A Monitoring Language for Run Time and Post-Mortem Behavior Analysis and Visualization

UFO is a new implementation of FORMAN, a declarative monitoring language, in which rules are compiled into execution monitors that run on a virtual machine supported by the Alamo monitor architecture.Comment: In M. Ronsse, K. De Bosschere (eds), proceedings of the Fifth International Workshop on Automated Debugging (AADEBUG 2003), September 2003, Ghent. cs.SE/030902

Rule-based Modeling of Cell Signaling: Advances in Model Construction, Visualization and Simulation

Rule-based modeling is a graph-based approach to specifying the kinetics of cell signaling systems. A reaction rule is a compact and explicit graph-based representation of a kinetic process, and it matches a class of reactions that involve identical sites and identical kinetics. Compact rule- based models have been used to generate large and combinatorially complex reaction networks, and rules have also been used to compile databases of kinetic interactions targeting specific cells and pathways. In this work, I address three technological challenges associated with rule-based modeling. First, I address the ability to generate an automated global visualization of a rule-based model as a network of signal flows. I showed how to analyze a reaction rule and extract a set of bipartite regulatory relationships, which can be aggregated across rules into a global network. I also provide a set of coarse-graining approaches to compress an automatically generated network into a compact pathway diagram, even for models with 100s of rules. Second, I resolved an incompatibility between two recent advances in rule-based modeling: network-free simulation (which enables simulation without generating a reaction network), and energy-based rule-based modeling (which enables specifying a model using cooperativity parameters and automated accounting of free energy). The incompatibility arose because calculating the reaction rate requires computing the reaction free energy in an energy-based model, and this requires knowledge of both reactants and products of the reaction, but the products are not available in a network-free simulation until after the reaction event has fired. This was resolved by expanding each energy- based rule into a number of normal reaction rules for which reaction free energies can be calculated unambiguously. Third, I demonstrated a particular type of modularization that is based on treating a set of rules as a module. This enables building models from combinations of modular hypotheses and supplements the other modularization strategies such as macros, types and energy-based compression

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization

Motivation: Biological systems are complex and challenging to model and therefore model reuse is highly desirable. To promote model reuse, models should include both information about the specifics of simulations and the underlying biology in the form of metadata. The availability of computationally tractable metadata is especially important for the effective automated interpretation and processing of models. Metadata are typically represented as machine-readable annotations which enhance programmatic access to information about models. Rule-based languages have emerged as a modelling framework to represent the complexity of biological systems. Annotation approaches have been widely used for reaction-based formalisms such as SBML. However, rule-based languages still lack a rich annotation framework to add semantic information, such as machine-readable descriptions, to the components of a model. Results: We present an annotation framework and guidelines for annotating rule-based models, encoded in the commonly used Kappa and BioNetGen languages. We adapt widely adopted annotation approaches to rule-based models. We initially propose a syntax to store machine-readable annotations and describe a mapping between rule-based modelling entities, such as agents and rules, and their annotations. We then describe an ontology to both annotate these models and capture the information contained therein, and demonstrate annotating these models using examples. Finally, we present a proof of concept tool for extracting annotations from a model that can be queried and analyzed in a uniform way. The uniform representation of the annotations can be used to facilitate the creation, analysis, reuse and visualization of rule-based models. Although examples are given, using specific implementations the proposed techniques can be applied to rule-based models in general

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization

Motivation: Biological systems are complex and challenging to model and therefore model reuse is highly desirable. To promote model reuse, models should include both information about the specifics of simulations and the underlying biology in the form of metadata. The availability of computationally tractable metadata is especially important for the effective automated interpretation and processing of models. Metadata are typically represented as machine-readable annotations which enhance programmatic access to information about models. Rule-based languages have emerged as a modelling framework to represent the complexity of biological systems. Annotation approaches have been widely used for reaction-based formalisms such as SBML. However, rule-based languages still lack a rich annotation framework to add semantic information, such as machine-readable descriptions, to the components of a model. Results: We present an annotation framework and guidelines for annotating rule-based models, encoded in the commonly used Kappa and BioNetGen languages. We adapt widely adopted annotation approaches to rule-based models. We initially propose a syntax to store machine-readable annotations and describe a mapping between rule-based modelling entities, such as agents and rules, and their annotations. We then describe an ontology to both annotate these models and capture the information contained therein, and demonstrate annotating these models using examples. Finally, we present a proof of concept tool for extracting annotations from a model that can be queried and analyzed in a uniform way. The uniform representation of the annotations can be used to facilitate the creation, analysis, reuse and visualization of rule-based models. Although examples are given, using specific implementations the proposed techniques can be applied to rule-based models in general. Availability and implementation: The annotation ontology for rule-based models can be found at http://purl.org/rbm/rbmo. The krdf tool and associated executable examples are available at http://purl.org/rbm/rbmo/krdf. Contact: or [email protected]

Visualization Techniques for Tongue Analysis in Traditional Chinese Medicine

Visual inspection of the tongue has been an important diagnostic method of Traditional Chinese Medicine (TCM). Clinic data have shown significant connections between various viscera cancers and abnormalities in the tongue and the tongue coating. Visual inspection of the tongue is simple and inexpensive, but the current practice in TCM is mainly experience-based and the quality of the visual inspection varies between individuals. The computerized inspection method provides quantitative models to evaluate color, texture and surface features on the tongue. In this paper, we investigate visualization techniques and processes to allow interactive data analysis with the aim to merge computerized measurements with human expert's diagnostic variables based on five-scale diagnostic conditions: Healthy (H), History Cancers (HC), History of Polyps (HP), Polyps (P) and Colon Cancer (C)

Construction safety and digital design: a review

As digital technologies become widely used in designing buildings and infrastructure, questions arise about their impacts on construction safety. This review explores relationships between construction safety and digital design practices with the aim of fostering and directing further research. It surveys state-of-the-art research on databases, virtual reality, geographic information systems, 4D CAD, building information modeling and sensing technologies, finding various digital tools for addressing safety issues in the construction phase, but few tools to support design for construction safety. It also considers a literature on safety critical, digital and design practices that raises a general concern about ‘mindlessness’ in the use of technologies, and has implications for the emerging research agenda around construction safety and digital design. Bringing these strands of literature together suggests new kinds of interventions, such as the development of tools and processes for using digital models to promote mindfulness through multi-party collaboration on safet

A framework for automated anomaly detection in high frequency water-quality data from in situ sensors

River water-quality monitoring is increasingly conducted using automated in situ sensors, enabling timelier identification of unexpected values. However, anomalies caused by technical issues confound these data, while the volume and velocity of data prevent manual detection. We present a framework for automated anomaly detection in high-frequency water-quality data from in situ sensors, using turbidity, conductivity and river level data. After identifying end-user needs and defining anomalies, we ranked their importance and selected suitable detection methods. High priority anomalies included sudden isolated spikes and level shifts, most of which were classified correctly by regression-based methods such as autoregressive integrated moving average models. However, using other water-quality variables as covariates reduced performance due to complex relationships among variables. Classification of drift and periods of anomalously low or high variability improved when we applied replaced anomalous measurements with forecasts, but this inflated false positive rates. Feature-based methods also performed well on high priority anomalies, but were also less proficient at detecting lower priority anomalies, resulting in high false negative rates. Unlike regression-based methods, all feature-based methods produced low false positive rates, but did not and require training or optimization. Rule-based methods successfully detected impossible values and missing observations. Thus, we recommend using a combination of methods to improve anomaly detection performance, whilst minimizing false detection rates. Furthermore, our framework emphasizes the importance of communication between end-users and analysts for optimal outcomes with respect to both detection performance and end-user needs. Our framework is applicable to other types of high frequency time-series data and anomaly detection applications