Getting Started in Biological Pathway Construction

Abstract

The increasingly extensive data on dynamic cellular processes are revo- lutionizing biology and medicine. Computational tools are necessary for exploring these data. A familiar and intuitive approach is to organize information into biolog- ical pathways. This chapter provides a general overview and an introduction to the specific software and notations used to store, construct, and analyze biological path- ways. Biological pathways are collected in public and private databases, which are often curated by many researchers. In these databases, information is represented in one of several standard notations, is usually viewable in several different layouts, and can be readily updated by multiple users. Specialized software allows users to manually or automatically mine the data in order to construct biological pathways.