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

VIRTUE : integrating CFD ship design

Novel ship concepts, increasing size and speed, and strong competition in the global maritime market require that a ship's hydrodynamic performance be studied at the highest level of sophistication. All hydrodynamic aspects need to be considered so as to optimize trade-offs between resistance, propulsion (and cavitation), seakeeping or manoeuvring. VIRTUE takes a holistic approach to hydrodynamic design and focuses on integrating advanced CFD tools in a software platform that can control and launch multi-objective hydrodynamic design projects. In this paper current practice, future requirements and a potential software integration platform are presented. The necessity of parametric modelling as a means of effectively generating and efficiently varying geometry, and the added-value of advanced visualization, is discussed. An illustrating example is given as a test case, a container carrier investigation, and the requirements and a proposed architecture for the platform are outlined

Grid simulation services for the medical community

The first part of this paper presents a selection of medical simulation applications, including image reconstruction, near real-time registration for neuro-surgery, enhanced dose distribution calculation for radio-therapy, inhaled drug delivery prediction, plastic surgery planning and cardio-vascular system simulation. The latter two topics are discussed in some detail. In the second part, we show how such services can be made available to the clinical practitioner using Grid technology. We discuss the developments and experience made during the EU project GEMSS, which provides reliable, efficient, secure and lawful medical Grid services

From SpaceStat to CyberGIS: Twenty Years of Spatial Data Analysis Software

This essay assesses the evolution of the way in which spatial data analytical methods have been incorporated into software tools over the past two decades. It is part retrospective and prospective, going beyond a historical review to outline some ideas about important factors that drove the software development, such as methodological advances, the open source movement and the advent of the internet and cyberinfrastructure. The review highlights activities carried out by the author and his collaborators and uses SpaceStat, GeoDa, PySAL and recent spatial analytical web services developed at the ASU GeoDa Center as illustrative examples. It outlines a vision for a spatial econometrics workbench as an example of the incorporation of spatial analytical functionality in a cyberGIS.

Parametric Surfaces for Augmented Architecture representation

Augmented Reality (AR) represents a growing communication channel, responding to the need to expand reality with additional information, offering easy and engaging access to digital data. AR for architectural representation allows a simple interaction with 3D models, facilitating spatial understanding of complex volumes and topological relationships between parts, overcoming some limitations related to Virtual Reality. In the last decade different developments in the pipeline process have seen a significant advancement in technological and algorithmic aspects, paying less attention to 3D modeling generation. For this, the article explores the construction of basic geometries for 3D model’s generation, highlighting the relationship between geometry and topology, basic for a consistent normal distribution. Moreover, a critical evaluation about corrective paths of existing 3D models is presented, analysing a complex architectural case study, the virtual model of Villa del Verginese, an emblematic example for topological emerged problems. The final aim of the paper is to refocus attention on 3D model construction, suggesting some "good practices" useful for preventing, minimizing or correcting topological problems, extending the accessibility of AR to people engaged in architectural representation