Some (possibly) helpful software for scientific paper writers

Scientific publication usually requires the inclusion of graphics, tables, or other kinds of figures into your manuscript. And your manuscript may have special formatting needs, like equations and non-ascii characters.

Commercial software packages such as the Microsoft Office suite can do specialized text formatting and help you create figures. Many authors who submit their work to the AAVSO use these packages for all of their text processing and plotting needs, and do just fine with them.

If you don't want to or can't afford to use for-purchase commercial packages, there are other options. One of the most famous of these is the OpenOffice suite, which is free, and quite powerful.

There are still other tools used for creating and typesetting your manuscript that are commonly used by the scientific community. For typesetting, LaTeX has become a major standard in scientific publication, due to its common availability in academia, and the fact that it has many features useful in scientific publication. It is also all but required for submitting papers to the astro-ph preprint archive. For graphics, Gnuplot is another common and powerful program useful for plotting data and creating "camera-ready" figures for publication. Below, we describe both of these, and suggest ways of obtaining and installing them.

Disclaimer

This document is intended as advice, not as a definitive instruction manual. You are on your own as far as figuring out what you need, where to get it, and how to install and use it. Installing (or attempting) to install any software downloaded over the internet has some risk. Please use common sense and caution when downloading files, and if you are not sure how to install something, please seek assistance. The AAVSO is not responsible for any damage done to your computer as a result of your following these directions. Proceed at your own risk!

1) Gnuplot

Gnuplot is a freely-available plotting package capable of making a variety of 2D and 3D plots from user-supplied data files (such as light curve data) or from predefined functions (like "sine" and "cosine"). You can create plots as you type via a command-line interface, or generate plots from pre-written scripts, tailored to give you exactly the output you want.

Gnuplot is available for a variety of systems in both binary and source code formats. For a Microsoft Windows-compatible binary, go to sourceforge. (I have tested that one on Windows 98 -- it works ok!) For a Mac OS X dmg file, also go to sourceforge. For linux, you can obtain the uncompiled sources from sourceforge , as well as your distribution CDs or a package manager like rpm or yum. You should visit the Gnuplot website at www.gnuplot.info for more installation instructions and tutorials.

If you are unsure whether you want to try learning gnuplot -- which does have a learning curve -- you can see how well it plots data on the fly by visiting the AAVSO's Light Curve Generator, which uses gnuplot! If you think this plot looks good, visit the gnuplot.info webpage for more. Gnuplot is very, very flexible, and can produce output on your screen, in png files, and in postscript. It can even use TrueType or other system fonts if you have them installed. It's a good program, and is 100% free.


2) LaTeX

LaTeX is a powerful text-formatting package that creates print-quality files from a text-based source file. The "latex programming language" is similar to but much more complete than the HTML markup language, and is designed for paper rather than screen output. It is the standard formatting program for most scientific fields, including astronomy, physics, and mathematics. One of the main benefits of using LaTeX is that it makes it incredibly easy to include mathematical, greek, and other special text formats in documents without the assistance of equation editors or other processing. It also has the benefit of being generated directly from a text file. In principle, a person experienced with latex can go from a text editor to postscript output without needing any graphical interface. And a latex-formatted document can be processed on any system running latex, regardless of its operating system.

One major problem is that LaTeX has a learning curve as well. After using it for ten years, I still have to reach for the manual to remember how to make an "infinity" sign or to put limits on a summation. And setting margins and formatting figure boxes have additional complications. It helps to get ahold of a good example of a formatted paper, that you can either study and learn from or simply cut and paste your text into. Like this one. It also helps to download a symbol guide, like this one which is one hundred and five pages long. (Fortunately, most of the ones you'll need are on just a few pages.) You might also look at the AASTeX homepage, and the IBVS information for authors page -- see the file ibvs2.sty.

LaTeX is a "unix-friendly" program. "Unix-friendly" programs are rarely simple to install, and LaTeX is no exception (even under Mac, yes). On *nix systems like linux and Mac OS X, you may have some or all of the required software installed. It is possible that your linux distribution has "tetex" package already, and if it is included in your distribution's default installation, you may already be ready to use it. (Hint: type "which latex" in a terminal window -- if it returns a pathname, you have it, but if it returns "Command not found", you don't.) On a Macintosh running OS X, you may have the GCC compiler installed that will be needed to build LaTeX from source. If not, you will need to install XCode Tools prior to trying any of this. You probably have XCode on one of your installation DVDs.

You definitely do not have LaTeX in any official release of Microsoft Windows. (There may be a template file that would allow you to load a latex file into Word, but I've never seen such a thing. And if you've got Word, don't bother with LaTeX.)

Because of its complexity, and because several scientific journals (including the JAAVSO) do accept documents in Microsoft Word and plain text, you should think awhile on whether to bother with this.

If you're still interested, read on...

Linux

Under linux, there may be packages available on your distribution cdroms. If not, you may download them from whichever mirror you like. You can use package manager tools like rpm or yum to do this. Refer to their manpage to find out how. I will assume you are familiar with such things if you are running linux. Using yum on FC4 for example, you can find the tetex package with the command "yum search tetex". The package you want will be something like "tetex.i386" or just "tetex". Note that "tetex" is a package which includes latex along with some other things. There is no "latex" package per se.

Macintosh OS X

If you have some familiarity with Unix as well as Macintosh, you can install tetex most painlessly with any of the *nix package managers that run under Mac OS X. I use and recommend Fink and the Fink Commander GUI. (This is how I installed LaTeX and several other packages on my personal laptop.) It's relatively painless, but you must have GCC installed, preferably from the XCode package that came with the install disks of your computer. If you have 10.4, or purchased a higher-end system with 10.3, it is probably already installed.

But there are other ways to do this, and you may even want a GUI LaTeX processor, like TeXshop for example (disclaimer: I've never tried it, use at your own risk). You can find out more at this How-to guide. They specifically recommend using the i-Installer program, i-Installer, to install teTeX, but the small size of that package (2.1 MB) is deceptive -- it will require that you download a very large package (more than 250MB) over the internet. If you don't have a cable modem, this might not be for you.

Windows

First, if you plan on submitting to the JAAVSO exclusively, we do accept Microsoft Word and plain text documents. LaTeX might not be necessary for you at all. But if you are curious, there are ways to install LaTeX. The Cygwin system allows you to compile and run *nix applications under Microsoft Windows. If you are running Cygwin, you can try to build from a tetex source package, as on a *nix system. I have never tested this, but presumably it's possible. There is also a package called MikTex which claims to run latex under all versions of Windows from Windows 98 through Windows Server 2003. (I say "claims" simply because I haven't tested it myself.) MikTex looks simpler, but I've used neither and can't recommend one over the other. Again, try at your own risk.