Connecting Scientific Data to Scientific Experiments with Provenance

As scientific workflows and the data they operate on, grow in size and complexity, the task of defining how those workflows should execute (which resources to use, where the resources must be in readiness for processing etc.) becomes proportionally more difficult. While "workflow compilers", such as Pegasus, reduce this burden, a further problem arises: since specifying details of execution is now automatic, a workflow's results are harder to interpret, as they are partly due to specifics of execution. By automating steps between the experiment design and its results, we lose the connection between them, hindering interpretation of results. To reconnect the scientific data with the original experiment, we argue that scientists should have access to the full provenance of their data, including not only parameters, inputs and intermediary data, but also the abstract experiment, refined into a concrete execution by the "workflow compiler". In this paper, we describe preliminary work on adapting Pegasus to capture the process of workflow refinement in the PASOA provenance system.

The Requirements of Using Provenance in e-Science Experiments

In e-Science experiments, it is vital to record the experimental process for later use such as in interpreting results, verifying that the correct process took place or tracing where data came from. The process that led to some data is called the provenance of that data, and a provenance architecture is the software architecture for a system that will provide the necessary functionality to record, store and use process documentation. However, there has been little principled analysis of what is actually required of a provenance architecture, so it is impossible to determine the functionality they would ideally support. In this paper, we present use cases for a provenance architecture from current experiments in biology, chemistry, physics and computer science, and analyse the use cases to determine the technical requirements of a generic, technology and application-independent architecture. We propose an architecture that meets these requirements and evaluate a preliminary implementation by attempting to realise two of the use cases.

Provenance-based Validation of E-Science Experiments

E-Science experiments typically involve many distributed services maintained by different organisations. After an experiment has been executed, it is useful for a scientist to verify that the execution was performed correctly or is compatible with some existing experimental criteria or standards, not necessarily anticipated prior to execution. Scientists may also want to review and verify experiments performed by their colleagues. There are no existing frameworks for validating such experiments in today's e-Science systems. Users therefore have to rely on error checking performed by the services, or adopt other ad hoc methods. This paper introduces a platform-independent framework for validating workflow executions. The validation relies on reasoning over the documented provenance of experiment results and semantic descriptions of services advertised in a registry. This validation process ensures experiments are performed correctly, and thus results generated are meaningful. The framework is tested in a bioinformatics application that performs protein compressibility analysis.

Provenance: The Bridge Between Experiments and Data

Current scientific applications are often structured as workflows and rely on workflow systems to compile abstract experiment designs into enactable workflows that utilise the best available resources. The automation of this step and of the workflow enactment, hides the details of how results have been produced. Knowing how compilation and enactment occurred allows results to be reconnected with the experiment design. We investigate how provenance helps scientists to connect their results with the actual execution that took place, their original experiment and its inputs and parameters.

Digital alchemy : two experiments in form processing

Programmatic form-finding and the visual analysis of creative works (architecture, sound, sculpture, painting, music or dance) can be combined to develop “alchemical” processes for the computational exploration of form. This paper reports two project-based form exploration experiments using such a process. The first experiment develops a process for capturing, manipulating and generating form based on a piece of dance choreography. The second experiment explores the decompression of space and architectural elements encoded within the Duchamp painting “Nude descending a staircase”. A discussion for incorporating programmatic strategies and for developing an innovative approach to conceptual form processing based on the language of geometry is presented.

Securing participation : experiments in a one-day introduction to economics

Classroom experiments and exercises served as a one-day introduction to economics for students who felt insecure about taking first-year business classes. The first experiment addresses demand in isolation, while the second addresses supply. Supply, demand and equilibrium are integrated in a pit market in which all students have equal expected profits. A monopoly pricing exercise addresses market failure. Exercises use many incremental questions to reveal principles of microeconomics. Evaluations show that at the end of the program, students were familiar with economic results and concepts, and were more comfortable with talking economics.

Heterologous microarray experiments used to identify the early gene response to heat stress in a coral reef fish

Coral reef fishes are expected to experience rising sea surface temperatures due to climate change. How well tropical reef fishes will respond to these increased temperatures and which genes are important in the response to elevated temperatures is not known. Microarray technology provides a powerful tool for gene discovery studies, but the development of microarrays for individual species can be expensive and time-consuming. In this study, we tested the suitability of a Danio rerio oligonucleotide microarray for application in a species with few genomic resources, the coral reef fish Pomacentrus moluccensis. Results from a comparative genomic hybridization experiment and direct sequence comparisons indicate that for most genes there is considerable sequence similarity between the two species, suggesting that the D. rerio array is useful for genomic studies of P. moluccensis. We employed this heterologous microarray approach to characterize the early transcriptional response to heat stress in P. moluccensis. A total of 111 gene loci, many of which are involved in protein processing, transcription, and cell growth, showed significant changes in transcript abundance following exposure to elevated temperatures. Changes in transcript abundance were validated for a selection of candidate genes using quantitative real-time polymerase chain reaction. This study demonstrates that heterologous microarrays can be successfully employed to study species for which specific microarrays have not yet been developed, and so have the potential to greatly enhance the utility of microarray technology to the field of environmental and functional genomics.

An Injection-locked Diode Laser for Cold Rydberg Atom Experiments

A free-running, temperature stabilized diode laser has been injection-locked to an external cavity diode laser for use in cold Rydberg atom experiments. Cold rubidium atoms in a magneto-optical trap (MOT) are excited to Rydberg states using a 10 ns laser pulse. The Rydberg atoms spontaneously ionize due to dipole forces, and the collisional ionization dynamics are observed as a function of atom density and principal quantum number of the Rydberg state, n. The injection-locked diode laser will be used as a repumper in conjunction with a dark spontaneous-force optical trap (SPOT) to increase the Rydberg state density. We report on the design of the injection-locked laser system.

South Pacific museums : experiments in culture

A collection of outstanding analyses of museums in the South Pacific, written by cultural, museum and architectural critics, and historians. A series of snapshots introduce the reader to key museums in the region and longer essays explore these museums in broad terms.

Democracy, global transitions, and education : using speculative fictions as thought experiments in anticipatory critical inquiry

The purpose of a thought experiment, as the term was used by quantum and relativity physicists in the early part of the twentieth century, was not prediction (as is the goal of classical experimental science), but more defensible representations of present 'realities'. Indeed, one of the best-known examples of a thought experiment ('Schrodinger's cat') demonstrates the impossibility of prediction at the quantum level. Speculative fictions, from Mary Shelley's Frankenstein to the Star Wars saga, can be read as socio-technical thought experiments that can help us to apprehend and comprehend present 'realities' and uncertainties, and to anticipate and critique possible futures. In this paper I will demonstrate how two examples of popular speculative fictions, Frank Herbert's Dune (1965) and Ursula Le Guin's The Telling (2000), can be read as thought experiments that describe problematic aspects of contemporary social and cultural transformations. I will argue that critical and deconstructive readings of these novels can help us to produce anticipatory critiques of possible ways in which democratic institutions are being transformed by globalisation. I will conclude by considering the implications of such anticipatory critiques for generating questions, problems and issues in educational inquiry and for choosing appropriate methodologies for investigating them.

Design of experiments and springback prediction for AHSS automotive components with complex geometry

With the drive towards implementing Advanced High Strength Steels (AHSS) in the automotive industry; stamping engineers need to quickly answer questions about forming these strong materials into elaborate shapes.
Commercially available codes have been successfully used to accurately predict formability, thickness and strains in complex parts. However, springback and twisting are still challenging subjects in numerical simulations of AHSS components. Design of Experiments (DOE) has been used in this paper to study the sensitivity of the implicit and explicit numerical results with respect to certain arrays ofuser input parameters in the forming ofan AHSS component. Numerical results were compared to experimental measurements of the parts stamped in an industrial production line. The forming predictions of the implicit and explicit codes were in good agreement with the experimental measurements for the conventional steel grade, while lower accuracies were observed for the springback predictions. The forming
predictions of the complex component with an AHSS material were also in good correlation with the respective experimental measurements. However, much lower accuracies were observed in its springback predictions. The number of integration points through the thickness and tool offset were found to be of significant importance, while coefficient of friction and Young's modulus (modeling input parameters) have no significant effect on the accuracy of the predictions for the complex geometry.