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

A compositional method for reliability analysis of workflows affected by multiple failure modes

We focus on reliability analysis for systems designed as workflow based compositions of components. Components are characterized by their failure profiles, which take into account possible multiple failure modes. A compositional calculus is provided to evaluate the failure profile of a composite system, given failure profiles of the components. The calculus is described as a syntax-driven procedure that synthesizes a workflows failure profile. The method is viewed as a design-time aid that can help software engineers reason about systems reliability in the early stage of development. A simple case study is presented to illustrate the proposed approach

Evaluation of linear classifiers on articles containing pharmacokinetic evidence of drug-drug interactions

Background. Drug-drug interaction (DDI) is a major cause of morbidity and mortality. [...] Biomedical literature mining can aid DDI research by extracting relevant DDI signals from either the published literature or large clinical databases. However, though drug interaction is an ideal area for translational research, the inclusion of literature mining methodologies in DDI workflows is still very preliminary. One area that can benefit from literature mining is the automatic identification of a large number of potential DDIs, whose pharmacological mechanisms and clinical significance can then be studied via in vitro pharmacology and in populo pharmaco-epidemiology. Experiments. We implemented a set of classifiers for identifying published articles relevant to experimental pharmacokinetic DDI evidence. These documents are important for identifying causal mechanisms behind putative drug-drug interactions, an important step in the extraction of large numbers of potential DDIs. We evaluate performance of several linear classifiers on PubMed abstracts, under different feature transformation and dimensionality reduction methods. In addition, we investigate the performance benefits of including various publicly-available named entity recognition features, as well as a set of internally-developed pharmacokinetic dictionaries. Results. We found that several classifiers performed well in distinguishing relevant and irrelevant abstracts. We found that the combination of unigram and bigram textual features gave better performance than unigram features alone, and also that normalization transforms that adjusted for feature frequency and document length improved classification. For some classifiers, such as linear discriminant analysis (LDA), proper dimensionality reduction had a large impact on performance. Finally, the inclusion of NER features and dictionaries was found not to help classification.Comment: Pacific Symposium on Biocomputing, 201

Usability of Scientific Workflow in Dynamically Changing Environment

Scientific workflow management systems are mainly data-flow oriented, which face several challenges due to the huge amount of data and the required computational capacity which cannot be predicted before enactment. Other problems may arise due to the dynamic access of the data storages or other data sources and the distributed nature of the scientific workflow computational infrastructures (cloud, cluster, grid, HPC), which status may change even during running of a single workflow instance. Many of these failures could be avoided with workflow management systems that provide provenance based dynamism and adaptivity to the unforeseen scenarios arising during enactment. In our work we summarize and categorize the failures that can arise in cloud environment during enactment and show the possibility of prediction and avoidance of failures with dynamic and provenance support

Flock together with CReATIVE-B: A roadmap of global research data infrastructures supporting biodiversity and ecosystem science

Biodiversity research infrastructures are providing the integrated data sets and support for studying scenarios of biodiversity and ecosystem dynamics. The CReATIVE-B project - Coordination of Research e-Infrastructures Activities Toward an International Virtual Environment for Biodiversity – explored how cooperation and interoperability of large-scale Research Infrastructures across the globe could support the challenges of biodiversity and ecosystem research. A key outcome of the project is that the research infrastructures agreed to continue cooperation after the end of the project to advance scientific progress in understanding and predicting the complexity of natural systems. By working together in implementing the recommendations in this Roadmap, the data and capabilities of the cooperating research infrastructures are better served to address the grand challenges for biodiversity and ecosystem scientists