Web-based Workflow System Research Articles

MitoLink: A generic integrated web-based workflow system to evaluate genotype-phenotype correlations in human mitochondrial diseases: Observations from the GenomeAsia Pilot project

MitoLink is a generic, scalable and modular web-based workflow system developed to study genotype-phenotype correlations in human mitochondrial diseases. MitoLink integrates applications for assessment of genomic variation and currently houses genome-wide datasets from GenomeAsia Pilot project, gnomAD, ClinVar and DisGenNet. In this study, a reference list of nearly 3975 proteins (both nuclear and mitochondrial encoded) with mitochondrial function is reported. This protein set is mapped to disease associated variants in the GenomeAsia Pilot Project and DisGenNet and evaluated for pathogenicity as defined by ClinVar. Observations of shared genetic components in potential comorbidities are discussed from gene-disease network in Asian population, however, the platform is generic and can be applied to any population dataset. MitoLink is a unique customized workflow system that allows for systematic storage, extraction, analysis and visualization of genomic variation to understand genotype-phenotype correlations for mitochondrial diseases. Given the modularity of tool and data integration, MitoLink is a scalable system that can accommodate a diverse set of applications linked via standard data structure within the framework of Galaxy. MitoLink is built on FAIR principles and supports creation of reproducible workflows towards understanding genotype-phenotype correlations across several disease phenotypes globally.

Ballaxy: web services for structural bioinformatics.

Web-based workflow systems have gained considerable momentum in sequence-oriented bioinformatics. In structural bioinformatics, however, such systems are still relatively rare; while commercial stand-alone workflow applications are common in the pharmaceutical industry, academic researchers often still rely on command-line scripting to glue individual tools together. In this work, we address the problem of building a web-based system for workflows in structural bioinformatics. For the underlying molecular modelling engine, we opted for the BALL framework because of its extensive and well-tested functionality in the field of structural bioinformatics. The large number of molecular data structures and algorithms implemented in BALL allows for elegant and sophisticated development of new approaches in the field. We hence connected the versatile BALL library and its visualization and editing front end BALLView with the Galaxy workflow framework. The result, which we call ballaxy, enables the user to simply and intuitively create sophisticated pipelines for applications in structure-based computational biology, integrated into a standard tool for molecular modelling. ballaxy consists of three parts: some minor modifications to the Galaxy system, a collection of tools and an integration into the BALL framework and the BALLView application for molecular modelling. Modifications to Galaxy will be submitted to the Galaxy project, and the BALL and BALLView integrations will be integrated in the next major BALL release. After acceptance of the modifications into the Galaxy project, we will publish all ballaxy tools via the Galaxy toolshed. In the meantime, all three components are available from http://www.ball-project.org/ballaxy. Also, docker images for ballaxy are available at https://registry.hub.docker.com/u/anhi/ballaxy/dockerfile/. ballaxy is licensed under the terms of the GPL.

MoBiFlow

Web-based problem solving environments provide sharing, execution and monitoring of scientific workflows. Where they depend on general purpose workflow development systems, the workflow notations are likely far too powerful and complex, especially in the area of biology, where programming skills are rare. On the other hand, application specific workflow systems may use special purpose languages and execution engines, suffering from a lack of standards, portability, documentation, stability of investment etc. In both cases, the need to support yet another application on the desk-top places a burden on the system administration of a research lab. In previous research the authors have developed the web based workflow systems Calvin and Hobbes, which enable biologists and computer scientists to approach these problems in collaboration. Both systems use a server-centric Web 2.0 based approach. Calvin is tailored to molecular biology applications, with a simple graphical workflow-language and easy access to existing BioMoby web services. Calvin workflows are compiled to industry standard BPEL workflows, which can be edited and refined in collaboration between researchers and computer scientists using the Hobbes tool. Together, Calvin and Hobbes form our workflow platform MoBiFlow, whose principles, design, and use cases are described in this paper.

분산 트랜잭션 워크플로우 모니터링 시스템의 설계 및 구현

This paper describes the design and implementation details of a distributed transactional workflow monitoring system. There have been prevalent research and development trends in the workflow literature - workflow systems tend to be completely distributed architectures to support very large-scale workflow applications on object-oriented and internet-based infrastructures. That is, the active (object), distributed (architecture), system-oriented (transaction), and large-scale (application) workflow systems are the key targets in terms of the research and development aspects. While the passive, centralized, human-oriented, and small/medium scale workflow systems are the typical instances of the traditional workflow systems. Unlike in the traditional (the client-server architecture) workflow systems, the workflow monitoring features should not be easily supported in the recent (the fully distributed architecture) workflow systems. At the same time, they need a set of additional monitoring features, such as gathering and displaying statistical (or overload status) information of the workflow architectural components dispersed on the internet. We, in this paper, introduce the additional workflow monitoring features that are necessarily required for the recent workflow systems, and show how to embed those features into a web-based distributed workflow system.

Emergency healthcare process automation using workflow technology and web services.

Emergency healthcare delivery involves a variety of interrelated activities performed from the time of a call to the ambulance service until the time of patient's exit from the emergency department of a hospital. As these activities can be viewed as parts of inter-organizational healthcare processes that involve at least two organizations (e.g. an ambulance service and a hospital), there is a need to provide the appropriate technological infrastructure for automating and managing these processes even in cases where the organizations involved use heterogeneous systems to support their internal services. Web-based workflow systems in conjunction with web services present a new way for service-oriented integration (SOI) of disparate systems and for developing distributed applications within and between organizations. Thus, process automation with the use of web services can provide an appropriate infrastructure for the integration of pre-hospital and in-hospital emergency healthcare. A prototype development of such a system is presented in this paper.

Developing a virtual patient record using XML and web-based workflow technologies

Virtual patient records (VPR) provide a means for integrated access to patient information that may be scattered around different healthcare settings. Within the boundaries of a health district providing all levels of care, this concept can be implemented in a corporate Intranet environment to support longitudinal patient care activities across the participating healthcare providers. In this context, a VPR implementation enables autonomous healthcare providers to operate in a cooperative working environment and apply continuity of care. Workflow systems bring this collaboration and cooperation into effect by automatically routing the medical information needed by authorised actors in a healthcare process. This paper presents a VPR framework that allows integrating geographically dispersed medical information within a health district and enhancing collaboration and coordination of authorised workgroups by means of a web-based workflow system. An implementation of the proposed framework is also presented.

Development of a web-based system for supporting sales in a mineral water manufacturing firm: A case study

In this paper, we present the findings of a case study of the development of a Web-based workflow system in a mineral water manufacturing firm for supporting sales management. The system aims at providing assistance in (i) performing efficient dissemination and management of information and sales documents, (ii) ordering and delivering mineral water, and (iii) improving the control processes. A framework for the development of Web-based workflow systems is proposed. The framework is examined and explained in the context of the case study. Finally, the case study illustrates and highlights the benefits and advantages of the system, which provides better support to teamwork as a result of better communication and monitoring, and which reduces sales cycle times.

Web-based Workflow Framework with CORBA

Workflow is an important class of applications in the daily business. A number of web-based workflow systems have been de veloped recently as a natural extension to traditional workflow systems to exploit the growing popularity of the Internet. However, most of them are designed based on the specific application at hand. In this paper, we distill out the fundamental elements of a workflow system into a general workflow framework. The framework provides appropriate application programming interfaces for programmers to fill in the application specific requirements of a workflow system at hand. This is realized through two object-wrappers: the Task interface and the Resource interface, which support the specification of the tasks involved in the workflow schedule and the resources accessed re spectively. A major characteristic of the framework is that the particular workflow schedule under execution is fluid, in the sense that the tasks involved as well as their precedence relationships can be modified dynamically. Consistency constraints will be examined in this paper which determine when such modifications are allowed. To maximize flexibility, we adhere our design to the CORBA architecture, which has been becoming highly popular in recent years, thus allowing tasks and resources of different types to interoperate in our framework. We demonstrate the feasibility of our framework with a small prototype that allows tasks in a workflow system to be sched uled and executed.

Echoes of Semiotically-Based Design in the Development and Testing of a Workflow System

Workflow systems are information-intensive task-oriented computer applications that typically involve a considerable number of users playing a wide variety of roles. Since communication, coordination and decision-making processes are essential for such systems, representing, interpreting and negotiating collective meanings are a crucial issue for software design and development processes. In this paper, we report and discuss our experience in implementing Qualitas, a web-based workflow system. Semiotic theory was extensively used to support design decisions and negotiations with users about technological signs. Taking scenarios as a type-sign exchanged throughout the whole process, we could trace the theoretic underpinnings of our experience and draw some revealing conclusions about the product and the process of technologically reified discourse. Although it is present in all information technology applications, this kind of discourse is seldom analyzed by software designers and developers. Our conjecture is that outside semiotic theory, professionals involved with human-computer interaction and software engineering practices have difficulty to coalesce concepts derived from such different disciplines as psychology, anthropology, linguistics and sociology, to name a few. Semiotics, however, can by itself provide a unifying ontological basis for interdisciplinary nowledge, raising issues and proposing alternatives, that may help professionals gain insights at lower learning costs. eywords: semiotic engineering, workflow systems, information-intensive task-oriented systems, scenario based design and development of computer systems, human-computer interaction