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 conceptual approach to gene expression analysis enhanced by visual analytics

The analysis of gene expression data is a complex task for biologists wishing to understand the role of genes in the formation of diseases such as cancer. Biologists need greater support when trying to discover, and comprehend, new relationships within their data. In this paper, we describe an approach to the analysis of gene expression data where overlapping groupings are generated by Formal Concept Analysis and interactively analyzed in a tool called CUBIST. The CUBIST workflow involves querying a semantic database and converting the result into a formal context, which can be simplified to make it manageable, before it is visualized as a concept lattice and associated charts