Dec 19, 2008

Edit PDF Files with pdfedit

Collaborative editing can be painful and in the end you might end up doing some changes to pdf versions of submitted files. pdfedit comes in handy. I needed some time searching the internet (very high noise level for this topic), while the program kept arguing "document is read-only." How to actually change files? Answer: tools > delinearize, open document, save document under new name, open again. The editor is comfortable enough (although the UI is kind of messy).

P.S.: Inkscape is a very comfortable editor. It allows import and export of many image formats including PDF and EPS. See my blog entry about creating print-quality figures with SVG, where I tell more about inkscape.

Dec 17, 2008

LaTex Poster Template (BAposter)

You can make great posters with LaTex. However hand-positioning elements through coordinates, adjusting size and margins can be very time-consuming and awkward. Already for quite some time I wanted to post about a particular latex poster template. I used it for two posters in ECRO 2008 and later a poster for FET 2009.

I like about this library that it is very elegant and that conversion from article to poster is effortless. You organize the poster in boxes, which have a header each, and which you align relative to each other using keywords such as below, top, column, row. A code snippet from my FET poster:

\item Some properties affect odor coding very strongly (sulfur--containing functional group).
\item Bond saturation affects also seems very relevant (alkyne, alkane, and alkene).
\item Carboxylic acid and aromatic, still seems to be important.
\item Results partly confirm relevance of dimensions of molecular properties suggested by Johnson and Leon

The image below shows a poster from Ecro 2008. I hope you can see the poster in the correct colors. The title bars should be blue.

The first figure on the left is made in GNU R and is so much better than the other ones created in matlab! The main problem with the matlab figures seems to be in matlab's inability in linux to save figures with transparent backgrounds. I learned a lot about exporting figures in the meantime. See my article on exporting figures from latex.

Thanks to Brian Amberg for his template, called baposter, (ba stands for his initials, I suppose).

For alternatives, another poster template which looks quite usable (I haven't tried it) is A0-poster. See the article about scribus posters on I found scribus poster templates: at scribus post and on the official scribus site.

What is your experience with poster presentations in latex?

You might also be interested in my article on exporting figures from matlab. I also wrote an articles about exporting data from matlab and how to get good combinations of linestyles and colors for plots.

Dec 14, 2008

Mythical Man Month

I am reading the Mythical Man Month, a book by Fred Brooks, about management of software projects. The titular man months refer to calculations in the planning of projects that equal men with months. It is in this book where Brooks quips famously: "adding manpower to a late software project, makes it later."

The book is a great read, short and to the point. Brooks shares from his experiences managing software projects, among others the OS/360, an operating system. The OS/360 was very ambitious and very late. One of Brooks' lessons is the second system effect, which predicts (I am simplifying) that the second system of a project manager will be much better than the first one.

Each chapter starts with a quote. Such as this one from genesis:
Chapter 11: 1 Now all the earth had one language and the words were common [to all].
2 And men moved east, and they found a plain in the land of Shinar 1 and they settled there.
3 And they said to each other, each to their fellow, "Come. Let us make bricks, and let us bake them with fire." They used brick instead of stone and tar instead of mortar.
4 Then they said, "Come. Let us build a city for ourselves, and a tower, the top of which reaches the heavens. So let us make a name for ourselves lest we be scattered over the face of the entire earth."
5 But Yahweh came down to see the city and the tower that the sons of man had built,
6 And Yahweh said, "See! The people are one and their language is the same for all of them. And now they have begun to do this; in the future nothing that they plan to do will be impossible for them.
7 Come. Let us go down and let us confuse their language so that they will not understand each other's language, each will not understand their fellow."
8 So Yahweh scattered them from there over the face of the entire earth, and they stopped building the city.
9 Because of this, the name of the city is called "Babel," 2 because Yahweh confused the language of the entire world, and Yahweh scattered them from there over the face of the entire world.

Bibel translation by Richard Hooker.

I wonder what other people think of this bible passage.

Dec 10, 2008

journal impact

I nearly always use google scholar to search articles and I suspect many people who do research do the same. If your article shows high up in the search list depends, except for appropriateness of search terms and the year of publication, on how many articles cite it, how often these are cited and so forth.

The eigenfactors web site uses a method similar to pagerank in order to rate journals based on know how well connected their articles. You also find a map of connections between sciences and top ten lists.

For example, to see the impact of Annnual Review of Neuroscience, here is the Eigenfactor, and here the isi web of knowledge result (for isi web, you need to access from a licensed computer). The results look very similar.