Digital provenance - models, systems, and applications

Data provenance refers to the history of creation and manipulation of a data object and is being widely used in various application domains including scientific experiments, grid computing, file and storage system, streaming data etc. However, existing provenance systems operate at a single layer of abstraction (workflow/process/OS) at which they record and store provenance whereas the provenance captured from different layers provide the highest benefit when integrated through a unified provenance framework. To build such a framework, a comprehensive provenance model able to represent the provenance of data objects with various semantics and granularity is the first step. In this thesis, we propose a such a comprehensive provenance model and present an abstract schema of the model. ^ We further explore the secure provenance solutions for distributed systems, namely streaming data, wireless sensor networks (WSNs) and virtualized environments. We design a customizable file provenance system with an application to the provenance infrastructure for virtualized environments. The system supports automatic collection and management of file provenance metadata, characterized by our provenance model. Based on the proposed provenance framework, we devise a mechanism for detecting data exfiltration attack in a file system. We then move to the direction of secure provenance communication in streaming environment and propose two secure provenance schemes focusing on WSNs. The basic provenance scheme is extended in order to detect packet dropping adversaries on the data flow path over a period of time. We also consider the issue of attack recovery and present an extensive incident response and prevention system specifically designed for WSNs

Digital provenance - models, systems, and applications

Data provenance refers to the history of creation and manipulation of a data object and is being widely used in various application domains including scientific experiments, grid computing, file and storage system, streaming data etc. However, existing provenance systems operate at a single layer of abstraction (workflow/process/OS) at which they record and store provenance whereas the provenance captured from different layers provide the highest benefit when integrated through a unified provenance framework. To build such a framework, a comprehensive provenance model able to represent the provenance of data objects with various semantics and granularity is the first step. In this thesis, we propose a such a comprehensive provenance model and present an abstract schema of the model. ^ We further explore the secure provenance solutions for distributed systems, namely streaming data, wireless sensor networks (WSNs) and virtualized environments. We design a customizable file provenance system with an application to the provenance infrastructure for virtualized environments. The system supports automatic collection and management of file provenance metadata, characterized by our provenance model. Based on the proposed provenance framework, we devise a mechanism for detecting data exfiltration attack in a file system. We then move to the direction of secure provenance communication in streaming environment and propose two secure provenance schemes focusing on WSNs. The basic provenance scheme is extended in order to detect packet dropping adversaries on the data flow path over a period of time. We also consider the issue of attack recovery and present an extensive incident response and prevention system specifically designed for WSNs

Semantically Resolving Type Mismatches in Scientific Workflows

Scientists are increasingly utilizing Grids to manage large data sets and execute scientific experiments on distributed resources. Scientific workflows are used as means for modeling and enacting scientific experiments. Windows Workflow Foundation (WF) is a major component of Microsoft’s .NET technology which offers lightweight support for long-running workflows. It provides a comfortable graphical and programmatic environment for the development of extended BPEL-style workflows. WF’s visual features ease the syntactic composition of Web services into scientific workflows but do nothing to assure that information passed between services has consistent semantic types or representations or that deviant flows, errors and compensations are handled meaningfully. In this paper we introduce SAWSDL-compliant annotations for WF and use them with a semantic reasoner to guarantee semantic type correctness in scientific workflows. Examples from bioinformatics are presented

BSML: A Binding Schema Markup Language for Data Interchange in Problem Solving Environments (PSEs)

We describe a binding schema markup language (BSML) for describing data interchange between scientific codes. Such a facility is an important constituent of scientific problem solving environments (PSEs). BSML is designed to integrate with a PSE or application composition system that views model specification and execution as a problem of managing semistructured data. The data interchange problem is addressed by three techniques for processing semistructured data: validation, binding, and conversion. We present BSML and describe its application to a PSE for wireless communications system design

Data Workflow - A Workflow Model for Continuous Data Processing

Online data or streaming data are getting more and more important for enterprise information systems, e.g. by integrating sensor data and workflows. The continuous flow of data provided e.g. by sensors requires new workflow models addressing the data perspective of these applications, since continuous data is potentially infinite while business process instances are always finite.\ud In this paper a formal workflow model is proposed with data driven coordination and explicating properties of the continuous data processing. These properties can be used to optimize data workflows, i.e., reducing the computational power for processing the workflows in an engine by reusing intermediate processing results in several workflows

HUDDL for description and archive of hydrographic binary data

Many of the attempts to introduce a universal hydrographic binary data format have failed or have been only partially successful. In essence, this is because such formats either have to simplify the data to such an extent that they only support the lowest common subset of all the formats covered, or they attempt to be a superset of all formats and quickly become cumbersome. Neither choice works well in practice. This paper presents a different approach: a standardized description of (past, present, and future) data formats using the Hydrographic Universal Data Description Language (HUDDL), a descriptive language implemented using the Extensible Markup Language (XML). That is, XML is used to provide a structural and physical description of a data format, rather than the content of a particular file. Done correctly, this opens the possibility of automatically generating both multi-language data parsers and documentation for format specification based on their HUDDL descriptions, as well as providing easy version control of them. This solution also provides a powerful approach for archiving a structural description of data along with the data, so that binary data will be easy to access in the future. Intending to provide a relatively low-effort solution to index the wide range of existing formats, we suggest the creation of a catalogue of format descriptions, each of them capturing the logical and physical specifications for a given data format (with its subsequent upgrades). A C/C++ parser code generator is used as an example prototype of one of the possible advantages of the adoption of such a hydrographic data format catalogue

Form, science, and narrative in the anthropocene

A significant strand of contemporary fiction engages with scientific models that highlight a constitutive interdependency between humanity and material realities such as the climate or the geological history of our planet. This article looks at the ways in which narrative may capture this human-nonhuman interrelation, which occupies the foreground of debates on the so-called Anthropocene. I argue that the formal dimension of scientific knowledge-as manifested by diagrams or metaphors used by scientists-is central to this narrative remediation. I explore two analogical strategies through which narrative may pursue a formal dialogue with science: clusters of metaphorical language and the global structuring of the plot. Rivka Galchen's novel Atmospheric Disturbances (2008), for instance, builds on a visual representation of meteorological patterns in a storm (lifted from an actual scientific paper) to stage the narrator's mental illness. Two other contemporary works (Orfeo by Richard Powers and A Tale for the Time Being by Ruth Ozeki) integrate scientific models through the overall design of the plot. By offering close readings of these novels, I seek to expand work in the area of New Formalism and show how formal choices are crucial to bringing together the human-scale world and more-than-human phenomena

Shingle 2.0: generalising self-consistent and automated domain discretisation for multi-scale geophysical models

The approaches taken to describe and develop spatial discretisations of the domains required for geophysical simulation models are commonly ad hoc, model or application specific and under-documented. This is particularly acute for simulation models that are flexible in their use of multi-scale, anisotropic, fully unstructured meshes where a relatively large number of heterogeneous parameters are required to constrain their full description. As a consequence, it can be difficult to reproduce simulations, ensure a provenance in model data handling and initialisation, and a challenge to conduct model intercomparisons rigorously. This paper takes a novel approach to spatial discretisation, considering it much like a numerical simulation model problem of its own. It introduces a generalised, extensible, self-documenting approach to carefully describe, and necessarily fully, the constraints over the heterogeneous parameter space that determine how a domain is spatially discretised. This additionally provides a method to accurately record these constraints, using high-level natural language based abstractions, that enables full accounts of provenance, sharing and distribution. Together with this description, a generalised consistent approach to unstructured mesh generation for geophysical models is developed, that is automated, robust and repeatable, quick-to-draft, rigorously verified and consistent to the source data throughout. This interprets the description above to execute a self-consistent spatial discretisation process, which is automatically validated to expected discrete characteristics and metrics.Comment: 18 pages, 10 figures, 1 table. Submitted for publication and under revie