BIOMICS

BIOMICS is a European Commission FP7 3-year STREP project that started on 1 October 2012. It falls under Objective ICT-2011-9.6: FET Proactive: Unconventional Computation (UCOMP)

Interaction Computing (IC) takes inspiration from cellular processes rather than from evolution. BIOMICS aims to leverage existing cell metabolic and regulatory mechanisms as the ontogenetic basis of a model for IC. However, because the knowledge to properly mimic, exploit and adapt these systems to computer science is lacking, BIOMICS will also advance the state of the art in the mathematics of biocomputing. The mathematical structure thus uncovered feeds into two different and complementary directions. On the one hand, it will inform the automata theory formalisms for IC; on the other hand, it will be mapped through category theory to the logic foundations of the BIOMICS specification language. Whereas the automata theory research will focus on the structural properties of self-organising systems, the BIOMICS specification language will instead focus on the specification of self-organising behaviour. By end of Year 2 we will have developed the formal tools and frameworks from both points of view of the behaviourrealisation dichotomy to be able to effect their synthesis in the form of an environment which, through interactions, is capable of generating useful software systems that match the biological structure template - and are therefore themselves based on interactions. This foundational mathematical work of BIOMICS will be applicable to software systems of a radically new kind and to systems biology, creating a unified mathematical framework for understanding, predicting, manipulating, and dynamically synthesising algorithmic activity-in-context based on interactions (i.e. interaction computation) in both realms. This will be demonstrated not only by the application of the framework to the analysis of complex-adaptive biological systems beyond those studied in the course of its development, but also by proof-of-concept implementations of software systems (for example demonstrating security properties) as a potential new paradigm for unconventional computing.

Objectives

The BIOMICS project was inspired by the observation that cell metabolic/regulatory systems are able to self-organise and/or construct order dynamically, through random interactions between their components and based on a wide range of possible inputs.
We are undertaking research into whether this behaviour can be reproduced in a controllable way through interacting finite-state automata. If so this will lead to a radically new model of "bottom-up computation" with equal applicability to computer science and systems biology that we call Interaction Computing (IC).

Role of University of Passau in BIOMICS 

• Lead on the design of a specification language which can be used by humans which are not required to have a deep understanding of algebra or category theory. We aim at a high-level language which mainly defines behavioural properties of a system and abstracts from the mathematical details.
   
• Lead on the creation of a proof-of-concept implementation which can validate the theoretical results, allowing experimental studies in both directions: the application fo our framework to computer science as well as to biological models.
   
• Analyse existing computer science systems through algebraic automata theory, also known as Krohn-Rhodes theory.