Biological computing

Biological computing as defined in this chapter focuses on computational approaches to explore the properties and functions of the fundamental molecules in biology: DNA, RNA, and proteins. The term is sometimes also used in describing biocomputers composed of biological parts, which is a completely different topic and will not be covered in this chapter. Ever since we entered the genomic era, the rapid development of biotechnology has provided more and more tools for acquiring data from these three molecules: microarray analysis, next-generation sequencing, mass spectrometry-based proteomics, etc. In the meantime, more and more online data resources, databases, and analytic software tools have become available to the public domain. For generated data, hundreds of thousands of computational approaches and analytical tools have been developed for downstream analysis. Network analysis have long been used in discover gene regulations in biological systems. In this chapter, we will overview data generation and analytical methods for DNA, RNA, and protein data and introduce some online databases that are necessary or helpful to biological data processing and analysis. Finally, we provide some case studies that involve either hypothesis generation or data driven network inference.