Sunday, March 25, 2012

Challenges in phylogenetic tree visualization

I recently read an excellent review by Roderic Page, on the challenges in phylogenetic tree representation and visualization. It provides an overview  on existing software and tools (although he missed our ETE package, see image below for an example of ETE's visualization features). The number and diversity of existing tools is overwhelming, but probably matches the diversity of different interests and possible applications of phylogenetic trees. One may be interested in  overlaying sequence information (see below), while other would be interested in displaying information on the geographical distribution of the species. Some may need to represent uncertainty and overly different topologies, or networks to represent transfers of genetic material, the possibilities are unlimited.

 Most importantly he mentions some of the challenges of tree visualization software such as the ability to represent huge trees and to allow interactive behavior with the user. In our group we have encountered such needs and this is the reason behind implementing more visualization features in ETE. Fortunately new technologies are offering new opportunities as well, and I enjoyed imagining the possibilities that 3D visualization and touchscreen technologies will provide to researchers. Definitely is a field to follow.

 If you are interested in the topic. I recommend this video.

Saturday, March 10, 2012

Open Letter for Research in Spain

As you surely have heard, Spain is facing a serious crisis in the context of a globalized market-economy (yes, it used to be a time when economical crisis related to something more tangible, such as a serious drought or a plague, but now one can only blame abstract fluxes of financial speculations). The new government is preparing a new budget which is predicted to include the most dramatic cuts in our history. Researchers here, who have already been hit by previous cuts (see this letter), are now embracing for the worst. 

 In this context, an open letter has been put together by the Confederation of Spanish Scientific Societies, the Federation of Young Researchers and others. I recommend you to read it (some cited figures and data are very revealing), and if yo agree with it sign it, as I just did.

 Open letter for research in Spain.

Sunday, March 4, 2012

Darwin's h-index

  I guess most scientists are nowadays familiar with the term "h-index", which is a metric of citations to your published articles. More specifically the h-index correspond to the number of articles (h) that have at least h citations. Given that this index is used by many funding agencies and by peers that evaluate you for a position or competitive grant, we all hope to see it grow year by year.

  Charles Darwin lived in completely different times, he had no need to apply for grants or positions every few years and there was no system to track citations or give a "number" to the supposed "impact" of his research.  He, nevertheless, has been absorbed by the current metrics obsession and has already an h-index, computed by google scholar. 

His magic number is 63. Will this change anyway our idea of how important was Darwin's impact to Science? or it will rather help us to put the h-index into context, and highlight the difficulty of measuring true impacts?