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Design and implementation of a domain specific language for phylogenetic inference
Enrico Pontelli1, Desh Ranjan, Gopal Gupta
1Knowledge Representation, Logic, and Advanced Programming Laboratory, Department of Computer Science, New Mexico State University, Box 30001/CS, Las Cruces, NM 88003 USA. epontell@cs.nmsu.edu
Journal of Bioinformatics and Computational Biology
|August 4, 2004
Summary
Biologists can now program phylogenetic inference solutions using phi LOG, a high-level domain-specific language. This approach simplifies complex phylogenetic analyses by leveraging automated software engineering for implementation infrastructure.
Area of Science:
- Computational Biology
- Bioinformatics
- Evolutionary Biology
Background:
- Domain experts operate at high levels of abstraction.
- Phylogenetic inference is a complex computational biology problem.
- Existing programming methods may not align with expert-level abstraction.
Purpose of the Study:
- Introduce phi LOG, a domain-specific language (DSL) for biologists.
- Enable high-level programming of phylogenetic inference solutions.
- Automate the creation of implementation infrastructure for the DSL.
Main Methods:
- Design and motivation for the phi LOG DSL.
- Utilize a software engineering framework based on Denotational Semantics.
- Employ Logic Programming for infrastructure generation (interpreter, compiler, debugger).
Main Results:
- A novel DSL, phi LOG, has been designed for phylogenetic inference.
- The DSL allows biologists to program at a high level of abstraction.
- Implementation infrastructure is automatically generated, reducing development overhead.
Conclusions:
- phi LOG empowers biologists to address phylogenetic inference challenges more effectively.
- Automated infrastructure generation through Denotational Semantics and Logic Programming is feasible.
- High-level DSLs can bridge the gap between domain expertise and computational solutions.