The complexity of the genomic structure and our limited understanding of biological processes require new computational methods to investigate the huge number of possible designs for circuits, pathways, and entire genomes, with the ideal being the ability to model, simulate and redesign a biological system in-silicon prior to fabrication, similar to CAD/CAM for physical devices.
Synthetic Biology aims to establish a standard and effective biological design flow, where biological systems are designed and verified computationally, before in vitro synthesis and in vivo experiments. Each phase of this process has multiple challenges ranging from managing high-throughput laboratory operations to developing new software and defining accurate and interoperable computational models.
The Special Interest Group in Biological Systems Design (BSD-SIG 2012) aims to provide a broad view of the current state-of-the-art for scientists from biology, chemistry, computer science, mathematics and engineering.
* Genome Design * Protein Design * Computer Aided Design Tools * Data management & standards
**Genome Design** The availability of high-fidelity techniques for the synthesis of long DNA strands constitutes the starting point for effective pathway engineering. The aim of this session is to present state-of-the-art methods for genome design, focusing, but not limited to, on the following topics: oligo-nucleotides design, Probe and watermark design, High-throughput techniques, theoretical aspects of DNA design.
**Protein Design** An important purpose of synthetic DNA is to express non-native or human-designed proteins. Protein expression and design introduce additional complexities. This session provides a forum to discuss the recent advances in this field, with particular emphasis on the design of therapeutic peptides and proteins.
**Computer Aided Design Tools** The design of biological systems is often characterized by ad hoc, human-centric procedures, which limit applications to small-scale problems. While Computer-Aided-Design (CAD) tools are standard in many engineering fields, CAD capabilities for synthetic biology are at a very early stage. This session gives a broad view of some emerging approaches in Biological Design Automation (BDA), with the aim of finding and discussing new areas where CAD tools can improve and accelerate the synthesis of living matter.
**Data management & standards** The enormous amount of data generated by high-throughput techniques and synthesis processes requires the introduction of new and specific representation schemes, along with efficient and open standards for interfacing different data sources. New systems are also required to collect information and performing on-line data analysis. The aim of this session is twofold: first, exploring data structures and representations for synthetic biology; second, promoting and discussing use-case scenarios for the Synthetic Biology Open Language (SBOL).