(Re-)construction, characterization and modeling of systems for synthetic biology.

Synthetic biology (SB) is a developing area of research that aims to design and build novel biological components and systems with functions that cannot generally be found in nature or biological systems. These systems are created with known properties using implementations or architectures different from those found in historical evolution. SB proposes a new paradigm for the analysis of biological systems and the development of practical applications. It is an inherently cross-disciplinary approach to biological sciences that integrates scientists, knowledge and techniques from fields like mathematics, physics, chemistry, engineering and computer science, within the large knowledge corpus developed in the different fields of biological sciences: molecular biology, systems biology, genetic engineering, comparative genomics, etc. This emerging discipline is not yet uniform and comprises a plethora of approaches, projects, and goals. As a result, no single definition has been agreed on by the members of the community. Broadly, five categories or branches can be defined within SB: bioengineering, synthetic genomics, protocell synthetic biology, unnatural molecular biology and in silico synthetic biology [1]. The bioengineering branch, represented by the ‘modularization, abstraction and standardization’ motto, aims to design and construct novel biological systems by assembling standard, simplified and well-characterized biological elements (parts) to form complex and functional modules (devices) that can be combined into new metabolic or regulatory pathways within the host (systems). This branch encourages an engineering approach to produce controllable and predictable constructs and aims at transforming biotechnology into a true engineering discipline [2]. Synthetic genomics aims at creating organisms with a (synthetic) minimal genome. Modern DNA chemical synthesis methods allow the synthesis of entire genomes that can serve to replace the original genome of the host and generate an artificial organism optimized for new targeted functionalities. The protocell branch aims at in vitro construction of fully artificial protocells endowed with the needed functions to be considered as living cells.The unnatural molecular biology branch pursuits the synthesis of new life forms, based on modification of the rules of molecular biology that evolution has shaped: new nucleic acids, new types of amino acids or existing ones with altered chiralities, different genetic code, orthogonal ribosomes, etc. SB should be model-driven especially since it has to deal with an increasing degree of complexity and relies on tools such as computational models of complex systems and bioinformatics for exploring interactions among the basic building blocks and to predict new properties emerging from their interaction among themselves and with the environment. Thus, the goals of the in silico branch are to produce detailed models of the elements of the synthetic circuits and tools for their design, to establish computational Biotech Highlight