example.tex

A simple example LaTeX file.

example.pdf

PDF file output for example.tex

Makefile

An example Makefile, showing one of many ways to produce a pdf file from a LaTeX file. You may wish to use Preview on the Mac, or freeware like ps2pdf to create the pdf file. (pdflatex has trouble with included .eps graphics, so I don't recommend it)

Simple on-line tutorial for LaTeX

The Art of Problem Solving website provides a LaTeX tutorial for high-school and middle-school students taking their on-line courses.

XyMTeX

A LaTeX package for drawing chemicals. A little hard to learn, but quite powerful, and supposedly easy to use once you've gotten past the initial hump. I've not used it myself (haven't needed chemical drawings in any of my papers), but one of my grad students has just learned it and likes it.

BibTeX

BibTeX is a free bibliography formatting tool for use with LaTeX (it comes with the LaTex distributions). It has been around a lot longer than commercial tools like EndNote and is likely to outlive them, as there is no commercial impetus to keep changing the product to force people to buy newer versions.

http://www.soe.ucsc.edu/~you/notes/ucthesis-ucsc/

I recommend using LaTeX for thesis proposals and theses. The ucthesis style file seems to be a good style to use.

DeTeXify

There is a cool tool for guessing the LaTeX code for hand-drawn symbols at http://detexify.kirelabs.org/classify.html Personally, I find it faster to scan a list of symbols (particularly since drawing with a touch pad on a laptop is tough), but others may find this drawing approach useful.

http://t16web.lanl.gov/Kawano/gnuplot/index-e.html

Gnuplot tutorial and tips

http://www.gnuplot.info/faq/faq.html

Official Gnuplot FAQ, including download information.

map_trim11_log

An example data file to use for gnuplot examples.

map_trim11-wrong.hist10000

An example data file to use for gnuplot examples. This one is the output of histogram-from-rdb, but the rdb file is 109Mbytes, so I did not want to put the full data set on the web.

fit-wrong.gnuplot

An example gnuplot script, illustrating fitting a complicated function.

cullpdb-phi-psi.2d

An example data file (output by histogram2-from-rdb), for illustrating contours and heat maps.

phi-psi-hist.gnuplot

An example gnuplot script, illustrating contours.

RDB is a collection of perl scripts that use files with tab-separated columns as a relational database. Rdb is very handy for handling modest amounts of data, where the effort of setting up a real database is not justified. It is very easy to read and write RDB files with almost any programming language, so this is a handy format for the output of analyses,

http://compbio.soe.ucsc.edu/rdb

Documentation for the standard scripts

http://compbio.soe.ucsc.edu/rdb/rdb2.6c+sort-patch.tar.gz

Finding old unix tools like RDB is sometimes difficult. It is included with some Linux installations, but if you need it on another machine, you can download our copy and untar it.

rdb2gnuplot

rdb2gnuplot is a locally-produced script to strip the rdb header off a file, to avoid confusing gnuplot. A typical use in gnuplot is

	  
plot '< column independent dependent < dummy-data.rdb | rdb2gnuplot' with lines

histogram-from-rdb

histogram-from-rdb is a locally-produced script for getting the histogram of a column in an rdb file. There are various options for adjusting how the bin sizes are set. The only documentation is in comments at the beginning of the script.

histogram2-from-rdb

histogram2-from-rdb is a locally-produced script for 2-d histograms from 2 columns of an rdb file. The only documentation is in comments at the beginning of the script.

correlate-rdb

correlate-rdb is a locally-produced script for computing the correlation between two columns of an rdb file.

smooth-rdb

smooth-rdb is a locally-produced script for producing a smoothed curve of one column as a function of another, by averaging over overlapping windows. The only documentation is in comments at the beginning of the script.

Note: there is a second edition, c2006.