A Survey of Data-Intensive Scientific Workflow Management <s> Taverna <s> Motivation:In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses. ::: ::: Results: The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community. The tool includes a workbench application which provides a graphical user interface for the composition of workflows. These workflows are written in a new language called the simple conceptual unified flow language (Scufl), where by each step within a workflow represents one atomic task. Two examples are used to illustrate the ease by which in silico experiments can be represented as Scufl workflows using the workbench application. ::: ::: Availability: The Taverna workflow system is available as open source and can be downloaded with example Scufl workflows from http://taverna.sourceforge.net <s> BIB001 </s> A Survey of Data-Intensive Scientific Workflow Management <s> Taverna <s> 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. <s> BIB002 </s> A Survey of Data-Intensive Scientific Workflow Management <s> Taverna <s> The Taverna workflow tool suite (http://www.taverna.org.uk) is designed to combine distributed Web Services and/or local tools into complex analysis pipelines. These pipelines can be executed on local desktop machines or through larger infrastructure (such as supercomputers, Grids or cloud environments), using the Taverna Server. In bioinformatics, Taverna workflows are typically used in the areas of high-throughput omics analyses (for example, proteomics or transcriptomics), or for evidence gathering methods involving text mining or data mining. Through Taverna, scientists have access to several thousand different tools and resources that are freely available from a large range of life science institutions. Once constructed, the workflows are reusable, executable bioinformatics protocols that can be shared, reused and repurposed. A repository of public workflows is available at http://www.myexperiment.org. This article provides an update to the Taverna tool suite, highlighting new features and developments in the workbench and the Taverna Server. <s> BIB003 </s> A Survey of Data-Intensive Scientific Workflow Management <s> Taverna <s> BackgroundScientific workflows management systems are increasingly used to specify and manage bioinformatics experiments. Their programming model appeals to bioinformaticians, who can use them to easily specify complex data processing pipelines. Such a model is underpinned by a graph structure, where nodes represent bioinformatics tasks and links represent the dataflow. The complexity of such graph structures is increasing over time, with possible impacts on scientific workflows reuse. In this work, we propose effective methods for workflow design, with a focus on the Taverna model. We argue that one of the contributing factors for the difficulties in reuse is the presence of "anti-patterns", a term broadly used in program design, to indicate the use of idiomatic forms that lead to over-complicated design. The main contribution of this work is a method for automatically detecting such anti-patterns, and replacing them with different patterns which result in a reduction in the workflow's overall structural complexity. Rewriting workflows in this way will be beneficial both in terms of user experience (easier design and maintenance), and in terms of operational efficiency (easier to manage, and sometimes to exploit the latent parallelism amongst the tasks).ResultsWe have conducted a thorough study of the workflows structures available in Taverna, with the aim of finding out workflow fragments whose structure could be made simpler without altering the workflow semantics. We provide four contributions. Firstly, we identify a set of anti-patterns that contribute to the structural workflow complexity. Secondly, we design a series of refactoring transformations to replace each anti-pattern by a new semantically-equivalent pattern with less redundancy and simplified structure. Thirdly, we introduce a distilling algorithm that takes in a workflow and produces a distilled semantically-equivalent workflow. Lastly, we provide an implementation of our refactoring approach that we evaluate on both the public Taverna workflows and on a private collection of workflows from the BioVel project.ConclusionWe have designed and implemented an approach to improving workflow structure by way of rewriting preserving workflow semantics. Future work includes considering our refactoring approach during the phase of workflow design and proposing guidelines for designing distilled workflows. <s> BIB004
Taverna  is an open-source SWfMS from the my Grid project to support workflow-based biological experiments. Taverna is used in multiple areas such as astronomy, bioinformatics, chemistry etc. In the presentation layer, Taverna takes a GUI for designing workflows and showing monitoring information while it uses a textual language to represent a workflow as a DAG BIB002 . The workflows can be designed in Taverna installed in the user's computer or an online web server. Moreover, this GUI can be installed in an Android mobile  In the user services layer, Taverna uses a state machine for the activities to achieve workflow monitoring BIB001 . The workflows designed through Taverna can be shared through "myExperiment" social network BIB003 . It gathers provenance data from local execution information and the remotely invoked web services  . In the WEP generation layer, Taverna automatically optimizes the workflow structure by identifying complex parts of workflow structures and simplifies them for easier design and workflow parallelization BIB004 . Taverna links the invocation of web services and the activities and checks the availability of the needed web services for generating a WEP. In the WEP execution layer, Taverna relies on web and grid services for task execution. In the infrastructure layer, Taverna is able to use the computing resources from grid or cloud. It also stores execution data in a database.