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

CONFIGEN: A tool for managing configuration options

This paper introduces CONFIGEN, a tool that helps modularizing software. CONFIGEN allows the developer to select a set of elementary components for his software through an interactive interface. Configuration files for use by C/assembly code and Makefiles are then automatically generated, and we successfully used it as a helper tool for complex system software refactoring. CONFIGEN is based on propositional logic, and its implementation faces hard theoretical problems.Comment: In Proceedings LoCoCo 2010, arXiv:1007.083

A Simulator for LLVM Bitcode

In this paper, we introduce an interactive simulator for programs in the form of LLVM bitcode. The main features of the simulator include precise control over thread scheduling, automatic checkpoints and reverse stepping, support for source-level information about functions and variables in C and C++ programs and structured heap visualisation. Additionally, the simulator is compatible with DiVM (DIVINE VM) hypercalls, which makes it possible to load, simulate and analyse counterexamples from an existing model checker

A novel R-package graphic user interface for the analysis of metabonomic profiles

Background Analysis of the plethora of metabolites found in the NMR spectra of biological fluids or tissues requires data complexity to be simplified. We present a graphical user interface (GUI) for NMR-based metabonomic analysis. The "Metabonomic Package" has been developed for metabonomics research as open-source software and uses the R statistical libraries. /Results The package offers the following options: Raw 1-dimensional spectra processing: phase, baseline correction and normalization. Importing processed spectra. Including/excluding spectral ranges, optional binning and bucketing, detection and alignment of peaks. Sorting of metabolites based on their ability to discriminate, metabolite selection, and outlier identification. Multivariate unsupervised analysis: principal components analysis (PCA). Multivariate supervised analysis: partial least squares (PLS), linear discriminant analysis (LDA), k-nearest neighbor classification. Neural networks. Visualization and overlapping of spectra. Plot values of the chemical shift position for different samples. Furthermore, the "Metabonomic" GUI includes a console to enable other kinds of analyses and to take advantage of all R statistical tools. /Conclusion We made complex multivariate analysis user-friendly for both experienced and novice users, which could help to expand the use of NMR-based metabonomics

Dynamic and Transparent Analysis of Commodity Production Systems

We propose a framework that provides a programming interface to perform complex dynamic system-level analyses of deployed production systems. By leveraging hardware support for virtualization available nowadays on all commodity machines, our framework is completely transparent to the system under analysis and it guarantees isolation of the analysis tools running on its top. Thus, the internals of the kernel of the running system needs not to be modified and the whole platform runs unaware of the framework. Moreover, errors in the analysis tools do not affect the running system and the framework. This is accomplished by installing a minimalistic virtual machine monitor and migrating the system, as it runs, into a virtual machine. In order to demonstrate the potentials of our framework we developed an interactive kernel debugger, nicknamed HyperDbg. HyperDbg can be used to debug any critical kernel component, and even to single step the execution of exception and interrupt handlers.Comment: 10 pages, To appear in the 25th IEEE/ACM International Conference on Automated Software Engineering, Antwerp, Belgium, 20-24 September 201

Interactive Chemical Reactivity Exploration

Elucidating chemical reactivity in complex molecular assemblies of a few hundred atoms is, despite the remarkable progress in quantum chemistry, still a major challenge. Black-box search methods to find intermediates and transition-state structures might fail in such situations because of the high-dimensionality of the potential energy surface. Here, we propose the concept of interactive chemical reactivity exploration to effectively introduce the chemist's intuition into the search process. We employ a haptic pointer device with force-feedback to allow the operator the direct manipulation of structures in three dimensions along with simultaneous perception of the quantum mechanical response upon structure modification as forces. We elaborate on the details of how such an interactive exploration should proceed and which technical difficulties need to be overcome. All reactivity-exploration concepts developed for this purpose have been implemented in the Samson programming environment.Comment: 36 pages, 14 figure