The cost required for the process of sequencing genomes has decreased drastically in the last few years. The knowledge of full genomes has increased the pace of the advancements in the field of functional genomics. Computational genomics, which analyses these sequences, has seen a similar growth. The multitude of sequencing technologies has resulted in various formats for storing the sequences. This has resulted in the creation of many tools for DNA analysis. There are various tools for sorting, indexing, analyzing read groups and other tasks. The analysis of genomics often requires the creation of pipelines, which processes the DNA sequences by chaining together many tools. This results in the creation of complex scripts that glue together these tools and pass the output from one stage to the other. Also, there are tools which allow creation of these pipelines with a graphical user interface. But these are complex to use and it is difficult to quickly add the new tools being developed to existing workflows. To solve these issues, we developed BioFlow; a web based genomic workflow management system. The use of BioFlow does not require any programming skills. The integrated workflow designer allows creation and saving workflows. The pipeline is created by connecting the tools with a visual connector. BioFlow provides an easy and simple interface that allows users to quickly add tools for use in any workflow. Audit logs are maintained at each stage, which helps users to easily identify errors and fix them. / Master of Science

Organizações modernas apresentam demandas relacionadas à automação dos seus processos de negócio devido à alta complexidade dos mesmos e à necessidade de maior eficácia na execução. Neste contexto, a tecnologia de workflow tem se mostrado bastante eficiente, principalmente para a automatização dos processos de negócio. No entanto, por ser uma tecnologia emergente e em evolução, workflow apresenta algumas limitações. Ainda que diversos (meta) modelos de workflow tenham sido propostos nos últimos, anos, seus sub-modelos para representação dos aspectos estruturais da organização apresentam baixo poder de expressão. Além disso, a maioria das ferramentas para modelagem de workflow não provêm funcionalidades para definição, consulta e reuso de padrões. Um dos principais problemas é falta de um mapeamento consolidado entre padrões de funções recorrentes em processos de negócio (ex: solicitação de execução de atividade, aprovação de documentos) e (meta) modelos e/ou ferramentas para modelagem de processos de negócio e workflow. Além disso, a maioria das abordagens em padrões de workflow não exploram a completude e necessidade dos seus padrões para modelagem de workflow. A primeira contribuição desta tese é um Modelo Transacional de Processos de Negócio (MTPN) com suporte aos aspectos estruturais da organização. O metamodelo possibilita a criação de (sub-)processos de negócio a partir do reuso de padrões, principalmente com base nestes aspectos. Adicionalmente, o metamodelo sugere a geração automática de padrões através da Linguagem de Execução para Web Services (BPEL4WS). Outra importante contribuição da tese é um conjunto de padrões de workflow representados como atividades de bloco. Cada padrão descreve uma função recorrente em processos de negócio. A mineração de 190 processos de workflow de mais de 10 organizações diferentes provou a existência dos padrões com alto suporte nos processos de workflow analisados. Além disso, o estudo mostrou que o conjunto de padrões é suficiente e necessário para modelar todos os 190 processos investigados. O estudo também resultou em um conjunto de regras de associação. As regras não apenas contribuem para uma melhor definição dos padrões de atividade de bloco, mas também para a combinação destes com padrões de controle de fluxo. / Modern organizations have demands related to the automation of their business processes since such processes are highly complex and need to be efficiently executed. Within this context, the workflow technology has shown to be very effective, mainly in the business process automation. However, as it is an emergent technology and in constant evolution, workflow presents some limitations. Though several workflow (meta) models have been proposed in recent years, their sub-models for organizational structure aspects representation show limited power of expression. On the other hand, most of the current workflow modeling tools do not provide functionalities that enable users to define, query, and reuse workflow patterns properly. One of the main problems is the non-availability of a consolidated mapping between patterns based on recurrent functions found in business processes (e.g., request for activity execution, notification, decision, or approval) and workflow (meta) models or workflow modeling tools. Relying on these problems, the first contribution of this thesis is a Transactional Metamodel of Business Process (TMBP) with support to organizational structure aspects. The metamodel makes feasible to create business (sub-)processes from the reuse of organizational –based workflow patterns. An additional feature of TMBP supports the generation of business (sub-)processes through the Business Process Execution Language for Web Services (BPEL4WS). Other important contribution of this thesis is a set of workflow patterns represented as block activity patterns. Each pattern refers to a recurrent business function frequently found in business processes. The mining of 190 workflow processes of more than 10 different organizations has evidenced the existence of the set of workflow patterns with high support in the workflow processes analyzed. Moreover, it became clear through this study that the set of patterns is both necessary and enough to design all 190 processes that were investigated. As a consequence of the mining process, a set of association rules was identified too. The rules not only help to better define specific workflow patterns, but also combine them with existent control flow patterns. These rules can be useful for building more complex workflows.

Organizações modernas apresentam demandas relacionadas à automação dos seus processos de negócio devido à alta complexidade dos mesmos e à necessidade de maior eficácia na execução. Neste contexto, a tecnologia de workflow tem se mostrado bastante eficiente, principalmente para a automatização dos processos de negócio. No entanto, por ser uma tecnologia emergente e em evolução, workflow apresenta algumas limitações. Ainda que diversos (meta) modelos de workflow tenham sido propostos nos últimos, anos, seus sub-modelos para representação dos aspectos estruturais da organização apresentam baixo poder de expressão. Além disso, a maioria das ferramentas para modelagem de workflow não provêm funcionalidades para definição, consulta e reuso de padrões. Um dos principais problemas é falta de um mapeamento consolidado entre padrões de funções recorrentes em processos de negócio (ex: solicitação de execução de atividade, aprovação de documentos) e (meta) modelos e/ou ferramentas para modelagem de processos de negócio e workflow. Além disso, a maioria das abordagens em padrões de workflow não exploram a completude e necessidade dos seus padrões para modelagem de workflow. A primeira contribuição desta tese é um Modelo Transacional de Processos de Negócio (MTPN) com suporte aos aspectos estruturais da organização. O metamodelo possibilita a criação de (sub-)processos de negócio a partir do reuso de padrões, principalmente com base nestes aspectos. Adicionalmente, o metamodelo sugere a geração automática de padrões através da Linguagem de Execução para Web Services (BPEL4WS). Outra importante contribuição da tese é um conjunto de padrões de workflow representados como atividades de bloco. Cada padrão descreve uma função recorrente em processos de negócio. A mineração de 190 processos de workflow de mais de 10 organizações diferentes provou a existência dos padrões com alto suporte nos processos de workflow analisados. Além disso, o estudo mostrou que o conjunto de padrões é suficiente e necessário para modelar todos os 190 processos investigados. O estudo também resultou em um conjunto de regras de associação. As regras não apenas contribuem para uma melhor definição dos padrões de atividade de bloco, mas também para a combinação destes com padrões de controle de fluxo. / Modern organizations have demands related to the automation of their business processes since such processes are highly complex and need to be efficiently executed. Within this context, the workflow technology has shown to be very effective, mainly in the business process automation. However, as it is an emergent technology and in constant evolution, workflow presents some limitations. Though several workflow (meta) models have been proposed in recent years, their sub-models for organizational structure aspects representation show limited power of expression. On the other hand, most of the current workflow modeling tools do not provide functionalities that enable users to define, query, and reuse workflow patterns properly. One of the main problems is the non-availability of a consolidated mapping between patterns based on recurrent functions found in business processes (e.g., request for activity execution, notification, decision, or approval) and workflow (meta) models or workflow modeling tools. Relying on these problems, the first contribution of this thesis is a Transactional Metamodel of Business Process (TMBP) with support to organizational structure aspects. The metamodel makes feasible to create business (sub-)processes from the reuse of organizational –based workflow patterns. An additional feature of TMBP supports the generation of business (sub-)processes through the Business Process Execution Language for Web Services (BPEL4WS). Other important contribution of this thesis is a set of workflow patterns represented as block activity patterns. Each pattern refers to a recurrent business function frequently found in business processes. The mining of 190 workflow processes of more than 10 different organizations has evidenced the existence of the set of workflow patterns with high support in the workflow processes analyzed. Moreover, it became clear through this study that the set of patterns is both necessary and enough to design all 190 processes that were investigated. As a consequence of the mining process, a set of association rules was identified too. The rules not only help to better define specific workflow patterns, but also combine them with existent control flow patterns. These rules can be useful for building more complex workflows.

Organizações modernas apresentam demandas relacionadas à automação dos seus processos de negócio devido à alta complexidade dos mesmos e à necessidade de maior eficácia na execução. Neste contexto, a tecnologia de workflow tem se mostrado bastante eficiente, principalmente para a automatização dos processos de negócio. No entanto, por ser uma tecnologia emergente e em evolução, workflow apresenta algumas limitações. Ainda que diversos (meta) modelos de workflow tenham sido propostos nos últimos, anos, seus sub-modelos para representação dos aspectos estruturais da organização apresentam baixo poder de expressão. Além disso, a maioria das ferramentas para modelagem de workflow não provêm funcionalidades para definição, consulta e reuso de padrões. Um dos principais problemas é falta de um mapeamento consolidado entre padrões de funções recorrentes em processos de negócio (ex: solicitação de execução de atividade, aprovação de documentos) e (meta) modelos e/ou ferramentas para modelagem de processos de negócio e workflow. Além disso, a maioria das abordagens em padrões de workflow não exploram a completude e necessidade dos seus padrões para modelagem de workflow. A primeira contribuição desta tese é um Modelo Transacional de Processos de Negócio (MTPN) com suporte aos aspectos estruturais da organização. O metamodelo possibilita a criação de (sub-)processos de negócio a partir do reuso de padrões, principalmente com base nestes aspectos. Adicionalmente, o metamodelo sugere a geração automática de padrões através da Linguagem de Execução para Web Services (BPEL4WS). Outra importante contribuição da tese é um conjunto de padrões de workflow representados como atividades de bloco. Cada padrão descreve uma função recorrente em processos de negócio. A mineração de 190 processos de workflow de mais de 10 organizações diferentes provou a existência dos padrões com alto suporte nos processos de workflow analisados. Além disso, o estudo mostrou que o conjunto de padrões é suficiente e necessário para modelar todos os 190 processos investigados. O estudo também resultou em um conjunto de regras de associação. As regras não apenas contribuem para uma melhor definição dos padrões de atividade de bloco, mas também para a combinação destes com padrões de controle de fluxo. / Modern organizations have demands related to the automation of their business processes since such processes are highly complex and need to be efficiently executed. Within this context, the workflow technology has shown to be very effective, mainly in the business process automation. However, as it is an emergent technology and in constant evolution, workflow presents some limitations. Though several workflow (meta) models have been proposed in recent years, their sub-models for organizational structure aspects representation show limited power of expression. On the other hand, most of the current workflow modeling tools do not provide functionalities that enable users to define, query, and reuse workflow patterns properly. One of the main problems is the non-availability of a consolidated mapping between patterns based on recurrent functions found in business processes (e.g., request for activity execution, notification, decision, or approval) and workflow (meta) models or workflow modeling tools. Relying on these problems, the first contribution of this thesis is a Transactional Metamodel of Business Process (TMBP) with support to organizational structure aspects. The metamodel makes feasible to create business (sub-)processes from the reuse of organizational –based workflow patterns. An additional feature of TMBP supports the generation of business (sub-)processes through the Business Process Execution Language for Web Services (BPEL4WS). Other important contribution of this thesis is a set of workflow patterns represented as block activity patterns. Each pattern refers to a recurrent business function frequently found in business processes. The mining of 190 workflow processes of more than 10 different organizations has evidenced the existence of the set of workflow patterns with high support in the workflow processes analyzed. Moreover, it became clear through this study that the set of patterns is both necessary and enough to design all 190 processes that were investigated. As a consequence of the mining process, a set of association rules was identified too. The rules not only help to better define specific workflow patterns, but also combine them with existent control flow patterns. These rules can be useful for building more complex workflows.

Dynamic changes in the business environment requires their business process to be up-to-date. The Workflow Management Systems supporting these business processes need to adapt to these changes rapidly. The Work Flow Management Systems however lacks the ability to dynamically propagate the process changes to their process model schemas (Workflow templates). The literature on workflow schema evolution emphasizes the impact of changes in control flow with very ittle attention to other aspects of a workflow schema. This thesis studies the data aspect (data flow and data model) of workflow schema during its evolution. Workflow schema changes can lead to inconsistencies between the underlying database model and the workflow. A rather straight forward approach to the problem would be to abandon the existing database model and start afresh. However this introduces data persistence issues. Also there could be significant system downtimes involved in the process of migrating data from the old database model to the current one. In this research we develop an approach to address this problem. The business changes demand various types of control flow changes to its business process model (workflow schema). The control flow changes include task insertion, deletion, swapping, movement, replacement, extraction, in-lining, Parallelizing etc. Many of the control flow changes to the workflow can be made by using the combination of a simple task insertion and deletion, while some like embedding task in loop/ conditional branch and Parallelizing tasks also requires the addition/removal of control dependency between the tasks. Since many of the control flow change patterns involves task insertion and deletion at its core, in this thesis we study its impact on the underlying data model. We propose algorithms to dynamically handle the changes in the underlying relational database schema. First we identify the basic change patterns that can be implemented using atomic task insertion and deletions. Then we characterize these basic pattern in terms of their data flow anomalies (Missing, Redundant, Conflicting data) that they can generate. The Data schema compliance criteria are developed to identify the data changes: (i) that makes the underlying database schema inconsistent with the modified workflow and (ii) generating the aforementioned data anomalies. The Data schema compliance criteria characterizes the change patterns in terms of its ability to work with the current relational data model. The Data schema compliance criteria show various properties required of the modified workflow to be consistent with the underlying database model. The data of any workflow instance conforming to Data schema compliance criteria can be directly accommodated in the database model. The data anomalies (of task insertion and deletion) identified using DSC are handled dynamically using respective Data adaptation algorithms. The algorithm uses the functional dependency constraints in the relational database model to adapt/handle these data anomalies. Such handled data (changes) that conform to DSC can be directly accommodated in the underlying database schema. Hence with this approach the workflow can be modified (using task insertion and deletion) and their data changes can be implemented on-the-fly using the Data adaptation algorithms. In this research the same old data model is evolved without abandoning it even after the modification of the workflow schema. This maintains the old data persistence in the existing database schema. Detailed implementation procedures to deploy the Data adaptation algorithms are presented with illustrative examples.

The the thesis deals with tools for workflow processes automation. It describes in general what workflow is. It also briefly describes tools such as MS BizTalk Server, SAP NetWeaver, IBM WebSphere, ORACLE BPEL. The main part deals with Windows Workflow Foundation. This tool is decribed in detail together with its parts workflow runtime, workflow instances and workflow activities. One part of the thesis is a application, which uses all the possibilities of Windows Workflow Foundation.

Um dos grandes problemas relacionados a modelagem de workflow consiste na utilização de técnicas de modelagem conceitual especificas a cada sistema de workflow, não havendo, dessa forma, urn modelo aceito consensualmente. Esta situação, decorrência do ambiente competitivo neste mercado, leva a não inclusão de muitas características conceitualmente importantes relacionadas a modelagem nos técnicas geralmente utilizadas. Um importante aspecto a ser tratado nos modelos conceituais e a questão da modelagem formal do workflow e que constitui o terra central deste trabalho. Esta dissertação apresenta uma técnica de modelagem de workflow utilizando como modelo de dados referencial o TF-ORM (Temporal Functionality in Objects with Roles Model). Esta técnica desenvolve uma especificação rigorosa de workflow em um nível conceitual, formalizando com a utilização de um modelo técnico seu comportamento interno (cooperação e interação entre tarefas) e seu relacionamento para o ambiente (designação de tarefas de trabalho para executores). Neste modelo, construções são apresentadas para representar, de forma eficiente, a modularização e o paralelismo. Uma linguagem textual de definição de workflow e apresentada. Adicionalmente é apresentada a utilização de descrições formais do workflow para gerar o esquema de dados do workflow e o conjunto de regras para seu gerenciamento. Em adição, o paradigma de regras oferece um formalismo conveniente para expressar computações reativas influenciadas por eventos externos, gerados fora do WFMS (Workflow Manager System). Finalmente é realizada uma analise sobre algumas ferramentas comerciais, procurando validar a praticidade dos modelos conceituais desenvolvidos. Os principais conceitos envolvidos em workflow são descritos e classificados de forma a possibilitar, a validação tanto dos conceitos quanto da modelagem através de um estudo de caso e a utilização de um sistema comercial. / One of the greatest problems in workflow modelling is the use of specific conceptual modelling techniques associated to each workflow system; there is not a consensual accepted model. This situation, a consequence of the strong competitive environment in this market, leads to the non-inclusion of many important conceptual characteristics. This restriction is a consequence of the restricted modelling techniques closely related with implementation models. An important aspect to be considered, and the central subject of this work, is the formal workflow modelling. A modelling technique using the TF-ORM (Temporary Functionality in Objects with Rolls Model) data model is here presented. The modelling technique develops a rigorous specification of workflow at the conceptual level, formalising in one model its internal behaviour (the co-operation and interaction among tasks) and its relationship with the environment (the designation of tasks). In this model, constructions where developed to represent, in an efficient form, the modularity and the parallelism of the activities. A formal language for the workflow definition is presented. Additionally, the use of formal workflow description is used to generate the data flow and rules set for its management. In addition, the rules paradigm offers a convenient formalism to express reactive computations influenced by external events generated outside the Workflow Manager System. Finally a case study is accomplished using some commercial modelling tools, to validate the developed conceptual models practicality.

Je weiter die Zivilisation vorranschreitet, um so komplexer werden deren Errungenschaften. Die Herstellungsprozesse ziehen auch ein komplexes Management während der Produktion nach sich, da viele Menschen und Maschinen am Produktionsprozess beteiligt sind. Der Manager stellt hier einen "Single Point of Failure" dar. Das bedeutet, dass die erfolgreiche Produktion nun abhängig von der Qualität und der Fehlerfreiheit des Managers bzw. des leitetenden Personals ist. Um diesen Mangel zu beseitigen, lohnt es sich auch an dieser Stelle gewisse Prozesse zu automatisieren. Man erreicht dadurch einen höheren Grad an Fehlerfreiheit und Zuverlässigkeit. Um dies zu realisieren, werden unter anderem die Prinzipien des Workflow-Managements benutzt. Je komplexer ein Workflow wird, um so mehr Rechenleistung wird benötigt, um diesen in einem Workflow-Management-System auszuführen. Eine technische Möglichkeit dieses Problem zu lösen, stellt die Verteilung der Workflow-Management-Software dar. Verteilung bedeutet im gleichen Atemzug eine Verkomplizierung der Softwarearchitektur, wodurch sie wiederum komplizierter zu entwickeln ist. Komplexe Softwaresysteme ziehen komplexe Testprogramme und Simulationsumgebungen nach sich. Um die Entwicklung eines verteilten Workflow-Management-Systems zu unterstützen, wird in dieser Arbeit ein Simulationssystem für Workflow-Management-Systeme entworfen und implementiert. Es wird den Entwicklern eines verteilten Workflow-Management- Systems ein wertvolles Tool während der Implementierung der Software sein.

Workflow Management Systems (WfMSs) are used to support the modelling, analysis, and enactment of business processes. The key benefits WfMSs seek to bring to an organisation include improved efficiency, better process control and improved customer service, which are realised by modelling rigidly structured business processes that in turn derive well-defined workflow process instances. However, the proprietary process definition frameworks imposed by WfMSs make it difficult to support (i) dynamic evolution and adaptation (i.e. modifying process definitions during execution) following unexpected or developmental change in the business processes being modelled; and (ii) exceptions, or deviations from the prescribed process model at runtime, even though it has been shown that such deviations are a common occurrence for almost all processes. These limitations imply that a large subset of business processes do not easily translate to the 'system-centric' modelling frameworks imposed. This research re-examines the fundamental theoretical principles that underpin workflow technologies to derive an approach that moves forward from the productionline paradigm and thereby offers workflow management support for a wider range of work environments. It develops a sound theoretical foundation based on Activity Theory to deliver an implementation of an approach for dynamic and extensible flexibility, evolution and exception handling in workflows, based not on proprietary frameworks, but on accepted ideas of how people actually perform their work activities. The approach produces a framework called worklets to provide an extensible repertoire of self-contained selection and exception-handling processes, coupled with an extensible ripple-down rule set. Using a Service-Oriented Architecture (SOA), a selection service provides workflow flexibility and adaptation by allowing the substitution of a task at runtime with a sub-process, dynamically selected from its repertoire depending on the context of the particular work instance. Additionally, an exceptionhandling service uses the same repertoire and rule set framework to provide targeted and multi-functional exception-handling processes, which may be dynamically invoked at the task, case or specification level, depending on the context of the work instance and the type of exception that has occurred. Seven different types of exception can be handled by the service. Both expected and unexpected exceptions are catered for in real time. The work is formalised through a series of Coloured Petri Nets and validated using two exemplary studies: one involving a structured business environment and the other a more creative setting. It has been deployed as a discrete service for the well-known, open-source workflow environment YAWL, and, having a service orientation, its applicability is in no way limited to that environment, but may be regarded as a case study in service-oriented computing whereby dynamic flexibility and exception handling for workflows, orthogonal to the underlying workflow language, is provided. Also, being open-source, it is freely available for use and extension.

Um dos grandes problemas relacionados a modelagem de workflow consiste na utilização de técnicas de modelagem conceitual especificas a cada sistema de workflow, não havendo, dessa forma, urn modelo aceito consensualmente. Esta situação, decorrência do ambiente competitivo neste mercado, leva a não inclusão de muitas características conceitualmente importantes relacionadas a modelagem nos técnicas geralmente utilizadas. Um importante aspecto a ser tratado nos modelos conceituais e a questão da modelagem formal do workflow e que constitui o terra central deste trabalho. Esta dissertação apresenta uma técnica de modelagem de workflow utilizando como modelo de dados referencial o TF-ORM (Temporal Functionality in Objects with Roles Model). Esta técnica desenvolve uma especificação rigorosa de workflow em um nível conceitual, formalizando com a utilização de um modelo técnico seu comportamento interno (cooperação e interação entre tarefas) e seu relacionamento para o ambiente (designação de tarefas de trabalho para executores). Neste modelo, construções são apresentadas para representar, de forma eficiente, a modularização e o paralelismo. Uma linguagem textual de definição de workflow e apresentada. Adicionalmente é apresentada a utilização de descrições formais do workflow para gerar o esquema de dados do workflow e o conjunto de regras para seu gerenciamento. Em adição, o paradigma de regras oferece um formalismo conveniente para expressar computações reativas influenciadas por eventos externos, gerados fora do WFMS (Workflow Manager System). Finalmente é realizada uma analise sobre algumas ferramentas comerciais, procurando validar a praticidade dos modelos conceituais desenvolvidos. Os principais conceitos envolvidos em workflow são descritos e classificados de forma a possibilitar, a validação tanto dos conceitos quanto da modelagem através de um estudo de caso e a utilização de um sistema comercial. / One of the greatest problems in workflow modelling is the use of specific conceptual modelling techniques associated to each workflow system; there is not a consensual accepted model. This situation, a consequence of the strong competitive environment in this market, leads to the non-inclusion of many important conceptual characteristics. This restriction is a consequence of the restricted modelling techniques closely related with implementation models. An important aspect to be considered, and the central subject of this work, is the formal workflow modelling. A modelling technique using the TF-ORM (Temporary Functionality in Objects with Rolls Model) data model is here presented. The modelling technique develops a rigorous specification of workflow at the conceptual level, formalising in one model its internal behaviour (the co-operation and interaction among tasks) and its relationship with the environment (the designation of tasks). In this model, constructions where developed to represent, in an efficient form, the modularity and the parallelism of the activities. A formal language for the workflow definition is presented. Additionally, the use of formal workflow description is used to generate the data flow and rules set for its management. In addition, the rules paradigm offers a convenient formalism to express reactive computations influenced by external events generated outside the Workflow Manager System. Finally a case study is accomplished using some commercial modelling tools, to validate the developed conceptual models practicality.