The CIPRES Software Effort

A key deliverable of the CIPRES project is freely-available, platform-independent software that can be installed on a laptop or desktop computer or run on a large supercomputer. To achieve this deliverable, the CIPRES software team, led by Mark Holder is actively developing software tools to serve practicing systematists (particularly those with large data-sets), computational systematists who implement algorithms, and algorithm designers. The basis for the enabling technology is a flexible, efficient library that allows for cooperation/communication between diverse phylogenetic modules. The libraries will make it possible for developers within the community to easily link their software to the software of other developers.

Biologists can access the CIPRES software services through multiple front-ends. Modules that allow the widely-used Mesquite software package to access CIPRES services will be released in Fall of 2006. The visual programming environment Kepler allows users to construct workflows by arranging and linking icons which represent distinct computational tasks. In addition to Mesquite and Kepler, the CIPRES software team has produced a simple Java application that uses CIPRES services to implement the recursive-iterative-DCM3 methods of Usman, Warnow, et al. All CIPRES software is still in the testing/pre-release stage.

 

Package 1: TheCIPRES libraries

 

The software development effort is a collaboration between developers at SDSC (Terri Liebowitz, Lucie Chan, Zhijie Guan) and systematists (Mark Holder, Paul Lewis, David Swofford, Wayne Maddison, David Maddison, Peter Midford, and Rutger Vos).

CIPRES software links:

• CIPRES software architecture
• CIPRES Releases
• CIPRES wikis
• CIPRES bug tracking
• CIPRES source code repository
• Nightly snapshots of the source code

CIPRES is a Collaboration of the Following Institutions:
American Museum of Natural History, Florida State University, New Jersey Institute of Technology, North Carolina State University, Rice University, San Diego Supercomputer Center, State University of New York at Buffalo, Texas A&M, University of Arizona, University of British Columbia, University of California at Berkeley, University of California at San Diego, University of Connecticut, University of Pennsylvania, Univ. of South Carolina, University of Texas at Austin, and Yale University. xhtml | css