CoSBiLab is a software platform implementing the new conceptual framework of algorithmic systems biology. It is centered on the idea of representing biological elements as programs and elements interaction as message passing between the corresponding programs. This idea is guiding the programming paradigm supported by the new programming language BlenX. This approach is higher level and provides a component-based view of systems rather than reaction-based descriptions that are usually adopted in ODE or rewriting system tools. CoSBiLab allows its users to exploit compositionality and stochasticity addressing in a native way concurrency and complexity.
To make the approach intuitive, CoSBiLab has a tabular interface to model systems and to grasp data from databases so that non-experts can use CoSBiLab; i.e., programming in BlenX without having programming skills. CoSBiLab has also tools that can help inferring missing data, perform network analysis, and visualize simulation outcomes. In addition to the introduction of the conceptual framework, demos will be provided to help in understanding the software that will support the e-scientists of the future in their work.
For more information, see “Algorithmic Systems Biology,” Communications of the ACM, 52(5):80–88, May 2009.