Download references in Medline format from
PubMed
In case you are interested - this is what
Medline format
looks like.
Use 'pybliographic' program on linux machines to organise your
references and write out a 'bibtex' format output file. You may need to
install this on your own machine as it is not 'on the system' or
run it remotely from a machine where it is already installed (e.g. bsmlx30).
'pybliographic' allows you to modify the KEYS to something logical.
I strongly recommend the use of {AUTHOR}:{DESCRIPTION}:{YEAR}
For example:
In case you are interested - this is what
Bibtex format
looks like.
Download natbib.sty file only
I used the 'natbib' package to handle all the issues with citations.
You can download the whole package and install it from scratch
but it is sufficient to only download the 'natbib.sty' file to actually
use this package.
I created a directory called tex in my home directory.
The 'natbib.sty' can go in here. If you have downloaded the whole package
then create a natbib directory inside of your tex directory
and put 'natbib.tar' in there before you extract the file. You have to
run the install script to generate a 'natbib.sty' file - see the README notes.
One way or another the 'natbib.sty' file should go in /home/bsm/james/tex
so that the chapter master latex file
and the thesis master latex file
knows where it is.
The main difference from the standard use of \cite is that all
citations must now be either \citep or \citet (see below).
The chapter master latex file
and the thesis master latex file must contain
the following two lines in the preamble.
The citation style of a given bibliography style is defined by the \bibpunct line.
This file needs to go in /home/bsm/james/tex directory.
Download Medline files from PubMed
Use pybliographic to organise your references
{AUTHOR} = most famous author on the paper
{DESCRIPTION} = descriptive key word
{YEAR} = last 2 digits of the year
Classic BLAST paper = Altschul:BLAST:90
Classic PSI-BLAST paper = Altschul:PSIBLAST:97
Classic SAM paper = Karplus:SAM:98
Classic CATH paper = Orengo:CATH:97
Classic DHS paper ;) = Bray:DHS:00
The 'natbib' package
Download the whole natbib.tar.gz file
Where do I put this file ?
Use \citet for in-text form and \citep for parenthetical citations:
\citet{key} ==>> Jones et al. (1990) (in-text form)
\citep{key} ==>> (Jones et al., 1990) (parenthetical form)
\citep{key1,key2} ==>> (Jones et al., 1990, 1992)
(multiple citations; common authors suppressed)
\citep[chap. 2]{key} ==>> (Jones et al., 1990, chap. 2)
\citep[see][]{key} ==>> (see Jones et al., 1990)
\citep[see][chap. 2]{key} ==>> (see Jones et al., 1990, chap. 2)
Defining the 'natbib' citation style
\usepackage{/home/bsm/james/tex/natbib}
\bibpunct{(}{)}{;}{a}{,}{,}
Use \bibpunct (in the preamble only) with 6 mandatory arguments:
1. opening bracket for citation
2. closing bracket
3. citation separator (for multiple citations in one \cite)
4. the letter n for numerical styles, s for superscripts else anything for author-year
5. punctuation between authors and date
6. punctuation between years (or numbers) when common authors missing
One optional argument is the character coming before post-notes. It
appears in square braces before all other arguments. May be left off.
Example (and default) \bibpunct[, ]{(}{)}{;}{a}{,}{,}
The JMB bibliography style file
The chapter master latex file
and the thesis master latex file must contain
the following line inside of the \begin{document} environment.
\bibliographystyle{/home/bsm/james/tex/jmb}