In this paper we describe our experience adopting the Research Object Bundle (RO-Bundle) format with BagIt serialization (BagIt-RO) for the design and implementation of "tales" in the Whole Tale platform. A tale is an executable research object intended for the dissemination of computational scientific findings that captures information needed to facilitate understanding, transparency, and re-execution for review and computational reproducibility at the time of publication. We describe the Whole Tale platform and requirements that led to our adoption of BagIt-RO, specifics of our implementation, and discuss migrating to the emerging Research Object Crate (RO-Crate) standard.

Research Objects have the potential to significantly enhance the reproducibility of scientific research. One important way Research Objects can do this is by encapsulating the means for re-executing the computational components of studies, thus supporting the new form of reproducibility enabled by digital computing-exact repeatability. However, Research Objects also can make scientific research more reproducible by supporting transparency, a component of reproducibility orthogonal to re-executability. We describe here our vision for making Research Objects more transparent by providing means for disambiguating claims about reproducibility generally, and computational repeatability specifically. We show how support for science-oriented queries can enable researchers to assess the reproducibility of Research Objects and the individual methods and results they encapsulate.

BACKGROUND: Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. RESULTS: We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip) datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data) and therefore are close to traditional shell scripting or R/BioConductor scripting approaches to pipeline design. Finally, we suggest that microarray data processing task workflows may provide a basis for future example-based comparison of different workflow systems. CONCLUSIONS: We provide a set of tools and complete workflows for microarray data analysis in the Kepler environment, which has the advantages of offering graphical, clear display of conceptual steps and parameters and the ability to easily integrate other resources such as remote data and web services.

Scientific workflows are commonplace in eScience applications. Yet, the lack of integrated support for data models, including streaming data, structured collections and files, is limiting the ability of workflows to support emerging applications in energy informatics that are stream oriented. This is compounded by the absence of Cloud data services that support reliable and performant streams. In this paper, we propose and present a scientific workflow framework that supports streams as first-class data, and is optimized for performant and reliable execution across desktop and Cloud platforms. The workflow framework features and its empirical evaluation on a private Eucalyptus cloud are presented.

Scientific workflow systems are used to integrate existing software components (actors) into larger analysis pipelines to perform in silico experiments. Current approaches for handling data in nested-collection structures, as required in many scientific domains, lead to many record-management actors (shims) that make the workflow structure overly complex, and as a consequence hard to construct, evolve and maintain. By constructing and executing workflows from bioinformatics and geosciences in the Kepler system, we will demonstrate how COMAD (Collection-Oriented Modeling and Design), an extension of conventional workflow design, addresses these shortcomings. In particular, COMAD provides a hierarchical data stream model (as in XML) and a novel declarative configuration language for actors that functions as a middleware layer between the workflow's data model (streaming nested collections) and the actor's data model (base data and lists thereof). Our approach allows actor developers to focus on the internal actor processing logic oblivious to the workflow structure. Actors can then be re-used in various workflows simply by adapting actor configurations. Due to streaming nested collections and declarative configurations, COMAD workflows can usually be realized as linear data processing pipelines, which often reflect the scientific data analysis intention better than conventional designs. This linear structure not only simplifies actor insertions and deletions (workflow evolution), but also decreases the overall complexity of the workflow, reducing future effort in maintenance.

BACKGROUND: For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly. RESULTS: We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform. CONCLUSIONS: By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable, easy-to-combine tools for asking increasingly complex microbial ecology questions.

Scientific workflow systems are increasingly used to automate complex data analyses, largely due to their benefits over traditional approaches for workflow design, optimization, and provenance recording. Many workflow systems employ a simple dependency model to represent the provenance of data produced by workflow runs. Although commonly adopted, this model does not capture explicit data dependencies introduced by "provenance-aware" processes, and it can lead to inefficient storage when workflow data is complex or structured. We present a provenance model, extending the conventional approach, that supports (i) explicit data dependencies and (ii) nested data collections. Our model adopts techniques from reference-based XML versioning, adding annotations for process and data dependencies. We present strategies and reduction techniques to store immediate and transitive provenance information within our model, and examine trade-offs among update time, storage size, and query response time. We evaluate our approach on real-world and synthetic workflow execution traces, demonstrating significant reductions in storage size, while also reducing the time required to store and query provenance information.

Abstract — XML process networks are a simple, yet power-ful programming paradigm for loosely coupled, coarse-grained dataflow applications such as data-centric scientific workflows. We describe a framework called ∆-XML that is well-suited for applications in which pipelines of data processors modify parts (“deltas”) of XML data collections while keeping the overall collection structure intact. We show how to optimize the execution of ∆-XML process networks by minimizing the data shipping cost in distributed settings. This X-CSR1 optimization employs static type inference based on XML Schema to determine the XML stream fragments that are relevant to a processor, allowing irrelevant fragments to be bypassed (“shipped”) to downstream pipeline steps. Finally, we present evaluation results for a real-world scientific workflow, which shows the practical feasibility of X-CSR. A long version of this paper is available as [1]. I.

Abstract We describe a provenance model tailored to scientific workflows based on the collection‐oriented modeling and design paradigm. Our implementation within the Kepler scientific workflow system captures the dependencies of data and collection creation events on preexisting data and collections, and embeds these provenance records within the data stream. A provenance query engine operates on self‐contained workflow traces representing serializations of the output data stream for particular workflow runs. We demonstrate this approach in our response to the first provenance challenge. Copyright © 2007 John Wiley & Sons, Ltd.

Abstract Scientific workflows often benefit from or even require advanced modeling constructs, e.g. nesting of subworkflows, cycles for executing loops, data‐dependent routing, and pipelined execution. In such settings, an often overlooked aspect of provenance takes center stage: a suitable model of provenance (MoP) for scientific workflows should be based upon the underlying model of computation (MoC) used for executing the workflows. We can derive an adequate MoP from a MoC (such as Kahn's process networks) by taking into account the assumptions that a MoC entails, and by recording the observables which it affords. In this way, a MoP captures or at least better approximates ‘real’ data dependencies for workflows with advanced modeling constructs. As a specific instance, we elaborate on the Read–Write–ReSet model, a simple and flexible MoP suitable for a number of different MoCs. Copyright © 2007 John Wiley & Sons, Ltd.

Abstract The first Provenance Challenge was set up in order to provide a forum for the community to understand the capabilities of different provenance systems and the expressiveness of their provenance representations. To this end, a functional magnetic resonance imaging workflow was defined, which participants had to either simulate or run in order to produce some provenance representation, from which a set of identified queries had to be implemented and executed. Sixteen teams responded to the challenge, and submitted their inputs. In this paper, we present the challenge workflow and queries, and summarize the participants' contributions. Copyright © 2007 John Wiley & Sons, Ltd.

We view scientific workflows as the domain scientist's way to harness cyberinfrastructure for e-Science. Domain scientists are often interested in "end-to-end" frameworks which include data acquisition, transformation, analysis, visualization, and other steps. While there is no lack of technologies and standards to choose from, a simple, unified framework combining data modeling and processoriented modeling and design of scientific workflows has yet to emerge. Towards this end, we introduce a number of concepts such as models of computation and provenance, actor-oriented modeling, adapters, hybrid types, and higher-order components, and then outline a particular composition of some of these concepts, yielding a promising new synthesis for describing scientific workflows, i.e., Collection-Oriented Modeling and Design (COMAD).