7,082 research outputs found
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
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Supporting Story Synthesis: Bridging the Gap between Visual Analytics and Storytelling
Visual analytics usually deals with complex data and uses sophisticated algorithmic, visual, and interactive techniques. Findings of the analysis often need to be communicated to an audience that lacks visual analytics expertise. This requires analysis outcomes to be presented in simpler ways than that are typically used in visual analytics systems. However, not only analytical visualizations may be too complex for target audience but also the information that needs to be presented. Hence, there exists a gap on the path from obtaining analysis findings to communicating them, which involves two aspects: information and display complexity. We propose a general framework where data analysis and result presentation are linked by story synthesis, in which the analyst creates and organizes story contents. Differently, from the previous research, where analytic findings are represented by stored display states, we treat findings as data constructs. In story synthesis, findings are selected, assembled, and arranged in views using meaningful layouts that take into account the structure of information and inherent properties of its components. We propose a workflow for applying the proposed framework in designing visual analytics systems and demonstrate the generality of the approach by applying it to two domains, social media, and movement analysis
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