Workflow resource pattern modelling and visualization

Workflow patterns have been recognized as the theoretical basis to modeling recurring problems in workflow systems. A form of workflow patterns, known as the resource patterns, characterise the behaviour of resources in workflow systems. Despite the fact that many resource patterns have been discovered, people still preclude them from many workflow system implementations. One of reasons could be obscurityin the behaviour of and interaction between resources and a workflow management system. Thus, we provide a modelling and visualization approach for the resource patterns, enabling a resource behaviour modeller to intuitively see the specific resource patterns involved in the lifecycle of a workitem. We believe this research can be extended to benefit not only workflow modelling, but also other applications, such as model validation, human resource behaviour modelling, and workflow model visualization

Petri Net Based Reliable Work Flow Framework for Nephrology Unit in Hospital Environment

The 21st century has witnessed a revolution in Biology and Medicine that has radically changed the way health, diagnosis, prognosis, etc., of a disease is monitored nowadays. Accordingly, hospital redesign, workforce planning and scheduling, patient flow, performance management, disease monitoring, and health care technology assessment need to be modeled efficiently. Mathematical modeling and computer simulation techniques have been shown to be increasingly valuable in providing useful information to aid planning and management. Petri Net (PN) is considered as a powerful model since it combines well-defined mathematical theory with a graphical representation which reflects the dynamic behavior of systems of interest. Due to dynamic characteristics, it is found to be more suitable for modeling Hospital Management System (HMS). In this paper, a Petri net model-based reliable workflow framework for Nephrology unit in hospital environment is proposed to track the movement of patients in the unit. The key objective of the proposed reliable workflow framework is to provide a well-organized health care unit to reduce the waiting time of the resource/ patient. The performance of the proposed Petri net model-based reliable workflow framework is simulated and validated through reachability graph using HPSim tool. The proposed Petri net workflow framework for the Nephrology unit can be used to deliver highly efficient and reliable healthcare services

Applying Process Mining Algorithms in the Context of Data Collection Scenarios

Despite the technological progress, paper-based questionnaires are still widely used to collect data in many application domains like education, healthcare or psychology. To facilitate the enormous amount of work involved in collecting, evaluating and analyzing this data, a system enabling process-driven data collection was developed. Based on generic tools, a process-driven approach for creating, processing and analyzing questionnaires was realized, in which a questionnaire is defined in terms of a process model. Due to this characteristic, process mining algorithms may be applied to event logs created during the execution of questionnaires. Moreover, new data that might not have been used in the context of questionnaires before may be collected and analyzed to provide new insights in regard to both the participant and the questionnaire. This thesis shows that process mining algorithms may be applied successfully to process-oriented questionnaires. Algorithms from the three process mining forms of process discovery, conformance checking and enhancement are applied and used for various analysis. The analysis of certain properties of discovered process models leads to new ways of generating information from questionnaires. Different techniques for conformance checking and their applicability in the context of questionnaires are evaluated. Furthermore, new data that cannot be collected from paper-based questionnaires is used to enhance questionnaires to reveal new and meaningful relationships

BioCAD: an information fusion platform for bio-network inference and analysis

Background : As systems biology has begun to draw growing attention, bio-network inference and analysis have become more and more important. Though there have been many efforts for bio-network inference, they are still far from practical applications due to too many false inferences and lack of comprehensible interpretation in the biological viewpoints. In order for applying to real problems, they should provide effective inference, reliable validation, rational elucidation, and sufficient extensibility to incorporate various relevant information sources. Results : We have been developing an information fusion software platform called BioCAD. It is utilizing both of local and global optimization for bio-network inference, text mining techniques for network validation and annotation, and Web services-based workflow techniques. In addition, it includes an effective technique to elucidate network edges by integrating various information sources. This paper presents the architecture of BioCAD and essential modules for bio-network inference and analysis. Conclusion : BioCAD provides a convenient infrastructure for network inference and network analysis. It automates series of users' processes by providing data preprocessing tools for various formats of data. It also helps inferring more accurate and reliable bio-networks by providing network inference tools which utilize information from distinct sources. And it can be used to analyze and validate the inferred bio-networks using information fusion tools.ope

A Semantic Framework for Declarative and Procedural Knowledge

In any scientic domain, the full set of data and programs has reached an-ome status, i.e. it has grown massively. The original article on the Semantic Web describes the evolution of a Web of actionable information, i.e.\ud information derived from data through a semantic theory for interpreting the symbols. In a Semantic Web, methodologies are studied for describing, managing and analyzing both resources (domain knowledge) and applications (operational knowledge) - without any restriction on what and where they\ud are respectively suitable and available in the Web - as well as for realizing automatic and semantic-driven work\ud ows of Web applications elaborating Web resources.\ud This thesis attempts to provide a synthesis among Semantic Web technologies, Ontology Research, Knowledge and Work\ud ow Management. Such a synthesis is represented by Resourceome, a Web-based framework consisting of two components which strictly interact with each other: an ontology-based and domain-independent knowledge manager system (Resourceome KMS) - relying on a knowledge model where resource and operational knowledge are contextualized in any domain - and a semantic-driven work ow editor, manager and agent-based execution system (Resourceome WMS).\ud The Resourceome KMS and the Resourceome WMS are exploited in order to realize semantic-driven formulations of work\ud ows, where activities are semantically linked to any involved resource. In the whole, combining the use of domain ontologies and work ow techniques, Resourceome provides a exible domain and operational knowledge organization, a powerful engine for semantic-driven work\ud ow composition, and a distributed, automatic and\ud transparent environment for work ow execution

Behavioral analysis of scientific workflows with semantic information

The recent development in scientific computing related areas has shown an increasing interest in scientific workflows because of their abilities to solve complex challenges. Problems and challenges that were too heavy or time-consuming can be solved now in a more efficient manner. Scientific workflows have been progressively improved by means of the introduction of new paradigms and technologies, being the semantic area one of the most promising ones. This paper focuses on the addition of semantic Web techniques to the scientific workflow area, which facilitates the integration of network-based solutions. On the other hand, a model checking technique to study the workflow behavior prior to its execution is also described. Using the Unary RDF annotated Petri net formalism (U-RDF-PN), scientific workflows can be improved by adding semantic annotations related to the task descriptions and workflow evolution. This technique can be applied using a complete environment for the model checking of this kind of workflows that is also depicted in this work. Finally, the proposed methodology is exemplified by its application to a couple of known scientific workflows: the First Provenance Challenge and the InterScan protein analysis workflow

Conceptual-level workflow modeling of scientific experiments using NMR as a case study

BACKGROUND: Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human reasoning are required. Workflows for experiments also highlight transitions among experimental phases, allowing intermediate results to be verified and supporting the proper handling of semantic mismatches and different file formats among the various tools used in the scientific process. Thus, scientific workflows are important for the modeling and subsequent capture of bioinformatics-related data. While much research has been conducted on the implementation of scientific workflows, the initial process of actually designing and generating the workflow at the conceptual level has received little consideration. RESULTS: We propose a structured process to capture scientific workflows at the conceptual level that allows workflows to be documented efficiently, results in concise models of the workflow and more-correct workflow implementations, and provides insight into the scientific process itself. The approach uses three modeling techniques to model the structural, data flow, and control flow aspects of the workflow. The domain of biomolecular structure determination using Nuclear Magnetic Resonance spectroscopy is used to demonstrate the process. Specifically, we show the application of the approach to capture the workflow for the process of conducting biomolecular analysis using Nuclear Magnetic Resonance (NMR) spectroscopy. CONCLUSION: Using the approach, we were able to accurately document, in a short amount of time, numerous steps in the process of conducting an experiment using NMR spectroscopy. The resulting models are correct and precise, as outside validation of the models identified only minor omissions in the models. In addition, the models provide an accurate visual description of the control flow for conducting biomolecular analysis using NMR spectroscopy experiment