament des d’Internet, tot i que aquesta última opció encara ha de millorar per arribar al nivell de Zotero (que a més sembla que també s’ha passat a les xarxes socials amb la versió 2.0). Des de Mendeley diuen que a més gent participant de la xarxa millor serà el reconeixement de les dades dels articles.

Inconvenients: el programa local no és en codi obert, i fa certa por invertir temps en construir una base de dades per a que llavors passi com a last.fm i converteixin gran part dels serveis a pagament.

After a long a tiring day, my RSS reader brought me some great news. Mendeley’s latest release now supports LaTeX. One more interesting new feature: Automatic library backups and easier restoration of backups.

as I am always looking for them, here’s a reference for the standard types.

I recently changed from using boring old BibTeX to exciting new BibLaTeX. There have been some slight problems with the transition (aren’t there always!). First, citations started appearing as: “Name, Year” instead of “Name (Year)” like I wanted them to. I got around this by adding the option “natbib=true” to the \usepackage{biblatex} command and replaced all my \cite commands with \citet commands. Not the most elegant solution, I’ll grant you, but it works. So I was casting around for a better solution. I thought I’d try the APA standards packages. They didn’t work at all until I did a “sudo texhash” and after that they didn’t solve the problem. (Though they did fix an annoying bibliography quirk: the biblatex standard authoryear bibliography style writes things as “Author, Year, Paper-title In: Journal” The APA packages do at least get rid of that annoying “In:” Tomorrow I’m going to see if Harvard or Chicago bbx and cbx files can get me out of that mess.

Two other outstanding gripes with biblatex. First is that I can’t have “X et al” appear in the citation while still having “X, Y and Z” appear in the bibliography. This was standard with whatever set-up I was using before (natbib and chicago probably). This is because the “maxnames” option controls both citations and bibliography. Not ideal.

Second gripe, I want my bibliography to be titled “References” rather than “bibliography” I had a work around for this using the memoir class and bibtex, but it no longer works with biblatex. I suppose I will explore this issue further tomorrow.

And why am I spending so much time playing with my bibliography? Well, because it’s a superb displacement activity and I have a huge project due in next week, that’s why!

This is a three part article describing different ways to handle bibliography and citation in LaTeX: (1) using  thebibliography environment, (2) using BibTeX, and (3) controlling BibTeX citations using natbib.

1. Using thebibliography environment to create bibliography:

The easiest way to create a bibliographic references for a scientific article is using thebibliography environment, especially when you have a very few references:

\begin{thebibliography}{99}
\bibitem[label1]{cite_key1} Mead, C. A.; Truhlar, D. G. {\it J. Chem. Phys.} {\bf 1979}, {\it 70}, 2284.
\bibitem[label2]{cite_key2} Mead, C. A.; Truhlar, D. G. {\it J. Chem. Phys.} {\bf 1983}, {\it 78}, 6344.
\end{thebibliography}


Notice that I have formatted the references in accordance with the requirement of the journal where I am going to send the article

Put the above environment in your LaTeX source file somewhere in between \begin{document} and \end{document}, where you want your bibliography to appear. The field with 99 in it indicates the maximum length of your entry labels. If you put 1 in place of 99, the bibligraphy cannot have more than 9 entries (because 10 has two digits, i.e. width=2). 99 is a safe number to use! The optional argument label at the beginning of each bibitem gives you an option to put your own label.

If you want to cite the second one, do it as

I am citing the second reference\cite{cite_key2} here.

Easy, isn’t it?

However, the problem with this is that you have to manually type each entry, and you cannot reuse the list for another journal unless you change the format by explicitly typing again. If you want to use the same bibliographic database again and again you should use BIBTeX (especially if you are going to stay long enough in this business!).

2. Using BibTeX to create bibliography:

A. First, create your bibliographic database.

I generally break it down into two parts: (1) abb.bib, which contains the 3-6 letter abberviations of the journal names and their expansion according to the journal where the article is going to be submitted, and (2) abb.bib, the actual bibliographic database with the 3-6 letter abbreviations in place of the journal names.

A sample of abb.bib:


@String{AnMath="Ann. Math."}
@String{CheRev="Chem. Rev."}
@String{CMP="Commun. Math. Phys."}


and a snippet of ref.bib:

@ARTICLE{agu71,
author = {J. Aguilar and J. M. Combes},
title = {A class of analytic perturbations for one-body Schr{\"o}dinger Hamiltonian},
journal = CMP,
year = {1971},
volume = {22},
pages = {269--279},
}

I use the graphical front-end Jabref package to maintain the ref.bib file (in fact, I used Jabref when I first created the database). Besides editing and entering new references, I can also link individual PDF files of the corresponding entries — thus it’s a PDF organizer as well. However, in order not to have to modify the journal names I always put there the abbreviations (e.g. CMP for Communications in Mathematical Physics above) and expand their names manually in abb.bib in accordance with the requirement of the journal where I am going to send the article. So if I have the same bibliographic database, ref.bib I can use it for all the journals as long as I modify abb.bib correctly.

B. Cite!

Cite the reference in the same way as above, e.g.

I'm citing Aguilar and Combes' complex scaling paper.\cite{agu71}

Use the cite command to your heart’s content in the LaTeX source file and then proceed to the next step. Needless to point out, if you use a reference not in the database, ref.bib,  you must enter it in the database (or else don’t cite it at all!).

C. Copy the correct bibliography style (*.bst) file in the working directory.

It’s usually available in the CTAN or TUG websites. For example, for American Chemical Society’s Journals, the achemnat style file may be used [link].

[Update (11/19/2009): The original achemnat.bst file seems to be missing in the above link;  here is a copy from Google's cache]

If you don’t want to use any style file, that’s OK, too (see below).

D. Link  the bibliographic style file and the database to the LaTeX source code.

Enter these two lines  where you want the bibliography to appear in the LaTeX source file:

The first one is to specify which style-file (here, achemnat.bst) is going to be used. If you don’t want to use any style file other than the default, just replace achemnat by plain above. Some styles files are in-built which comes with other packages. Some useful style files may be found here.

In the second line, the stuff in the curly brakcets tells LaTeX where to look for the bibliographic database. Here, abb refers to the file abb.bib, and ref to ref.bib [see 2. A above]. You need to copy these two files in your working directory.

E. Lastly, compile!

Compilation  is the trickiest part — you have to compile it twice (maybe, thrice!) with latex:

$ latex source.tex
$ bibtex source
$ latex source
$ latex source


3. Citation using natbib:
More control over citations for BibTeX can be achieved using natbib package [download link]  — include these in the preamble:

Let’s try to explain above options one-by-one:

• First: the terms within the square bracket mean (in respective order) cite as superscripts; separate two citations by a comma; use numbers (not alphabet) for the citations; sort in increasing order and compress, i.e. if the references 1 and 3 through 5 are cited then show the citation as 1,3-5.
• Second: give the bibliography the title “REFERENCES”.
• Third: make the number format in the bibliography as (1), (2), etc.

Cite the references in the same way as above [see 2. B above].

See this link (PDF) for more details on natbib.

I’m writing a report and I had to cite an article from a book. It’s one of this book which every article can also be used as a standalone paper. The problem is that if you use an article record, you will miss the book and if you use the book record, you will miss the article.

How to solve it? Google it! (somebody has already solved it and post it somewhere)

And it is. The solution is to use @incollection:

@InCollection{Doe05,
author = {John Doe},
title = {Dynamic Ambient Paradigms},
booktitle = {Paradigm Gems 2},
pages = {223--233},
publisher = {Addison Wesley},
year = 2005,
editor = {Averell Doe}
}


More BiBTeX tips (where I found this solution) on this page.

Mirando un poco sobre la creación de referencias bibliográficas con el programa BiBTeX de   (ver aquí) y navegando un poco en la internet encontré un programa bastante interesante que simplifica la creación de bases bibliográficas que uno usualmente trabaja en documentos de como artículos, libros, monografías, etc.

El programa JabRef (ver aquí) es un gestor de referencias bibliográficas con el cual se puede incorporar varias referencias de diferentes bases para crear la necesaria a utilizar, solo es llenar los espacios claves y demás. Además se cuenta con servicio para buscar las bibliografías en bases de datos como JStor, IEEEXplorer, arXiv, entre otras.

Para conocer la mécanica de la creación y edición de bases de datos con el BiBTeX pueden ver la siguiente entrada de un blog bastante interesante (dar click aquí).

Ver tambien: como escribir un documento en , como hacer un poster

By default LaTeX does not display the bibliography section in the table of contents (TOC). This article describes how to add it.

Teksten som skrives foran referanselista (som overskrift) er inneholdt i en LaTeX-variabel. Dersom dokumentklassen er article heter variabelen \refname. Dersom dokumentklassen er book, heter variabelen \bibname.

Innholdet i variabelen avhenger av dokumentspråket. Dersom språket er norsk, så er innholdet hhv Referanser og Bibliografi, på engelsk blir det References og Bibliography

Dersom du ønsker å endre innholdet i variablene, må du gi en slik kommando


\renewcommand{\refname}{Litteraturliste}
\renewcommand{\bibname}{Litteratur brukt i utarbeidelsen}


Denne kommandoen kan du like greitt sette inn rett før \bibliography-kommandoen, f.eks:


\newpage
\renewcommand{\refname}{Litteraturliste}
\addcontentsline{toc}{section}{\refname}
\bibliography{referansenemine}
\bibliographystyle{plain}


så har du god kontroll på overskrift og hva som kommer inn i innholdsfortegnelsen.

Henvisning til referanselista kommer ikke automatisk inn i innholdsfortegnelsen.
For å få den inn, må du gi følgende kommando rett før
bibliography-kommandoen i latex-filen:


\addcontentsline{toc}{section}{Referanser}


Her forteller toc at det hele skal inn i table-of-contents,
section hvilket dokumentnivå innførselen skal ha og
Referanser hvilken tekst som skal inn i innholdsfortegnelsen.

I BibTeX fins det definert en rekke stiler for bibliografien og du kan også lage dine egne. Her er noen vanlige stiler:

• plain
  lista blir sortert alfabetisk på førsteforfatter og nummerert fortløpende. På siteringsplassen kommer numrene.
• unsrt
  som plain i utseende, men referansene kommer i den rekkefølgen de har i dokumentet og den første siteringen får nummer 1, den neste nummer 2 osv.
• abbrv
  som plain, men med mer kompakte referanser.

Dag Langmyhr (IFI) har oversatt disse tre stilene til norske varianter (norplain, norunsrt og norabbrv) der diverse småord er oversatt til norsk.

Det fins en rekke andre stiler og mange tidsskrifter har publisert sine BibTeX-stiler for dem som skal skrive artikler. Pakkene Chicago og harvard inneholder hyppig brukte stiler, se mer om dette i Langmyhrs guide.