SUMMARY: The Infobiotics Workbench is an integrated software suite incorporating model specification, simulation, parameter optimization and model checking for Systems and Synthetic Biology. A modular model specification allows for straightforward creation of large-scale models containing many compartments and reactions. Models are simulated either using stochastic simulation or numerical integration, and visualized in time and space. Model parameters and structure can be optimized with evolutionary algorithms, and model properties calculated using probabilistic model checking. AVAILABILITY: Source code and binaries for Linux, Mac and Windows are available at http://www.infobiotics.org/infobiotics-workbench/; released under the GNU General Public License (GPL) version 3. CONTACT: [email protected].

Compartmentalisation is thought to have been a crucial step in the origin of life. To help us bridge the gap between selfassembly processes behind the formation of bio-compartments and metabolic and information bearing processes we refer to DPD and P Systems Simulations. In this paper we computational formalism (P Systems) with a molecular scale model (Dissipative Particle Dynamics) by linking the membranes which delimit the cellular regions within P Systems to self-assembled phospholipid based vesicles in DPD. We test the platform by modelling a passive transport process involving vesicles containing membrane inclusions similar to pore complexes such as α-hemolysin. In doing so, we illustrate the usefulness of the modelling approach and derive a more realistic parameter set for the P system through the dissipative particle dynamics simulation.