Thesis of Søren B. Vrist
The world of biocomputing or biomolecular computing a mix of biomolecular research and computer science. Research by Neil D. Jones, Jakob Grue Simonsen and Lars Hartmann has uncovered a niche virtually untouched: Regular programs as written by computer science programmers. Others have addressed ``hardware/wetware'' for computation as one of the facets while others research computer science approaches for aiding and modeling biology. The niche explored by Jones et al. and this thesis somewhat joins the ideas of both worlds and suggests a novel contribution; A biomolecular plausible instruction set, with the promise of programmability on level which will be familiar to regular computer science programmers. This thesis will expand on the biomolecular instruction set - defined as a part of the Blob programming model in [1] - by designing and devloping an intermediate level programming language -\bplc\. The Blob model was lacking in formal semantics and a formal operational semantics for both the blob instruction set and the developed programming language will be provided. The related work of the biocomputing community will be sampled and presented and the contribution of a programming language for a biomolecular computational model will be compared and held into perspective. A compiler for the programming language into the blob instruction set is provided
A Programming Language for a Biomolecular Computational Model
Søren Bjerregaard Vrist
Department of Computer Science, University of Copenhagen (DIKU), Copenhagen, Denmark
Thesis
(english) 2.4MB (bibtex)
[1] "Programming in Biomolecular Computation", by Hartmann, Simonsen and Jones,Computer Science to Biology, June 2010, CS2Bio