Papers by Natallia Kokash
Ensuring transactional behavior of business processes and web service compositions is an essentia... more Ensuring transactional behavior of business processes and web service compositions is an essential issue in the area of service-oriented computing. Transactions in this context may require long periods of time to complete and must be managed using non-blocking techniques. Data integrity in Long-Running Transactions (LRTs) is preserved using compensations, that is, activities explicitly programmed to eliminate the effects of a process terminated by a user or that failed to complete due to another reason. In this paper, we present a framework for behavioral modeling of business processes, focusing on their transactional properties. Our solution is based on the channel-based coordination language Reo, which is an expressive, compositional and semantically precise design language admitting formal reasoning. The operational semantics of Reo is given by constraint automata. We illustrate how Reo can be used for modeling termination and compensation handling in a number of commonly-used workflow patterns, including sequential and parallel compositions, nested transactions, discriminator choice and concurrent flows with link dependencies. Furthermore, we show how essential properties of LRTs can be expressed in LTL and CTL-like logics and verified using model checking technology. Our framework is supported by a number of Eclipse plug-ins that provide facilities for modeling, animation, and verification of LRTs to generate executable code for them.
In this paper, we present the implementation of a novel domain-specific language (DSL) for pharma... more In this paper, we present the implementation of a novel domain-specific language (DSL) for pharmacometric modeling called the Modelling Description Language (MDL). MDL is a modular, declarative language with block structures that allows users to abstract data, processes and mathematical models from auxiliary code, and hence, improves model readability, reusability and opportunities for collaborative research. The main aim of this DSL is interoperability between core software tools used in pharmacometrics. We describe the MDL-IDE, an integrated development environment for MDL, which assists users in writing MDL code. The paper focuses on language constructs and design decisions, briefly explains how models are validated and converted to a machine-readable format for processing by existing model simulation and estimation software tools.
The paradigms of service-oriented computing and modeldriven development are becoming of increasin... more The paradigms of service-oriented computing and modeldriven development are becoming of increasing importance in the field of software engineering. According to these paradigms, new systems are composed with added value from existing stand-alone services to support business processes across organizations. Services comprising a system but originating from various sources need to be coordinated. The Reo coordination language is a state-of-the-art computer supported approach to channel-based coordination. Reo introduces various types of channels which can be composed to build complex connectors to represent various behavioral protocols. This makes Reo suitable for the modeling of servicebased business processes. In previous work we presented a framework for model checking data-aware Reo connectors using the mCRL2 toolset. In this paper, we extend this result with a proof of correctness, evaluation of optimization techniques, and support for context-sensitive analysis.
Motivation: This work describes the underlying notion and formal representation of tissue motifs ... more Motivation: This work describes the underlying notion and formal representation of tissue motifs in terms of simple combinations of cell types that are co-located in the same tissue. The composition of tissue motifs is characterised on the basis that particular forms of biological interaction can take place between the cells in the motif. One such biological interaction involves the diffusion of gene products that are secreted into the surrounding tissue fluid to reach binding receptors attached to nearby plasma membranes.
Reo, an exogenous channel-based coordination language, is a model for service coordination wherei... more Reo, an exogenous channel-based coordination language, is a model for service coordination wherein services communicate through connectors formed by joining binary communication channels. In order to establish transactional communication among services as prescribed by connector semantics, distributed ports exchange "handshaking" messages signalling which parties are ready to provide or consume data. In this paper, we present a formal implementation model for distributed Reo with communication delays and outline ideas for its proof of correctness. To reason about Reo implementation formally, we introduce Timed Action Constraint Automata (TACA) and explain how to compare TACA with existing automata-based semantics for Reo. We use TACA to describe "handshaking" behavior of Reo modeling primitives and argue that in any distributed circuit remote Reo nodes and channels exposing such behavior commit to perform transitions envisaged by the network semantics.
The lack of a common exchange format for mathematical models in pharmacometrics has been a long-s... more The lack of a common exchange format for mathematical models in pharmacometrics has been a long-standing problem. Such a format has the potential to increase productivity and analysis quality, simplify the handling of complex workflows, ensure reproducibility of research, and facilitate the reuse of existing model resources. Pharmacometrics Markup Language (PharmML), currently under development by the Drug Disease Model Resources (DDMoRe) consortium, is intended to become an exchange standard in pharmacometrics by providing means to encode models, trial designs, and modeling steps.
Reo is an exogenous channel-based coordination language that acts as glue code to tie together so... more Reo is an exogenous channel-based coordination language that acts as glue code to tie together software components and services. The building blocks of Reo models are connectors that impose constraints on the data-flow in component or service-based architectures in terms of data synchronization, buffering, mutual exclusion, etc. Several semantic models have been introduced to formalize the behavior of Reo. These models differ in terms of expressiveness, computation complexity and purposes that they serve. In this paper, we present a method and a tool for building formal automata-based semantics of Reo that unifies various aspects of existing semantics. We express the behavior of a Reo network as a mixed system of Boolean and numerical constraints constructed compositionally by conjuncting the assertions for its constituent parts. The solutions of this system are found with the help of off-the-shelf constraint solvers and are used to construct the constraint automaton with state memory that gives the sound and complete semantics of Reo with respect to existing models. Our approach is more efficient and scalable compared to the existing methods for generating formal semantics of Reo connectors.
Treemapping is a method for displaying hierarchical data using nested rectangles. Each branch of ... more Treemapping is a method for displaying hierarchical data using nested rectangles. Each branch of the tree is given its rectangle, which then is tiled with smaller rectangles representing sub-branches. A node's shape has an area proportional to a specified dimension of the data. To create a treemap, one must define a tiling algorithm, i.e., a way to divide a rectangle into sub-rectangles of specified areas. There are several problems with existing tiling algorithms: (i) they allow tiles to shift when the main window or some of the tiles are resized affecting the user perception of the information; (ii) they do not allow users to place selected elements into desired positions w.r.t. each other. In this paper, we present a method for creating treemaps with customized layouts. The method is based on reusable templates and supports zooming into specific areas of the treemap without affecting its initial layout. We illustrate the use of template-based treemaps to the visualization of biomedical data. Furthermore, we present an algorithm for automated generation of layouts satisfying positional constraints for a particular class of constraints.
A key challenge for the physiology modeling community is to enable the searching, objective compa... more A key challenge for the physiology modeling community is to enable the searching, objective comparison and, ultimately, re-use of models and associated data that are interoperable in terms of their physiological meaning. In this work, we outline the development of a workflow to modularize the simulation of tissue-level processes in physiology. In particular, we show how, via this approach, we can systematically extract, parcellate and annotate tissue histology data to represent component units of tissue function. These functional units are semantically interoperable, in terms of their physiological meaning. In particular, they are interoperable with respect to [i] each other and with respect to [ii] a circuitboard representation of long-range advective routes of fluid flow over which to model long-range molecular exchange between these units. We exemplify this approach through the combination of models for physiology-based pharmacokinetics and pharmacodynamics to quantitatively depict biological mechanisms across multiple scales. Links to the data, models and software components that constitute this workflow are found at http://open-physiology.org/. Keywords: functional tissue units, histology, physiology-based pharmacokinetics, fluid flow modeling, physiology circuit-boarding, ApiNATOMY, visual knowledge management www.frontiersin.org February 2015 | Volume 6 | Article 24 | 1 de Bono et al. The Open Physiology workflow Frontiers in Physiology | Computational Physiology and Medicine February 2015 | Volume 6 | Article 24 | 2 de Bono et al. The Open Physiology workflow www.frontiersin.org February 2015 | Volume 6 | Article 24 | 9 de Bono et al. The Open Physiology workflow RA (2015) The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units. Front. Physiol. 6:24.
Physiology experts deal with complex biophysical relationships, across multiple spatial and tempo... more Physiology experts deal with complex biophysical relationships, across multiple spatial and temporal scales. Automating the discovery of such relationships, in terms of physiological meaning, is a key goal to the physiology community. ApiNATOMY is an effort to provide an interface between the physiology expert's knowledge and all ranges of data relevant to physiology. It does this through an intuitive graphical interface for managing semantic metadata and ontologies relevant to physiology. In this paper, we present a web-based ApiNATOMY environment, allowing physiology experts to navigate through circuitboard visualizations of body components, and their cardiovascular and neural connections, across different scales. Overlaid on these schematics are graphical renderings of organs, neurons and gene products, as well as mathematical models of processes semantically annotated with this knowledge.
International banks need to estimate their operational risk due to external regulations. Based on... more International banks need to estimate their operational risk due to external regulations. Based on their estimations they need to provide private capital to cover potential losses caused by these risks. Therefore, operational risks need to be properly measured and managed in order to reduce the required private capital. In this paper we discuss operational risk related to a typical banking business process that is enabled by an IT landscape. We present how risks related to the operational behavior of the IT landscape can be simulated. The simulation results help to estimate risk measures like the expected loss, the value-at-risk and the expected shortfall. We further sketch how control theory could be used to actively manage the dynamic reconfiguration of an service landscape in order to minimize operational risks. First experimental simulation results illustrate our approach.
The paradigm of service-oriented computing revolutionized the field of software engineering. Acco... more The paradigm of service-oriented computing revolutionized the field of software engineering. According to this paradigm, new systems are composed of existing stand-alone services to support complex cross-organizational business processes. Correct communication of these services is not possible without a proper coordination mechanism. The Reo coordination language is a channel-based modeling language that introduces various types of channels and their composition rules. By composing Reo channels, one can specify Reo connectors that realize arbitrary complex behavioral protocols. Several formalisms have been introduced to give semantics to Reo. In their most basic form, they reflect service synchronization and dataflow constraints imposed by connectors. To ensure that the composed system behaves as intended, we need a wide range of automated verification tools to assist service composition designers. In this paper, we present our framework for the verification of Reo using the mCRL2 toolset. We unify our previous work on mapping various semantic models for Reo, namely, constraint automata, timed constraint automata, coloring semantics and the newly developed action constraint automata, to the process algebraic specification language of mCRL2, address the correctness of this mapping, discuss tool support, and present a detailed example that illustrates the use of Reo empowered with mCRL2 for the analysis of dataflow in service-based process models.
Business process management is an operational management approach that focuses on improving busin... more Business process management is an operational management approach that focuses on improving business processes. Business processes, i.e., collections of important activities in an organization, are represented in the form of a workflow, an orchestrated and repeatable pattern of activities amenable to automated analysis and control. Priority is an important concept in modeling workflows. We need priority to model cancelable and compensable tasks within transactional business processes. We use the Reo coordination language to model and formally analyze workflows. In this paper, we propose a constraint-based approach to formalize priority in Reo. We introduce special channels to propagate and block priority flows, define their semantics as constraints, and model priority propagation as a constraint satisfaction problem.
The correct behavior of a service composition depends on the appropriate coordination of its serv... more The correct behavior of a service composition depends on the appropriate coordination of its services. According to the idea of channelbased coordination, services exchange messages though channels without any knowledge about each other. The Reo coordination language aims at building connectors out of basic channels to implement arbitrarily complex interaction protocols. The activity within a Reo connector consists of two types of communication, each of which incurs a delay: internal coordination and data transfer. Semantic models have been proposed for Reo that articulate data transfer delays, but none of them explicitly considers coordination delays. More importantly, these models implicitly assume that (1) internal coordination and data transfer activities take place in two separate phases, and (2) data transfer delays do not affect the coordination phase. This assumptions prevent maximal concurrency in data exchange and distort the evaluation of end-to-end delays in service composition models. In this paper, we introduce a novel compositional automata-based semantic model for Reo that explicitly represents both internal coordination and data transfer aspects in channel-based connectors. Furthermore, we map the proposed model to the process algebra mCRL2, which allows us to generate state spaces for connectors with time delays and analyze them automatically.
Compliance management is essential for ensuring that organizational business processes and suppor... more Compliance management is essential for ensuring that organizational business processes and supporting information systems are in accordance with a set of prescribed requirements originating from laws, regulations, and various legislative or technical documents such as Sarbanes-Oxley Act or ISO 17799. As the violation of such requirements may lead to significant punishment for an organization, compliance management should be supported at the very early stages of business process development. In this paper, we present an integrated approach to compliance management that helps process designers to adhere to compliance requirements relevant for their processes. Firstly, we introduce a conceptual model for specifying compliance requirements originating from various compliance sources. Secondly, we propose a framework for augmenting business processes with reusable fragments to ensure process compliance to certain requirements by design. Furthermore, we discuss the formalization of compliance requirements using mathematical logics and integrate the framework for process reuse with automated software verification tools.
In this paper, we present a toolset to automate the transformation of Business Process Modeling N... more In this paper, we present a toolset to automate the transformation of Business Process Modeling Notation (BPMN), UML Sequence Diagrams, and Business Process Execution Language (BPEL), into their proposed formal semantics expressed in the channel-based coordination language Reo. Such transformations enable the animated execution and verification of the aforementioned notations with the help of verification and model checking tools available for Reo.
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Papers by Natallia Kokash