View source for Paper/Thesis Guide

This is a reference for how to write papers and theses. I spent a lot of time messing with different tools and these are the ones I settled on. You may wish to substitute your personal favorite here and there, but these are a very good basic set. I like them because they are free, portable, and stable. You will be able to work on your paper from any machine. In other words, if you lose your laptop or your hard drive crashes, you don't need that special license for a piece of software and you don't have to borrow one or find a hack to get your data back.

==Picky Things==

Please take a look at my [[Paper/Thesis Checklist]]
  
 
==Word Processing==



I prefer to use LaTeX. Any other word processor (except perhaps Framemaker) is a pain to get to have the right format. Word is horrible because every time you make an edit you have to replace your figures. Given that, you can start with several document classes that have the formatting done for you:

<UL>
<LI>[https://support.soe.ucsc.edu/latex/thesis UCSC official thesis format]</LI> <-- link needs to be updated
<LI>[https://support.soe.ucsc.edu/latex/porting UCSC technical report format]</LI>
<LI>[http://www.soe.ucsc.edu/~mrg/UCSC-thesis-tex.tar.gz Javi Martinez's thesis format]</LI>
<LI>[http://www.ieee.org/web/publications/authors/transjnl/index.html IEEE style guide]</LI>
<LI>Other conferences will generally provide you with a LaTeX template</LI>
</UL>

Some other (mostly Mac) utilities I have found useful for LaTeX:
<UL>
<LI>[http://evolve.lse.ac.uk/software/EquationEditor EquationEditor] - for putting equations on slides</LI>
<LI>[http://www.uoregon.edu/~koch/texshop TexShop] - for quickly updating/viewing your LaTeX results</LI>
</UL>

==Drawing Graphics==

For making images, I try to be consistent. It is important to have the ability to always modify the image. If you need some fancy tool like Visio, you may not have a license. Photoshop, for example, costs thousands of dollars. Therefore, I recommend these tools for vector graphics (simple line-based shapes) in the order of my preference:
<UL>
<LI>[http://www.inkscape.org Inkscape]</LI>
<LI>[http://www.xfig.org Xfig]</LI>
<LI>[http://live.gnome.org/Dia Dia]</LI>
</UL>
You should store both the original file and an eps or pdf copy for use in a LaTeX document.

Sometimes, you may not have a vector graphic file. For example, screen captures. To edit (or create) these, you can use [http://www.gimp.org The Gimp]. 

==Screen Captures==

This depends on your platform. On the Linux machines in the lab, you can use the print screen button like on Windows. Often, Unix/Linux machines will have "xv" which has a grab option. On OSX machines, you can use Grab.app.

==Results==

For making plots, there are also many options. I prefer to use (in order):
<UL>
<LI>[http://www.gnuplot.info gnuplot]</LI>
<LI>Matlab (but this requires a license)</LI>
</UL>
For computing results, you should also look at the [http://www.r-project.org R project].


==Converting Image Formats==

To convert formats, I highly recommend the ImageMagick tool suite. The interface is through the command 'convert' and it pretty much automatically recognizes extensions. So, for example, you can do:
<PRE>
convert myimage.gif myimage.eps
</PRE>
You can also specify rotation (-rotate 90), scale, resolution, etc. It works with almost any image format you will find. Type "man convert" for more information.

To convert an eps to a pdf, you can also use
<PRE>
epstopdf myimage.eps
</PRE>
which will save a file called myimage.pdf.

==Revision Control==

See the new separate [[Tutorial on SVN]].

==Feedback==


If any of the above tools (except Matlab) are missing from a group machine, please let me know and I will install it.

Please feel free to update this information with other things I may forget.