Interactive DNA Sequence and Structure Design for DNA Nanotechnology and DNA Computation

DNA sequence and structure design are very important for DNA nanotechnology and DNA computation. A computer aided design tool is needed for exploring DNA sequence and structure of interests before experimental synthesis, which is a very time and labor consuming process. In this paper, an interactive DNA sequence and structure design software tool called DNA shop is proposed and implemented

Support for energy-oriented design in the Australian context

There is a need for decision support tools that integrate energy simulation into early design in the context of Australian practice. Despite the proliferation of simulation programs in the last decade, there are no ready-to-use applications that cater specifically for the Australian climate and regulations. Furthermore, the majority of existing tools focus on achieving interaction with the design domain through model-based interoperability, and largely overlook the issue of process integration. This paper proposes an energy-oriented design environment that both accommodates the Australian context and provides interactive and iterative information exchanges that facilitate feedback between domains. It then presents the structure for DEEPA, an openly customisable system that couples parametric modelling and energy simulation software as a means of developing a decision support tool to allow designers to rapidly and flexibly assess the performance of early design alternatives. Finally, it discusses the benefits of developing a dynamic and concurrent performance evaluation process that parallels the characteristics and relationships of the design process

Analysing Reverse Engineering Techniques for Interactive Systems

Reverse engineering is the process of discovering a model of a software system by analyzing its structure and functions. Reverse engineering techniques applied to interactive software applications (e.g. applications with user interfaces (UIs)) are very important and significant, as they can help engineers to detect defects in the software and then improve or complete them. There are several approaches, and many different tools, which are able to reverse-engineer software applications into formal models. These can be classified into two main types: dynamic tools and static tools. Dynamic tools interact with the application to find out the run-time behaviours of the software, simulating the actions of a user to explore the system’s state space, whereas static tools focus on static structure and architecture by analysing the code and documents. Reverse engineering techniques are not common for interactive software systems, but nowadays more and more organizations recognize the importance of interactive systems, as the trend in software used in computers is for applications with graphical user interfaces. This has in turn led to a developing interest in reverse engineering tools for such systems. Many reverse engineering tools generate very big models which make analysis slow and resource intensive. The reason for this is the large amount of information that is generated by the existing reverse engineering techniques. Slicing is one possible technique which helps with reducing un-necessary information for building models of software systems. This project focuses on static analysis and slicing, and considers how they can aid reverse engineering techniques for interactive systems, particularly with respect to the generation of a particular set of models, Presentation Models (PModels) and Presentation Interaction Models (PIMs)

Groupware Support for Software Inspections: The Impact of Group Interaction and Interface on Performance

The software inspection meeting is one of the best- known techniques for quality assurance in software development and has become a standard practice in many software development groups (Ebenau and Strauss, 1994). The application of groupware has been suggested as a particularly promising way to improve the inspection process (Johnson, 1998). This paper discusses a “research in progress” study that concerns the application of groupware to software inspection meetings. A controlled experimental study involving eighty teams is presently being conducted to address two fundamental research questions relating to the use of groupware to support software inspections: 1) Is it more effective to use groupware in an interactive or nominal group mode?; and 2) Is it worthwhile to incorporate task structure into the design of the groupware interface? The research design is a 2 X 2 factorial design using the inspection team as the unit of analysis. One independent variable manipulates the type of group interaction (nominal vs. interactive) and the second independent variable manipulates task structure (a partitioned groupware interface vs. an unpartitioned interface). The dependent variable will be team performance

Interactive DNA Sequence and Structure Design for DNA Nanoapplications

DNA sequence and structure design is very important for DNA nanoapplications. A computer-aided design tool is needed for exploring DNA sequence and structure of interests before experimental synthesis, which is a time- and labor-consuming process. In this paper, an interactive DNA sequence and structure design software tool called DNA shop is proposed and implemented. The visualization tool can generate DNA structures by specifying, selecting, and moving DNA sequences around and display corresponding structures. Using the tool, DNA sequence and structure can be visually inspected in three-dimensional space before experimental studies

From Autonomous to Performative Control of Timbral Spatialisation

Timbral spatialisation is one such process that requires the independent control of potentially thousands of parameters (Torchia, et al., 2003). Current research on controlling timbral spatialisation has focussed either on automated generative systems, or suggested that to design trajectories in software is to write every movement line by line (Normandeau, 2009). This research proposes that Wave Terrain Synthesis may be used as an effective bridging control structure for timbral spatialisation, enabling the performative control of large numbers of parameter sets associated with software. This methodology also allows for compact interactive mapping possibilities for a physical controller, and may also be effectively mapped gesturall

The Connectome Visualization Utility: Software for Visualization of Human Brain Networks

In analysis of the human connectome, the connectivity of the human brain is collected from multiple imaging modalities and analyzed using graph theoretical techniques. The dimensionality of human connectivity data is high, and making sense of the complex networks in connectomics requires sophisticated visualization and analysis software. The current availability of software packages to analyze the human connectome is limited. The Connectome Visualization Utility (CVU) is a new software package designed for the visualization and network analysis of human brain networks. CVU complements existing software packages by offering expanded interactive analysis and advanced visualization features, including the automated visualization of networks in three different complementary styles and features the special visualization of scalar graph theoretical properties and modular structure. By decoupling the process of network creation from network visualization and analysis, we ensure that CVU can visualize networks from any imaging modality. CVU offers a graphical user interface, interactive scripting, and represents data uses transparent neuroimaging and matrix-based file types rather than opaque application-specific file formats

Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS

Novel algorithms are presented for automated NOESY peak picking and NOE signal identification in homonuclear 2D and heteronuclear-resolved 3D [1H,1H]-NOESY spectra during denovoprotein structure determination by NMR, which have been implemented in the new software ATNOS (automated NOESY peak picking). The input for ATNOS consists of the amino acid sequence of the protein, chemical shift lists from the sequence-specific resonance assignment, and one or several 2D or 3D NOESY spectra. In the present implementation, ATNOS performs multiple cycles of NOE peak identification in concert with automated NOE assignment with the software CANDID and protein structure calculation with the program DYANA. In the second and subsequent cycles, the intermediate protein structures are used as an additional guide for the interpretation of the NOESY spectra. By incorporating the analysis of the raw NMR data into the process of automated denovoprotein NMR structure determination, ATNOS enables direct feedback between the protein structure, the NOE assignments and the experimental NOESY spectra. The main elements of the algorithms for NOESY spectral analysis are techniques for local baseline correction and evaluation of local noise level amplitudes, automated determination of spectrum-specific threshold parameters, the use of symmetry relations, and the inclusion of the chemical shift information and the intermediate protein structures in the process of distinguishing between NOE peaks and artifacts. The ATNOS procedure has been validated with experimental NMR data sets of three proteins, for which high-quality NMR structures had previously been obtained by interactive interpretation of the NOESY spectra. The ATNOS-based structures coincide closely with those obtained with interactive peak picking. Overall, we present the algorithms used in this paper as a further important step towards objective and efficient de novoprotein structure determination by NM

Formal Object Interaction Language: Modeling and Verification of Sequential and Concurrent Object-Oriented Software

As software systems become larger and more complex, developers require the ability to model abstract concepts while ensuring consistency across the entire project. The internet has changed the nature of software by increasing the desire for software deployment across multiple distributed platforms. Finally, increased dependence on technology requires assurance that designed software will perform its intended function. This thesis introduces the Formal Object Interaction Language (FOIL). FOIL is a new object-oriented modeling language specifically designed to address the cumulative shortcomings of existing modeling techniques. FOIL graphically displays software structure, sequential and concurrent behavior, process, and interaction in a simple unified notation, and has an algebraic representation based on a derivative of the π-calculus. The thesis documents the technique in which FOIL software models can be mathematically verified to anticipate deadlocks, ensure consistency, and determine object state reachability. Scalability is offered through the concept of behavioral inheritance; and, FOIL’s inherent support for modeling concurrent behavior and all known workflow patterns is demonstrated. The concepts of process achievability, process complete achievability, and process determinism are introduced with an algorithm for simulating the execution of a FOIL object model using a FOIL process model. Finally, a technique for using a FOIL process model as a constraint on FOIL object system execution is offered as a method to ensure that object-oriented systems modeled in FOIL will complete their processes based activities. FOIL’s capabilities are compared and contrasted with an extensive array of current software modeling techniques. FOIL is ideally suited for data-aware, behavior based systems such as interactive or process management software