Tag Archives: Web Resources

A new phylogeneticist blogger

I’d like to advertise a newcomer among bloggers in phylogenetics: Nicolas Lartillot, now a researcher in Lyon. Nicolas just started blogging a couple of weeks ago but, judging from the number of posts he has already contributed, he seems bound to become a very prolific blogger.

Nicolas has made several noteworthy contributions to the field of phylogenetics, in particular Bayesian phylogenetics. For instance he has developed the CAT model of protein evolution, which seems to be more resilient against the Long Branch Attraction artifact, he has proposed Thermodynamic Integration for computing Bayes factors, he has developed a model for investigating correlations between continuous traits and rates of molecular evolution along a phylogeny, and he maintains the PhyloBayes package.

His blog is called “The Bayesian kitchen”, which I believe means that, underneath the nice theoretical properties of Bayesian inference, a fair amount of cooking is sometimes necessary to get things to work. So far his posts have been about the Bayesian/frequentist divide, about the philosophy of Bayesian inference, or about the interpretation of posterior probabilities, among other things. He uses examples from phylogenetics (e.g. dating, diversification models, ), comparative methods, or gene tree-species tree methods) or population genetics to help make his points. I’m certain I’m going to learn a lot from his posts, and I believe some of the readers of this blog will enjoy them too!

Has CIPRES helped you out?

cipresCipres is preparing their annual useage report which, among other things, helps determine the size of their XSEDE allocation from year to year. Please read the email from Mark Miller (copied below) and participate in their short survey (available at http://www.surveymonkey.com/s/QLCB7WZ).

Dear CIPRES Science Gateway User,

We need your help to keep the CIPRES Science Gateway operating. You received this email because you are one of the 2800+ users who submitted a job from the CIPRES Science Gateway during the past year. Each year we must report on user activities to continue receiving annual allocations of computer time for our Gateway.

In the last year, strong user response to this survey helped us increase the amount of time we received from the XSEDE allocations committee, and an NSF award to create a new set of CIPRES Web Services. Soon you will be able to access CIPRES through tools like Mesquite, or through scripts you write yourself, as well as through the browser interface.

Even if you just used it for a class, you can help by completing a brief survey (just a few questions) describing your activities on the CIPRES Science Gateway, and providing opinions about how the CIPRES Gateway should continue to operate.  The survey is located here:   http://www.surveymonkey.com/s/QLCB7WZ

The survey results help us continue to provide the community with easy access to computational resources for phylogenetic programs, and help us plan for sustainability of the resource. It requires only a few minutes to complete, but your feedback is a key element in justifying access to NSF resources.
If you do not wish to complete the survey, please help by sending me citations for any publications that were enabled by the CIPRES Gateway.
Thanks for your help,

Mark Miller
Principal Investigator