Software for systems biology: from tools to integrated platforms

Software is crucial for biological research, has an impact on research productivity and enables researchers to explore massive databases and knowledge-bases.The workflow in systems biology generally consists of iterative cycles of: experiments; data acquisition and analysis; modelling; and computational analysis. Each of these processes is supported by software tools.Standardization and interoperability are crucial for the efficient use of software tools and data resources.A software platform enables various software tools, data resources and knowledge sources to be accessible in a consistent manner. This dramatically improves the productivity of research and reduces potential errors in the workflow.In the future, software platforms and data or knowledge resources need to be supported through community-wide efforts. However, this requires a broader understanding of social dynamics, psychology and the economics of research activities; additionally, platforms need to be supported by user-friendly software tools.