MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments

A look at cloud architecture interoperability through standards

Enabling cloud infrastructures to evolve into a transparent platform while preserving integrity raises interoperability issues. How components are connected needs to be addressed. Interoperability requires standard data models and communication encoding technologies compatible with the existing Internet infrastructure. To reduce vendor lock-in situations, cloud computing must implement universal strategies regarding standards, interoperability and portability. Open standards are of critical importance and need to be embedded into interoperability solutions. Interoperability is determined at the data level as well as the service level. Corresponding modelling standards and integration solutions shall be analysed