Which layout software do you use for creating publication quality figures?

Dr Engelbert Buxbaum engelbert_buxbaum at hotmail.com
Wed May 25 09:10:25 EST 2005

paul_wary at yahoo.com wrote:

> Hi,
> This may not be directly a molecular biology question but nonetheless
> most of you here have already had to deal with this I suppose. I am
> familiar with the MS Office suite programs but do not have any
> experience with DTP/layout software. For a publication I need to create
> multi-part figures with some annotation (not the actual caption, which
> will be on separate pages, just some basic graphics elements like
> frames, arrows, and labels). The "problem" is that the output should
> also be high quality (e.g. TIFF or EPS). Which software do you use for
> this purpose or which software would you recommend?

For publication quality texts (thesis for example) nothing beats
(La)TeX, the support for graphic inclusion, tables, formulas, index,
cross-references and other specialties of scientific texts is truely
excelent. Special applications like typesetting DNA-sequences,
hiroglyphs sanskrit or chess problems are available as packages, if
required. In addition, there are free versions of this software
available (see your nearest CTAN node www.tug.org, www.tex.ac.uk,
www.dante.de and others) for virtually any operating system, making
document exchange between coworkers a snap. Since LaTeX documents are
plain ASCII texts, you can go back to them after decades, something no
proprietary format offers. An active  user community exists on
comp.text.tex for rapid advice and help, your computer centre probably
also has a "TeXnician".

For the graphical presentation of laboratory data the Gnuplot system
(www.gnuplot.org) offers unparalleld flexibility and quality. Gnuplot
too is free software, available for all operating systems and works with
plain ASCII data files. Output can be for different devices like
plotters, printers or various graphic file formats. The recently
released version 4 is truely awsome. Support is found on
comp.graphics.apps.gnuplot. Commercial systems like SigmaPlot or Origin
are simply too expensive and offer little if any advantages.

Vektor drawings can be produced with xfig (www.xfig.org) under *nix, an
operating system independent Java version (jfig) is also available,
albeit slower. If you are prepared to spend money and are working on a
Windozze platform, Turbo-CAD by IMSI is not half bad, easy to learn and
not too expensive. Unfortunately they have stopped to distribute their
free learning edition.

Pixel graphics and photos can be edited and converted between formats by
the Gnu Immage Manipulation Package, Gimp. Whether this program is
better, equal or worse than its commercial rival, Photoshop, is a matter
of intense flame wars, to which I do not wish to contribute. Drawing of
such pictures can be done by programs that are part of most operating
systems like (x)paint, and converted from their proprietary format into
something more open by Gimp. There are also more comfortable commercial
programs available, but in general I would advice to use vector graphics
as much as possible and limit pixels to photos.

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