Saturday, May 24, 2008

The CIPRES Portal

Supercomputers or computing clusters are now a popular solution to the computational challenges posed by increasingly large phylogenetic datasets. By using a cluster, you can speed a typical MrBayes run up by at least eight times (by running each of the eight chains required by the default MCMCMC settings on a different processor). The obvious problem with these resources, of course, is that many users don't have access to a cluster. Fortunately, this is beginning to change. One emerging resource is the CIPRES portal, which offers public access to computing resources at the San Diego Supercomputing Center. Although some have complained that this massively multi-PI, NSF-funded resource has been slow to develop, there has been tangible and important progress over the past few years. At this point, users can implement some of the most popular applications in phylogenetics (e.g., PAUP*, MrBayes, RaxML) through a web interface. In most cases, unfortunately, this interface is limiting; for example, some of the most popular options in MrBayes (e.g., parititioning) and PAUP* (e.g., multiple randomized sequence addition replicates in a heuristic search) are remain unavailable. Nevertheless, they're aware of these limitations and I've been told that improvements are on the horizon. This is an important resource and I want very much for it to succeed.

1 comment:

Anonymous said...

Hi, I supervise the CIPRES Portal at SDSC, and wish to thank you for your kind words. I want to mention three things:

1) the command line options you mentioned that are not available on Portal V 1.0 are now available on Portal V 2.0,; along with many new tools, many new options, and a place to store your data indefinitely.

2)We are working to make the project scalable by blurring the line between developers and users. For example, using a variant of the PISE XML standard users and developers can add options for existing tools, or create interfaces for tools we have not exposed already, using our webtooldev project.

You can find information on creating XML as well as docs, templates, and examples at
You can use this web application to build and test an interface in a working version of the portal.
A few developers have already contributed their own tools or other popular tools from the community.