Tag Archives: Science

Science and KDE: kile

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During the course of my research work, I may obtain results that are worthy of publication in scientific journals. Since my master’s thesis I’ve been using LaTeX as my writing platform, mainly because I can concentrate on content rather than presentation (I find it useful also for writing non-scientific stuff as well). Also, I can handle bibliography (essential for a scientific publication) very well without using expensive proprietary applications (such as Endnote).

In my early days I used kLyX first, then LyX, but I found the platform to be too limited for my tastes, and also LaTeX errors were difficult to diagnose. I needed a proper editor, and that’s when I heard of kile, a KDE front-end for LaTeX. Kile is currently at version 2.0.2 and is a KDE 3 application. However, in KDE SVN work is ongoing to produce a KDE4 version (2.1) and that’s what I’ll look at in this entry.

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Science and KDE: rkward

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I try to use FOSS extensively for my scientific work. In fact, when possible, I use only FOSS tools. Among these there is the R programming language. It’s a Free implementation of the S-plus language, and it’s mainly aimed at statistics and mathematics. As the people who read my scientific posts know, I don’t like R much. But sometimes it’s the only alternative.

Well, what does R have to do with KDE? With this post I’d like to start a series (hopefully) of articles that deals with KDE programs used for scientific purposes. In this particular entry, I’ll focus on rkward, a GUI front-end for R.
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Published! (and it matters more)

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Finally I can lift the curtain of silence and tell the reason why I’ve been very busy before Christmas: it all lies in the publication of a paper, “Using Pathway Signatures as Means of Identifying Similarities among Microarray Experiments”, which is finally out on this week’s issue of PLoS ONE. It’s different from the previous paper I mentioned (which was not my first publication, either), for two main reasons:

  • It’s a bioinformatics paper;
  • I am first author there.

The second point is very important because usually for a person doing bioinformatics is more difficult to end up as first author in a paper, since most we do is “something in the middle” like data analysis. Therefore, this paper is quite important for me. Also, it deals with an interest of mine, mainly analysis of biological networks using high-throughput platforms such as microarrays. Actually I’m also interested in network reconstruction, but I need to study far more than what I’m doing right now.

In any case, let’s hope this is the first of a (hopefully long) series!