Fine-Grained Workflow Interoperability in Life Sciences

In den vergangenen Jahrzehnten führten Fortschritte in den Schlüsseltechnologien der Lebenswissenschaften zu einer exponentiellen Zunahme der zur Verfügung stehenden biologischen Daten. Um Ergebnisse zeitnah generieren zu können werden sowohl spezialisierte Rechensystem als auch Programmierfähigkeiten benötigt: Desktopcomputer oder monolithische Ansätze sind weder in der Lage mit dem Wachstum der verfügbaren biologischen Daten noch mit der Komplexität der Analysetechniken Schritt zu halten. Workflows erlauben diesem Trend durch Parallelisierungsansätzen und verteilten Rechensystemen entgegenzuwirken. Ihre transparenten Abläufe, gegeben durch ihre klar definierten Strukturen, ebenso ihre Wiederholbarkeit, erfüllen die Standards der Reproduzierbarkeit, welche an wissenschaftliche Methoden gestellt werden. Eines der Ziele unserer Arbeit ist es Forschern beim Bedienen von Rechensystemen zu unterstützen, ohne dass Programmierkenntnisse notwendig sind. Dafür wurde eine Sammlung von Tools entwickelt, welche jedes Kommandozeilenprogramm in ein Workflowsystem integrieren kann. Ohne weitere Anpassungen kann unser Programm zwei weit verbreitete Workflowsysteme unterstützen. Unser modularer Entwurf erlaubt zudem Unterstützung für weitere Workflowmaschinen hinzuzufügen. Basierend auf der Bedeutung von frühen und robusten Workflowentwürfen, haben wir außerdem eine wohl etablierte Desktop–basierte Analyseplattform erweitert. Diese enthält über 2.000 Aufgaben, wobei jede als Baustein in einem Workflow fungiert. Die Plattform erlaubt einfache Entwicklung neuer Aufgaben und die Integration externer Kommandozeilenprogramme. In dieser Arbeit wurde ein Plugin zur Konvertierung entwickelt, welches nutzerfreundliche Mechanismen bereitstellt, um Workflows auf verteilten Hochleistungsrechensystemen auszuführen—eine Aufgabe, die sonst technische Kenntnisse erfordert, die gewöhnlich nicht zum Anforderungsprofil eines Lebenswissenschaftlers gehören. Unsere Konverter–Erweiterung generiert quasi identische Versionen desselben Workflows, welche im Anschluss auf leistungsfähigen Berechnungsressourcen ausgeführt werden können. Infolgedessen werden nicht nur die Möglichkeiten von verteilten hochperformanten Rechensystemen sowie die Bequemlichkeit eines für Desktopcomputer entwickelte Workflowsystems ausgenutzt, sondern zusätzlich werden Berechnungsbeschränkungen von Desktopcomputern und die steile Lernkurve, die mit dem Workflowentwurf auf verteilten Systemen verbunden ist, umgangen. Unser Konverter–Plugin hat sofortige Anwendung für Forscher. Wir zeigen dies in drei für die Lebenswissenschaften relevanten Anwendungsbeispielen: Strukturelle Bioinformatik, Immuninformatik, und Metabolomik.Recent decades have witnessed an exponential increase of available biological data due to advances in key technologies for life sciences. Specialized computing resources and scripting skills are now required to deliver results in a timely fashion: desktop computers or monolithic approaches can no longer keep pace with neither the growth of available biological data nor the complexity of analysis techniques. Workflows offer an accessible way to counter against this trend by facilitating parallelization and distribution of computations. Given their structured and repeatable nature, workflows also provide a transparent process to satisfy strict reproducibility standards required by the scientific method. One of the goals of our work is to assist researchers in accessing computing resources without the need for programming or scripting skills. To this effect, we created a toolset able to integrate any command line tool into workflow systems. Out of the box, our toolset supports two widely–used workflow systems, but our modular design allows for seamless additions in order to support further workflow engines. Recognizing the importance of early and robust workflow design, we also extended a well–established, desktop–based analytics platform that contains more than two thousand tasks (each being a building block for a workflow), allows easy development of new tasks and is able to integrate external command line tools. We developed a converter plug–in that offers a user–friendly mechanism to execute workflows on distributed high–performance computing resources—an exercise that would otherwise require technical skills typically not associated with the average life scientist's profile. Our converter extension generates virtually identical versions of the same workflows, which can then be executed on more capable computing resources. That is, not only did we leverage the capacity of distributed high–performance resources and the conveniences of a workflow engine designed for personal computers but we also circumvented computing limitations of personal computers and the steep learning curve associated with creating workflows for distributed environments. Our converter extension has immediate applications for researchers and we showcase our results by means of three use cases relevant for life scientists: structural bioinformatics, immunoinformatics and metabolomics

Exact and Approximated Log Alignments for Processes with Inter-case Dependencies

The execution of different cases of a process is often restricted by inter-case dependencies through e.g., queueing or shared resources. Various high-level Petri net formalisms have been proposed that are able to model and analyze coevolving cases. In this paper, we focus on a formalism tailored to conformance checking through alignments, which introduces challenges related to constraints the model should put on interacting process instances and on resource instances and their roles. We formulate requirements for modeling and analyzing resource-constrained processes, compare several Petri net extensions that allow for incorporating inter-case constraints. We argue that the Resource Constrained $\nu$-net is an appropriate formalism to be used the context of conformance checking, which traditionally aligns cases individually failing to expose deviations on inter-case dependencies. We provide formal mathematical foundations of the globally aligned event log based on theory of partially ordered sets and propose an approximation technique based on the composition of individually aligned cases that resolves inter-case violations locally

A Taxonomy of Workflow Management Systems for Grid Computing

With the advent of Grid and application technologies, scientists and engineers are building more and more complex applications to manage and process large data sets, and execute scientific experiments on distributed resources. Such application scenarios require means for composing and executing complex workflows. Therefore, many efforts have been made towards the development of workflow management systems for Grid computing. In this paper, we propose a taxonomy that characterizes and classifies various approaches for building and executing workflows on Grids. We also survey several representative Grid workflow systems developed by various projects world-wide to demonstrate the comprehensiveness of the taxonomy. The taxonomy not only highlights the design and engineering similarities and differences of state-of-the-art in Grid workflow systems, but also identifies the areas that need further research.Comment: 29 pages, 15 figure

Knowledge Modeling for Developing Program Planning Agents

This paper describes a method of domain knowledge modeling for program planning and scheduling in intelligent e-Learning advising systems, focusing on the modeling and representation of precedence relations among course learning objects encoded in model curricular and the representation of domain experts’ knowledge using Petri nets formalism and a XML-based markup language. We developed a Web-based program model editor

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

Methodologies synthesis

This deliverable deals with the modelling and analysis of interdependencies between critical infrastructures, focussing attention on two interdependent infrastructures studied in the context of CRUTIAL: the electric power infrastructure and the information infrastructures supporting management, control and maintenance functionality. The main objectives are: 1) investigate the main challenges to be addressed for the analysis and modelling of interdependencies, 2) review the modelling methodologies and tools that can be used to address these challenges and support the evaluation of the impact of interdependencies on the dependability and resilience of the service delivered to the users, and 3) present the preliminary directions investigated so far by the CRUTIAL consortium for describing and modelling interdependencies

Model Driven Development and Maintenance of Business Logic for Information Systems

Since information systems become more and more important in today\''s society, business firms, organizations, and individuals rely on these systems to manage their daily business and social activities. The dependency of possibly critical business processes on complex IT systems requires a strategy that supports IT departments in reducing the time needed to implement changed or new domain requirements of functional departments. In this context, software models help to manage system\''s complexity and provide a tool for communication and documentation purposes. Moreover, software engineers tend to use automated software model processing such as code generation to improve development and maintenance processes. Particularly in the context of web-based information systems, a number of model driven approaches were developed. However, we believe that compared to the user interface layer and the persistency layer, there could be a better support of consistent approaches providing a suitable architecture for the consistent model driven development of business logic. To ameliorate this situation, we developed an architectural blueprint consisting of meta models, tools, and a method support for model driven development and maintenance of business logic from analysis until system maintenance. This blueprint, which we call Amabulo infrastructure, consists of five layers and provides concepts and tools to set up and apply concrete infrastructures for model driven development projects. Modeling languages can be applied as needed. In this thesis we focus on business logic layers of J2EE applications. However, concrete code generation rules can be adapted easily for different target platforms. After providing a high-level overview of our Amabulo infrastructure, we describe its layers in detail: The Visual Model Layer is responsible for all visual modeling tasks. For this purpose, we discuss requirements for visual software models for business logic, analyze several visual modeling languages concerning their usefulness, and provide an UML profile for business logic models. The Abstract Model Layer provides an abstract view on the business logic model in the form of a domain specific model, which we call Amabulo model. An Amabulo model is reduced to pure logical information concerning business logic aspects. It focuses on information that is relevant for the code generation. For this purpose, an Amabulo model integrates model elements for process modeling, state modeling, and structural modeling. It is used as a common interface between visual modeling languages and code generators. Visual models of the Visual Model Layer are automatically transformed into an Amabulo model. The Abstract System Layer provides a formal view onto the system in the form of a Coloured Petri Net (CPN). A Coloured Petri Net representation of the modeled business logic is a formal structure and independent of the actual business logic implementation. After an Amabulo model is automatically transformed into a CPN, it can be analyzed and simulated before any line of code is generated. The Code Generation Layer is responsible for code generation. To support the design and implementation of project-specific code generators, we discuss several aspects of code integration issues and provide object-oriented design approaches to tackle the issues. Then, we provide a conceptual mapping of Amabulo model elements into architectural elements of a J2EE infrastructure. This mapping explicitly considers robustness features, which support a later manual integration of generated critical code artifacts and external systems. The Application Layer is the target layer of an Amabulo infrastructure and comprises generated code artifacts. These artifacts are instances of a specific target platform specification, and they can be modified for integration purposes with development tools. Through the contributions in this thesis, we aim to provide an integrated set of solutions to support an efficient model driven development and maintenance process for the business logic of information systems. Therefore, we provide a consistent infrastructure blueprint that considers modeling tasks, model analysis tasks, and code generation tasks. As a result, we see potential for reducing the development and maintenance efforts for changed domain requirements and simultaneously guaranteeing robustness and maintainability even after several changes

APQL: A process-model query language

As business process management technology matures, organisations acquire more and more business process models. The management of the resulting collections of process models poses real challenges. One of these challenges concerns model retrieval where support should be provided for the formulation and efficient execution of business process model queries. As queries based on only structural information cannot deal with all querying requirements in practice, there should be support for queries that require knowledge of process model semantics. In this paper we formally define a process model query language that is based on semantic relationships between tasks in process models and is independent of any particular process modelling notation

The program is the model: Enabling [email protected]

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-36089-3_7Revised Selected Papers of 5th International Conference, SLE 2012, Dresden, Germany, September 26-28, 2012The increasing application of Model-Driven Engineering in a wide range of domains, in addition to pure code generation, raises the need to manipulate models at runtime, as part of regular programs. Moreover, certain kinds of programming tasks can be seen as model transformation tasks, and thus we could take advantage of model transformation technology in order to facilitate them. In this paper we report on our works to bridge the gap between regular programming and model transformation by enabling the manipulation of Java APIs as models. Our approach is based on the specification of a mapping between a Java API (e.g., Swing) and a meta-model describing it. A model transformation definition is written against the API meta-model and we have built a compiler that generates the corresponding Java bytecode according to the mapping. We present several application scenarios and discuss the mapping between object-oriented meta-modelling and the Java object system. Our proposal has been validated by a prototype implementation which is also contributed.Work funded by the Spanish Ministry of Economy and Competitivity (TIN2011-24139), and the R&D programme of Madrid Region (S2009/TIC-1650)