25,048 research outputs found
Global transaction support for workflow management systems: from formal specification to practical implementation
In this paper, we present an approach to global transaction management in workflow environments. The transaction mechanism is based on the well-known notion of compensation, but extended to deal with both arbitrary process structures to allow cycles in processes and safepoints to allow partial compensation of processes. We present a formal specification of the transaction model and transaction management algorithms in set and graph theory, providing clear, unambiguous transaction semantics. The specification is straightforwardly mapped to a modular architecture, the implementation of which is first applied in a testing environment, then in the prototype of a commercial workflow management system. The modular nature of the resulting system allows easy distribution using middleware technology. The path from abstract semantics specification to concrete, real-world implementation of a workflow transaction mechanism is thus covered in a complete and coherent fashion. As such, this paper provides a complete framework for the application of well-founded transactional workflows
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Kronos: a workflow assembler for genome analytics and informatics.
BackgroundThe field of next-generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into "best practices" for automated analysis of next-generation sequencing datasets) still requires significant programming investment and expertise.ResultsWe present Kronos, a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by compiling a text configuration file into executable Python applications. Making analysis modules would still require programming. The framework of each workflow includes a run manager to execute the encoded workflows locally (or on a cluster or cloud), parallelize tasks, and log all runtime events. The resulting workflows are highly modular and configurable by construction, facilitating flexible and extensible meta-applications that can be modified easily through configuration file editing. The workflows are fully encoded for ease of distribution and can be instantiated on external systems, a step toward reproducible research and comparative analyses. We introduce a framework for building Kronos components that function as shareable, modular nodes in Kronos workflows.ConclusionsThe Kronos platform provides a standard framework for developers to implement custom tools, reuse existing tools, and contribute to the community at large. Kronos is shipped with both Docker and Amazon Web Services Machine Images. It is free, open source, and available through the Python Package Index and at https://github.com/jtaghiyar/kronos
A novel framework for the use of workflow system in the integration of supply chain tiers
The global competition has imposed challenges to supply chain integration, mainly, during the process of obtain information to make demand management decisions. This paper proposes an integrated framework for data collection, analysis and results dissemination in the supply chain management (SCM), contributing to research and alternatives for \u201cThe Bullwhip Effect\u201d issue. In this sense, it is necessary to discuss the integration of supply chain management, Enterprise Resources Planning (ERP) functionality and others systems, to enlarge this scope to the total supply chain players. The ERP web-based tool and Workflow Systems (WS) can contribute to solve issues related to supply chain management. Starting from a detailed analysis of the research background regarding current SCM definitions and integration problems, Information Technology and Communication (ITC) development and WS in order to map and ensure flow fluency; the paper proposes a model to increase the overall integrations and an application in a case study for supporting the decisions that are aligned with the company\u2019s strategic objectives. This paper is divided in: research background; proposed model of the SC integration; case study, conclusions and future research
Italian center for Astronomical Archives publishing solution: modular and distributed
The Italian center for Astronomical Archives tries to provide astronomical
data resources as interoperable services based on IVOA standards. Its VO
expertise and knowledge comes from active participation within IVOA and VO at
European and international level, with a double-fold goal: learn from the
collaboration and provide inputs to the community. The first solution to build
an easy to configure and maintain resource publisher conformant to VO standards
proved to be too optimistic. For this reason it has been necessary to re-think
the architecture with a modular system built around the messaging concept,
where each modular component speaks to the other interested parties through a
system of broker-managed queues. The first implemented protocol, the Simple
Cone Search, shows the messaging task architecture connecting the parametric
HTTP interface to the database backend access module, the logging module, and
allows multiple cone search resources to be managed together through a
configuration manager module. Even if relatively young, it already proved the
flexibility required by the overall system when the database backend changed
from MySQL to PostgreSQL+PgSphere. Another implementation test has been made to
leverage task distribution over multiple servers to serve simultaneously: FITS
cubes direct linking, cubes cutout and cubes positional merging. Currently the
implementation of the SIA-2.0 standard protocol is ongoing while for TAP we
will be adapting the TAPlib library. Alongside these tools a first
administration tool (TASMAN) has been developed to ease the build up and
maintenance of TAP_SCHEMA-ta including also ObsCore maintenance capability.
Future work will be devoted at widening the range of VO protocols covered by
the set of available modules, improve the configuration management and develop
specific purpose modules common to all the service components.Comment: SPIE Astronomical Telescopes + Instrumentation 2018, Software and
Cyberinfrastructure for Astronomy V, pre-publishing draft proceeding (reduced
abstract
Clinical guidelines as plans: An ontological theory
Clinical guidelines are special types of plans realized by collective agents. We provide an ontological theory of such plans that is designed to support the construction of a framework in which guideline-based information systems can be employed in the management of workflow in health care organizations.
The framework we propose allows us to represent in formal terms how clinical guidelines are realized through the actions of are realized through the actions of individuals organized into teams. We provide various levels of implementation representing different levels of conformity on the part of health care organizations.
Implementations built in conformity with our framework are marked by two dimensions of flexibility that are designed to make them more likely to be accepted by health care professionals than standard guideline-based management systems. They do justice to the fact 1) that responsibilities within a health care organization are widely shared, and 2) that health care professionals may on different occasions be non-compliant with guidelines for a variety of well justified reasons.
The advantage of the framework lies in its built-in flexibility, its sensitivity to clinical context, and its ability to use inference tools based on a robust ontology. One disadvantage lies in its complicated implementation
Distributed Access Control for Web and Business Processes
Middleware influenced the research community in developing a number of systems for controlling access to distributed resources. Nowadays a new paradigm for the lightweight integration of business resources from different partners is starting to take hold â Web Services and Business Processes for Web Services. Security and access control policies for Web Services protocols and distributed systems are well studied and almost standardized, but there is not yet a comprehensive proposal for an access control architecture for business processes. So, it is worth looking at the available approaches to distributed authorization as a starting point for a better understanding of what they already have and what they still need to address the security challenges for business processes
The OMII Software â Demonstrations and Comparisons between two different deployments for Client-Server Distributed Systems
This paper describes the key elements of the OMII software and the scenarios which OMII software can be deployed to achieve distributed computing in the UK e-Science Community, where two different deployments for Client-Server distributed systems are demonstrated. Scenarios and experiments for each deployment have been described, with its advantages and disadvantages compared and analyzed. We conclude that our first deployment is more relevant for system administrators or developers, and the second deployment is more suitable for usersâ perspective which they can send and check job status for hundred job submissions
Modularity for Security-Sensitive Workflows
An established trend in software engineering insists on using components
(sometimes also called services or packages) to encapsulate a set of related
functionalities or data. By defining interfaces specifying what functionalities
they provide or use, components can be combined with others to form more
complex components. In this way, IT systems can be designed by mostly re-using
existing components and developing new ones to provide new functionalities. In
this paper, we introduce a notion of component and a combination mechanism for
an important class of software artifacts, called security-sensitive workflows.
These are business processes in which execution constraints on the tasks are
complemented with authorization constraints (e.g., Separation of Duty) and
authorization policies (constraining which users can execute which tasks). We
show how well-known workflow execution patterns can be simulated by our
combination mechanism and how authorization constraints can also be imposed
across components. Then, we demonstrate the usefulness of our notion of
component by showing (i) the scalability of a technique for the synthesis of
run-time monitors for security-sensitive workflows and (ii) the design of a
plug-in for the re-use of workflows and related run-time monitors inside an
editor for security-sensitive workflows
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