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
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
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
which offers a 30 day free trial and enables you to produce a
bibliography with RTF files created by OpenOffice.org.
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
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
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.
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
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.
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
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.
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
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.
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.
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.
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
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