Using open-source tools for documenting research [LWN.net]

January 18, 2006

This article was contributed by Carl Bolduc

Introduction

Getting published is a major concern for students conducting graduate studies in science. I'm a PhD student in molecular biology and I started using Linux at the beginning of my graduate studies. Public science research mostly looks like open-source software development. You work hard and give your methods and results to everyone through publications in scientific journals. Ironically, the majority of people working in the field of science use only proprietary software. I myself work in a Microsoft Windows environment.

A typical scientific article will require the use of several tools to reach its final published state. First, most researchers use Microsoft Word and Excel for text writing and tables. They also use EndNote to manage and create the bibliographies you will find in every scientific article. Finally, scientists use a graphics suite, such as Adobe's Photoshop, for figures and PDF creation. This software listing scales up to more than one thousand dollars. It's practically impossible for the regular student to purchase such a platform. In some laboratories, when the head researcher is kind enough, you will find a computer where most of these tools are installed and shared by all members of the team. But what if you could create your own open-source research writing box for free? In fact, you can. You can accomplish the entire array of tasks associated with scientific writing with any good Linux distribution.

The easiest step

One of the most popular open source application that has boosted the Microsoft to Linux transition is certainly OpenOffice.org. For anybody working in science reporting, it is a first and easy step that enables you to step out of proprietary software and remain compatible with Microsoft Office formats. In addition, several journals will ask that the submissions should be in the .doc or PDF format. OpenOffice.org saves you a lot of trouble with its useful PDF export tool.

Although OpenOffice.org can complete a fair portion of the job, it doesn't contain a bibliographic manager tool such as EndNote yet. Such a facility is necessary for academic writer and OpenOffice.org is supposed to fill the blank with some bibliographic extensions in its next version. For now, there is a commercial web-based tool called WriteNote which offers a 30 day free trial and enables you to produce a bibliography with RTF files created by OpenOffice.org.

LaTeX

While OpenOffice.org may be a first step toward writing scientific articles under Linux, the true power resides inside LaTeX. As it is mentioned on the latex project website: "LaTeX is a high-quality typesetting system, with features designed for the production of technical and scientific documentation". "LaTeX is the de facto standard for the communication and publication of scientific documents."

Some of the LaTeX features include insertion of tables and figures as well as the capacity to create complex mathematical equations. Additionally, there are tremendous advantages in learning to write with LaTeX. In fact, BibTeX could get you out of proprietary software tomorrow. You can gather your bibliographic references in a simple text file with the BibTeX syntax and easily insert quotations inside your LaTeX documents, automatically generating a bibliography at the end of your articles.

While the LaTeX format requires a minimum of learning, you can rely on the useful TeXmed web-based tool to query NCBI PubMed and generate BibTeX entries for you. You must specify, in your LaTeX document, a bibliography style to format it according to the journal's recommendations. In fact, many journals now offer their bibliography style on their website. If you can't find the format that you need on the web, you can use custom-bib to create the style you need.

LyX and friends

LaTeX basics can be learned quite easily, but you might need to read a lot from the web or buy some books (like I did) to use its full potential. But do you really need to go through all this trouble? That's where LyX comes into play.

LyX is a GUI front end to LaTeX. Though it has its own file format, it can import and export to LaTeX. LyX looks like a word processor while taking care of all the formatting, just like LaTeX. LyX is fully featured and let you insert figures, tables, mathematical equations and more. Though managing a bibtex text file is very easy, you can rely on graphical tools here too. Software like gBib and JabRef will help you deal with your numerous references and even let you insert them in LyX, just like EndNote does with Word.

Gnuplot

Continuing in your path to build an open-source research writing box, you need a powerful tool to generate plots from your precious experiment results. That is where Gnuplot enters the scene, with its almost limitless possibilities. Gnuplot is a command-line plotting utility with easy to learn commands that enable you to create high quality 2D and 3D plots suitable for scientific publications. It can output LaTeX and EPS code which can be inserted in your LaTeX documents. You can check out this demo that shows the wide variety of Gnuplot's capabilities.

Inkscape

One thing that was really missing in Linux in the past was a good vector graphics editor. I had to install Adobe Illustrator under Wine to be able to draw high quality figures showing various metabolic pathways. Now, with Inkscape, I have everything that I need to create high quality vector graphics which can be exported to EPS and inserted in my LaTeX documents. Inkscape can draw shapes, paths, text and can also export to PNG.

The Gimp

To complete your open-source research writing box, you need a powerful image manipulation program to process your photos and to generate figures from them. That's where The Gimp comes into play. With The Gimp, you can process gel photos, crop the area that you like, obtain negatives of your originals and add labels where you want, all with a few mouse clicks.

Linux drawbacks

While this path can be rewarding, a significant effort will be required. The first thing you need to do is to install a Linux distribution. This might seem frightening to the newcomer, but there are powerful Linux distributions such as Mandriva, Fedora and Ubuntu which are very easy to install and have packaged most of the tools mentioned it this article.

You also need to learn how to use new software. A few of the applications mentioned above only have a command-line interface, but most operations can be performed using GUI-based tools. There is plenty of documentation online, and you can always join an IRC channel to get live help. In a short time, you will become very functional, and you will reach new levels of productivity.

The worst drawback of using Linux in a Microsoft-based environment may involve compatibility issues with your coworkers. Since my boss insists on working with .doc files, I have to convert my papers to RTF using latex2rtf before I send him anything, even if PDF is the most portable format out there. But this doesn't stop me from benefiting of the LaTeX functionality.

Finally, you must rely on the Internet for support. Most of the system administrators in the research field don't know much about Linux (at least not in Quebec, where I'm working) and won't be able to support you if you have problems.

Linux superiority

Beside the fact that Linux and all this software is free, there are many advantages in building an open-source research writing box. Linux provides a robust environment that is a virtually virus-free. Interoperability among applications is quite good, all of the applications mentioned in this article can share data through the LaTeX and EPS file formats.

With little experience, you will start working faster and more efficiently. Serious page formatting issues found in Windows-based WYSIWYG software will be gone. Finally, you will be able to easily share your work by creating high quality PDF files.

An example screenshot of my desktop publishing environment can be seen here.

(Log in to post comments)

Nice article!

Posted Jan 26, 2006 6:45 UTC (Thu) by moxfyre (subscriber, #13847) [Link]

I'm also a grad student (physics) and, like you, I've figured out my own set of tools for productive science work under Linux:

LaTeX
BibTex
Octave (MATLAB clone, super awesome!!) for crunching data and graphing
Gnuplot
Xcircuit for drawing schematics (free as in speech)
Eagle for drawing schematics (free as in beer)

Another important task for me is automated data taking. I use Perl with GPIB modules to control programmable lab instruments. For me, this is vastly better than using LabView which is proprietary, and in my opinion damaging to the brain of any real programmer. :-)

LaTeX is utterly, completely, and totally superior to Word for technical writing. You can't make a Word document too long before you start getting all kinds of problems with graphs mysteriously jumping around, images not scaling properly, table of contents not building correctly, etc. With LaTeX you get exactly what you want and once you've had a bit of practice you can write very quickly.

I took a lab course last semester where the professor did all his handouts in Word. Most of the graphs were anti-aliased to the point that they were barely legible (bad rasterization?) and there were lots of weird formatting quirks. He had no way to generate an index for the 100-page lab manual. Me and other LaTeX-using students would hand in perfectly formatted 30 page reports with flawless graphs and schematics and he'd look on enviously...