Research Projects:

A Domain-specific Computational Workbench for Evolutionary Biology.

The primary goal of this subproject is the design and implementation of a domain-specific framework for the development and execution of phylogenetic inference applications. The framework is based on a novel Domain Specifis Language (DSL), called ΦLog.

The specification of ΦLog will be developed using a novel semantic-based formation, which will allow the agent-based paltform to support program executions. The platform will view existing pertinent data sources and applications as bioinformatic services; the agent infrastructure will automatically develop execution plans by extracting high-level actions from the source ΦLog programs and instantiating each high-level action into invocations of the relevant services.

The design of ΦLog will be driven by close interaction between language designers (computer scientists) and its users (biologists). These users will be both local biologists at NMSU and scientists from other institutions. The language will enable biologists to express—at a high level of abstraction—the analytical tasks associated with extracting genetic and genomic data from databases, aligning sequences to define homology of characters, modeling the evolutionary change of characteristics, and evaluating distinct phylogenetic trees.

PI: Enrico Pontelli
Co-Investigators: B. Milligan, D. Ranjan, J. Spalding, S. Tran
Collaborators: C. Baral (Arizona State U.), G. Gupta (U.T. Dallas), S. McIlraith (Stanford & U. Toronto)

Other Research Projects

Computational Methods and Tools for Promoter Identification.

An Information Management System for Emerging Pathogen Data.

Bridging the Resolution Gap: Automatic Sequence Mapping for Intermediate Resolution Macro-molecular Structures from Electron Cryo-Microscopy.