BlobVis ScreenShot

Abstract

In the connection between biology and compution, which has been researched and discussed in decades, one question seems notable by its absence: Where are the programs?
The report below provides a short introduction to biomolecular computing from Von Neumann to recent advances using process alegra for modeling biochemical interactions. as well as a description of the ``blob-model''. The ``blob-model'' is a model of computation devised by Hartmann, Jones and Simonsen[1]. The model provides machine instructions possibly executable in a biomolecular setting and aim to enable programmers to write programs which could be executed in a biomolecular context. The model is claimed to be biological plausible, demonstrated programmable and provably stored-program, universal, uniform and Turing-complete[1].
In an effort to support or disprove these claims as well as explore the properties of the model, a visualization tool for running the programs in the blob-model has been developed. This site provides the downloadable program as well as
Based on the tool the report below provide a discussion on previously undiscovered aspects of the blob-model.

[1] "Programming in Biomolecular Computation", by Hartmann, Simonsen and Jones,Computer Science to Biology, June 2010, CS2Bio

Report

Report (english) 2.2MB (bibtex)

Source code

Download the code via github: svrist/blobvis