BUILD: A Tool for Maintaining Consistency in Modular Systems

Build is a tool for keeping modular systems in a consistent state by managing the construction tasks (e.g. compilation, linking, etc.) associated with such systems. It employs a user supplied system model and a procedural description of a task to be performed in order to perform the task. This differs from existing tools which do not explicitly separate knowledge about systems from knowledge about how systems are manipulated. BUILD provides a static framework for modeling systems and handling construction requests that makes use of programming environment specific definitions. By altering the set of definitions, BUILD can be extended to work with new programming environments to perform new tasks.

An integrated firewall policy validation tool.

Security policies are increasingly being implemented by organisations. Policies are mapped to device configurations to enforce the policies. This is typically performed manually by network administrators. The development and management of these enforcement policies is a difficult and error prone task. This thesis describes the development and evaluation of an off-line firewall policy parser and validation tool. This provides the system administrator with a textual interface and the vendor specific low level languages they trust and are familiar with, but the support of an off-line compiler tool. The tool was created using the Microsoft C#.NET language, and the Microsoft Visual Studio Integrated Development Environment (IDE). This provided an object environment to create a flexible and extensible system, as well as simple Web and Windows prototyping facilities to create GUI front-end applications for testing and evaluation. A CLI was provided with the tool, for more experienced users, but it was also designed to be easily integrated into GUI based applications for non-expert users. The evaluation of the system was performed from a custom built GUI application, which can create test firewall rule sets containing synthetic rules, to supply a variety of experimental conditions, as well as record various performance metrics. The validation tool was created, based around a pragmatic outlook, with regard to the needs of the network administrator. The modularity of the design was important, due to the fast changing nature of the network device languages being processed. An object oriented approach was taken, for maximum changeability and extensibility, and a flexible tool was developed, due to the possible needs of different types users. System administrators desire, low level, CLI-based tools that they can trust, and use easily from scripting languages. Inexperienced users may prefer a more abstract, high level, GUI or Wizard that has an easier to learn process. Built around these ideas, the tool was implemented, and proved to be a usable, and complimentary addition to the many network policy-based systems currently available. The tool has a flexible design and contains comprehensive functionality. As opposed to some of the other tools which perform across multiple vendor languages, but do not implement a deep range of options for any of the languages. It compliments existing systems, such as policy compliance tools, and abstract policy analysis systems. Its validation algorithms were evaluated for both completeness, and performance. The tool was found to correctly process large firewall policies in just a few seconds. A framework for a policy-based management system, with which the tool would integrate, is also proposed. This is based around a vendor independent XML-based repository of device configurations, which could be used to bring together existing policy management and analysis systems.

The Development of a Holistic and Quantitative Tool for the Assessment and Improvement of Survey Quality.

There are a variety of guidelines and methods available to measure and assess survey quality. Most of these are based on qualitative descriptions. In practice, they are not easy to implement and it is very difficult to make comparisons between surveys. Hence there is a theoretical and pragmatic demand to develop a mainly quantitative based survey assessment tool. This research aimed to meet this need and make contributions to the evaluation and improvement of survey quality. Acknowledging the critical importance of measurement issues in survey research, this thesis starts with a comprehensive introduction to measurement theory and identifies the types of measurement errors associated with measurement procedures through three experiments. Then it moves on to describe concepts, guidelines and methods available for measuring and assessing survey quality. Combining these with measurement principles leads to the development of a quantitative based statistical holistic tool to measure and assess survey quality. The criteria, weights and subweights for the assessment tool are determined using Multi-Criteria Decision-Making (MCDM) and a survey questionnaire based on the Delphi method. Finally the model is applied to a database of surveys which was constructed to develop methods of classification, assessment and improvement of survey quality. The model developed in this thesis enables survey researchers and/or commissioners to make a holistic assessment of the value of the particular survey(s). This model is an Excel based audit which takes a holistic approach, following all stages of the survey from inception, to design, construction, execution, analysis and dissemination. At each stage a set of criteria are applied to assess quality. Scores attained against these assessments are weighted by the importance of the criteria and summed to give an overall assessment of the stage. The total score for a survey can be obtained by a combination of the scores for every stage weighted again by the importance of each stage. The advantage of this is to construct a means of survey assessment which can be used in a diagnostic manner to assess and improve survey quality.

ART: An ontology based tool for the translation of papers into Semantic Web format

To be presented at SIG/ISMB07 ontology workshop: http://bio-ontologies.org.uk/index.php To be published in BMC Bioinformatics. Sponsorship: JISC

Safe Compositional Network Sketches: NetSketch Tool Implementation

Numerous problems exist that can be modeled as traffic through a network in which constraints exist to regulate flow. Vehicular road travel, computer networks, and cloud based resource distribution, among others all have natural representations in this manner. As these networks grow in size and/or complexity, analysis and certification of the safety invariants becomes increasingly costly. The NetSketch formalism introduces a lightweight verification framework that allows for greater scalability than traditional analysis methods. The NetSketch tool was developed to provide the power of this formalism in an easy to use and intuitive user interface.

Safe Compositional Network Sketches: Tool & Use Cases

NetSketch is a tool that enables the specification of network-flow applications and the certification of desirable safety properties imposed thereon. NetSketch is conceived to assist system integrators in two types of activities: modeling and design. As a modeling tool, it enables the abstraction of an existing system so as to retain sufficient enough details to enable future analysis of safety properties. As a design tool, NetSketch enables the exploration of alternative safe designs as well as the identification of minimal requirements for outsourced subsystems. NetSketch embodies a lightweight formal verification philosophy, whereby the power (but not the heavy machinery) of a rigorous formalism is made accessible to users via a friendly interface. NetSketch does so by exposing tradeoffs between exactness of analysis and scalability, and by combining traditional whole-system analysis with a more flexible compositional analysis approach based on a strongly-typed, Domain-Specific Language (DSL) to specify network configurations at various levels of sketchiness along with invariants that need to be enforced thereupon. In this paper, we overview NetSketch, highlight its salient features, and illustrate how it could be used in applications, including the management/shaping of traffic flows in a vehicular network (as a proxy for CPS applications) and in a streaming media network (as a proxy for Internet applications). In a companion paper, we define the formal system underlying the operation of NetSketch, in particular the DSL behind NetSketch's user-interface when used in "sketch mode", and prove its soundness relative to appropriately-defined notions of validity.

Music Maker – A Camera-based Music Making Tool for Physical Rehabilitation

The therapeutic effects of playing music are being recognized increasingly in the field of rehabilitation medicine. People with physical disabilities, however, often do not have the motor dexterity needed to play an instrument. We developed a camera-based human-computer interface called "Music Maker" to provide such people with a means to make music by performing therapeutic exercises. Music Maker uses computer vision techniques to convert the movements of a patient's body part, for example, a finger, hand, or foot, into musical and visual feedback using the open software platform EyesWeb. It can be adjusted to a patient's particular therapeutic needs and provides quantitative tools for monitoring the recovery process and assessing therapeutic outcomes. We tested the potential of Music Maker as a rehabilitation tool with six subjects who responded to or created music in various movement exercises. In these proof-of-concept experiments, Music Maker has performed reliably and shown its promise as a therapeutic device.

A Self-Organizing Neural Network Model for Redundant Sensory-Motor Control, Motor Equivalence, and Tool Use

A neural network is introduced which provides a solution of the classical motor equivalence problem, whereby many different joint configurations of a redundant manipulator can all be used to realize a desired trajectory in 3-D space. To do this, the network self-organizes a mapping from motion directions in 3-D space to velocity commands in joint space. Computer simulations demonstrate that, without any additional learning, the network can generate accurate movement commands that compensate for variable tool lengths, clamping of joints, distortions of visual input by a prism, and unexpected limb perturbations. Blind reaches have also been simulated.

A Self-Organizing Neural Model of Motor Equivalent Reaching and Tool Use by a Multijoint Arm

This paper describes a self-organizing neural model for eye-hand coordination. Called the DIRECT model, it embodies a solution of the classical motor equivalence problem. Motor equivalence computations allow humans and other animals to flexibly employ an arm with more degrees of freedom than the space in which it moves to carry out spatially defined tasks under conditions that may require novel joint configurations. During a motor babbling phase, the model endogenously generates movement commands that activate the correlated visual, spatial, and motor information that are used to learn its internal coordinate transformations. After learning occurs, the model is capable of controlling reaching movements of the arm to prescribed spatial targets using many different combinations of joints. When allowed visual feedback, the model can automatically perform, without additional learning, reaches with tools of variable lengths, with clamped joints, with distortions of visual input by a prism, and with unexpected perturbations. These compensatory computations occur within a single accurate reaching movement. No corrective movements are needed. Blind reaches using internal feedback have also been simulated. The model achieves its competence by transforming visual information about target position and end effector position in 3-D space into a body-centered spatial representation of the direction in 3-D space that the end effector must move to contact the target. The spatial direction vector is adaptively transformed into a motor direction vector, which represents the joint rotations that move the end effector in the desired spatial direction from the present arm configuration. Properties of the model are compared with psychophysical data on human reaching movements, neurophysiological data on the tuning curves of neurons in the monkey motor cortex, and alternative models of movement control.

An automated calibration tool for high performance wireless inertial measurement in professional sports

Traditional motion capture techniques, for instance, those employing optical technology, have long been used in the area of rehabilitation, sports medicine and performance analysis, where accurately capturing bio-mechanical data is of crucial importance. However their size, cost, complexity and lack of portability mean that their use is often impractical. Low cost MEMS inertial sensors when combined and assembled into a Wireless Inertial Measurement Unit (WIMU) present a possible solution for low cost and highly portable motion capture. However due to the large variability inherent to MEMS sensors, such a system would need extensive characterization to calibrate each sensor and ensure good quality data capture. A completely calibrated WIMU system would allow for motion capture in a wider range of real-world, non-laboratory based applications. Calibration can be a complex task, particularly for newer, multi-sensing range capable inertial sensors. As such we present an automated system for quickly and easily calibrating inertial sensors in a packaged WIMU, demonstrating some of the improvements in accuracy attainable.

A medical study on wireless inertial measurement technology as a tool for identifying patients at risk of death or imminent clinical deterioration

This paper provides a system description and preliminary results for an ongoing clinical study currently being carried out at the Mid-Western Regional Hospital, Nenagh, Ireland. The goal of the trial is to determine if wireless inertial measurement technology can be employed to identify elderly patients at risk of death or imminent clinical deterioration. The system measures cumulative movement and provides a score that will help provide a robust early warning to clinical staff of clinical deterioration. In addition the study examines some of the logistical barriers to the adoption of wearable wireless technology in front-line medical care.

Mainstream technology as an occupational therapy tool: technophobe or technogeek?

Occupational therapists need to embrace the use of mainstream technology in their quest to ensure that therapy remains current and meaningful to their clients. Technology can be useful to improve both functional independence and occupational performance. This opinion piece introduces how occupational therapists can apply mainstream technologies, including information and communication technologies such as the internet, computer software, portable devices and computer games, in their everyday interventions.

Hepcidin as a therapeutic tool to limit iron overload and improve anemia in β-thalassemic mice.

Excessive iron absorption is one of the main features of β-thalassemia and can lead to severe morbidity and mortality. Serial analyses of β-thalassemic mice indicate that while hemoglobin levels decrease over time, the concentration of iron in the liver, spleen, and kidneys markedly increases. Iron overload is associated with low levels of hepcidin, a peptide that regulates iron metabolism by triggering degradation of ferroportin, an iron-transport protein localized on absorptive enterocytes as well as hepatocytes and macrophages. Patients with β-thalassemia also have low hepcidin levels. These observations led us to hypothesize that more iron is absorbed in β-thalassemia than is required for erythropoiesis and that increasing the concentration of hepcidin in the body of such patients might be therapeutic, limiting iron overload. Here we demonstrate that a moderate increase in expression of hepcidin in β-thalassemic mice limits iron overload, decreases formation of insoluble membrane-bound globins and reactive oxygen species, and improves anemia. Mice with increased hepcidin expression also demonstrated an increase in the lifespan of their red cells, reversal of ineffective erythropoiesis and splenomegaly, and an increase in total hemoglobin levels. These data led us to suggest that therapeutics that could increase hepcidin levels or act as hepcidin agonists might help treat the abnormal iron absorption in individuals with β-thalassemia and related disorders.

SplicerAV: a tool for mining microarray expression data for changes in RNA processing.

BACKGROUND: Over the past two decades more than fifty thousand unique clinical and biological samples have been assayed using the Affymetrix HG-U133 and HG-U95 GeneChip microarray platforms. This substantial repository has been used extensively to characterize changes in gene expression between biological samples, but has not been previously mined en masse for changes in mRNA processing. We explored the possibility of using HG-U133 microarray data to identify changes in alternative mRNA processing in several available archival datasets. RESULTS: Data from these and other gene expression microarrays can now be mined for changes in transcript isoform abundance using a program described here, SplicerAV. Using in vivo and in vitro breast cancer microarray datasets, SplicerAV was able to perform both gene and isoform specific expression profiling within the same microarray dataset. Our reanalysis of Affymetrix U133 plus 2.0 data generated by in vitro over-expression of HRAS, E2F3, beta-catenin (CTNNB1), SRC, and MYC identified several hundred oncogene-induced mRNA isoform changes, one of which recognized a previously unknown mechanism of EGFR family activation. Using clinical data, SplicerAV predicted 241 isoform changes between low and high grade breast tumors; with changes enriched among genes coding for guanyl-nucleotide exchange factors, metalloprotease inhibitors, and mRNA processing factors. Isoform changes in 15 genes were associated with aggressive cancer across the three breast cancer datasets. CONCLUSIONS: Using SplicerAV, we identified several hundred previously uncharacterized isoform changes induced by in vitro oncogene over-expression and revealed a previously unknown mechanism of EGFR activation in human mammary epithelial cells. We analyzed Affymetrix GeneChip data from over 400 human breast tumors in three independent studies, making this the largest clinical dataset analyzed for en masse changes in alternative mRNA processing. The capacity to detect RNA isoform changes in archival microarray data using SplicerAV allowed us to carry out the first analysis of isoform specific mRNA changes directly associated with cancer survival.

Dissecting Policy Designs: An Application of the Institutional Grammar Tool

An enduring challenge for the policy and political sciences is valid and reliable depiction of policy designs. One emerging approach for dissecting policy designs is the application of Sue Crawford and Elinor Ostrom's institutional grammar tool. The grammar tool offers a method to identify, systematically, the core elements that comprise policies, including target audiences, expected patterns of behavior, and formal modes of sanctioning for noncompliance. This article provides three contributions to the study of policy designs by developing and applying the institutional grammar tool. First, we provide revised guidelines for applying the institutional grammar tool to the study of policy design. Second, an additional component to the grammar, called the oBject, is introduced. Third, we apply the modified grammar tool to four policies that shape Colorado State Aquaculture to demonstrate its effectiveness and utility in illuminating institutional linkages across levels of analysis. The conclusion summarizes the contributions of the article as well as points to future research and applications of the institutional grammar tool. © 2011 Policy Studies Organization.