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

IGUANA Architecture, Framework and Toolkit for Interactive Graphics

IGUANA is a generic interactive visualisation framework based on a C++ component model. It provides powerful user interface and visualisation primitives in a way that is not tied to any particular physics experiment or detector design. The article describes interactive visualisation tools built using IGUANA for the CMS and D0 experiments, as well as generic GEANT4 and GEANT3 applications. It covers features of the graphical user interfaces, 3D and 2D graphics, high-quality vector graphics output for print media, various textual, tabular and hierarchical data views, and integration with the application through control panels, a command line and different multi-threading models.Comment: Presented at the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003, 6 pages LaTeX, 4 eps figures. PSN MOLT008 More and higher res figs at http://iguana.web.cern.ch/iguana/snapshot/main/gallery.htm

rpanel: Simple Interactive Controls for R Functions Using the tcltk Package

In a variety of settings it is extremely helpful to be able to apply R functions through buttons, sliders and other types of graphical control. This is particularly true in plotting activities where immediate communication between such controls and a graphical display allows the user to interact with a plot in a very effective manner. The tcltk package provides extensive tools for this and the aim of the rpanel package is to provide simple and well documented functions which make these facilities as accessible as possible. In addition, the operations which form the basis of communication within tcltk are managed in a way which allows users to write functions with a more standard form of parameter passing. This paper describes the basic design of the software and illustrates it on a variety of examples of interactive control of graphics. The tkrplot system is used to allow plots to be integrated with controls into a single panel. An example of the use of a graphical image, and the ability to interact with this, is also discussed.

Creating R Packages: A Tutorial

This tutorial gives a practical introduction to creating R packages. We discuss how object oriented programming and S formulas can be used to give R code the usual look and feel, how to start a package from a collection of R functions, and how to test the code once the package has been created. As running example we use functions for standard linear regression analysis which are developed from scratch

Emerging from the MIST: A Connector Tool for Supporting Programming by Non-programmers

Software development is an iterative process. As user re-quirements emerge software applications must be extended to support the new requirements. Typically, a programmer will add new code to an existing code base of an application to provide a new functionality. Previous research has shown that such extensions are easier when application logic is clearly separated from the user interface logic. Assuming that a programmer is already familiar with the existing code base, the task of writing the new code can be considered to be split into two sub-tasks: writing code for the application logic; that is, the actual functionality of the application; and writing code for the user interface that will expose the functionality to the end user. The goal of this research is to reduce the effort required to create a user interface once the application logic has been created, toward supporting scientists with minimal pro-gramming knowledge to be able to create and modify pro-grams. Using a Model View Controller based architecture, various model components which contain the application logic can be built and extended. The process of creating and extending the views (user interfaces) on these model components is simplified through the use of our Malleable Interactive Software Toolkit (MIST), a tool set an infrastructure intended to simplify the design and extension of dynamically reconfigurable interfaces. This paper focuses on one tool in the MIST suite, a connec-tor tool that enables the programmer to evolve the user interface as the application logic evolves by connecting related pieces of code together; either through simple drag-and-drop interactions or through the authoring of Python code. The connector tool exemplifies the types of tools in the MIST suite, which we expect will encourage collabora-tive development of applications by allowing users to inte-grate various components and minimizing the cost of de-veloping new user interfaces for the combined compo-nents

User interface development and software environments : the Chiron-1 system

User interface development systems for software environments have to cope with the broad, extensible and dynamic character of such environments, must support internal and external integration, and should enable various software development strategies. The Chiron-1 system adapts and extends key ideas from current research in user interface development systems to address the particular demands of software environments. Important Chiron-1 concepts are: separation of concerns, dynamism, and open architecture. We discuss the requirements on such user interface development systems, present the Chiron-1 architecture and a scenario of its usage, detail the concepts it embodies, and report on its design and prototype implementation

Distributed storage manager system for synchronized and scalable AV services across networks

This article has been made available through the Brunel Open Access Publishing Fund - Copyright @ 2011 Hindawi Publishing CorporationThis paper provides an innovative solution, namely, the distributed storage manager that opens a new path for highly interactive and personalized services. The distributed storage manager provides an enhancement to the MHP storage management functionality acting as a value added middleware distributed across the network. The distributed storage manager system provides multiple protocol support for initializing and downloading both streamed and file-based content and provides optimum control mechanisms to organize the storing and retrieval of content that are remained accessible to other multiple heterogeneous devices

The future of technology enhanced active learning – a roadmap

The notion of active learning refers to the active involvement of learner in the learning process, capturing ideas of learning-by-doing and the fact that active participation and knowledge construction leads to deeper and more sustained learning. Interactivity, in particular learnercontent interaction, is a central aspect of technology-enhanced active learning. In this roadmap, the pedagogical background is discussed, the essential dimensions of technology-enhanced active learning systems are outlined and the factors that are expected to influence these systems currently and in the future are identified. A central aim is to address this promising field from a best practices perspective, clarifying central issues and formulating an agenda for future developments in the form of a roadmap