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 Combined Release and Radiation Effects Satellite Program, CRRES : a unique series of scientific experiments.

Mode of access: Internet.

The resources of the sea as shown in the scientific experiments to test the effects of trawling and of the closure of certain areas off the Scottish shores,

Mode of access: Internet.

Conservation of Computational Scientific Execution Environments for Workflow-based Experiments Using Ontologies

La reproducibilidad de estudios y resultados científicos es una meta a tener en cuenta por cualquier científico a la hora de publicar el producto de una investigación. El auge de la ciencia computacional, como una forma de llevar a cabo estudios empíricos haciendo uso de modelos matemáticos y simulaciones, ha derivado en una serie de nuevos retos con respecto a la reproducibilidad de dichos experimentos. La adopción de los flujos de trabajo como método para especificar el procedimiento científico de estos experimentos, así como las iniciativas orientadas a la conservación de los datos experimentales desarrolladas en las últimas décadas, han solucionado parcialmente este problema. Sin embargo, para afrontarlo de forma completa, la conservación y reproducibilidad del equipamiento computacional asociado a los flujos de trabajo científicos deben ser tenidas en cuenta. La amplia gama de recursos hardware y software necesarios para ejecutar un flujo de trabajo científico hace que sea necesario aportar una descripción completa detallando que recursos son necesarios y como estos deben de ser configurados. En esta tesis abordamos la reproducibilidad de los entornos de ejecución para flujos de trabajo científicos, mediante su documentación usando un modelo formal que puede ser usado para obtener un entorno equivalente. Para ello, se ha propuesto un conjunto de modelos para representar y relacionar los conceptos relevantes de dichos entornos, así como un conjunto de herramientas que hacen uso de dichos módulos para generar una descripción de la infraestructura, y un algoritmo capaz de generar una nueva especificación de entorno de ejecución a partir de dicha descripción, la cual puede ser usada para recrearlo usando técnicas de virtualización. Estas contribuciones han sido aplicadas a un conjunto representativo de experimentos científicos pertenecientes a diferentes dominios de la ciencia, exponiendo cada uno de ellos diferentes requisitos hardware y software. Los resultados obtenidos muestran la viabilidad de propuesta desarrollada, reproduciendo de forma satisfactoria los experimentos estudiados en diferentes entornos de virtualización. ABSTRACT Reproducibility of scientific studies and results is a goal that every scientist must pursuit when announcing research outcomes. The rise of computational science, as a way of conducting empirical studies by using mathematical models and simulations, have opened a new range of challenges in this context. The adoption of workflows as a way of detailing the scientific procedure of these experiments, along with the experimental data conservation initiatives that have been undertaken during last decades, have partially eased this problem. However, in order to fully address it, the conservation and reproducibility of the computational equipment related to them must be also considered. The wide range of software and hardware resources required to execute a scientific workflow implies that a comprehensive description detailing what those resources are and how they are arranged is necessary. In this thesis we address the issue of reproducibility of execution environments for scientific workflows, by documenting them in a formalized way, which can be later used to obtain and equivalent one. In order to do so, we propose a set of semantic models for representing and relating the relevant information of those environments, as well as a set of tools that uses these models for generating a description of the infrastructure, and an algorithmic process that consumes these descriptions for deriving a new execution environment specification, which can be enacted into a new equivalent one using virtualization solutions. We apply these three contributions to a set of representative scientific experiments, belonging to different scientific domains, and exposing different software and hardware requirements. The obtained results prove the feasibility of the proposed approach, by successfully reproducing the target experiments under different virtualization environments.

Pattern-Based Evaluation of Scientific Workflow Management Systems

In recent years several scientific Workflow Management Systems (WfMSs) have been developed with the aim to automate large scale scientific experiments. As yet, many offerings have been developed, but none of them has been promoted as an accepted standard. In this paper we propose a pattern-based evaluation of three among the most widely used scientific WfMSs: Kepler, Taverna and Triana. The aim is to compare them with traditional business WfMSs, emphasizing the strengths and deficiencies of both systems. Moreover, a set of new patterns is defined from the analysis of the three considered systems.

The scientific project of the small satellite of china

The efforts involved in developing a small satellite for scientific purposes in China in recent years are introduced in the present paper. The project is arranged on a case to case principle depending upon requirements and financial support. The space technology of a satellite and rockets, which have been developed over a relatively longer period in China, have been transferred to the scientific research of small satellites for improvement of the quality requirements. The surplus payloads of the rocket and satellite are used as the payloads of the small satellite and scientific experiments at a low cost. As an example, the project of balloon satellites for atmospheric research was successfully completed in 1991. The experience of the project management is of great benefit for further organization and arrangement of other projects. Opportunities exist for surplus payloads to be used in the future, and a small satellite for magnetospheric research will be launched in 1993.

Enabling Scientific Workflow Sharing through Coarse-Grained Interoperability

E-scientists want to run their scientific experiments on Distributed Computing Infrastructures (DCI) to be able to access large pools of resources and services. To run experiments on these infrastructures requires specific expertise that e-scientists may not have. Workflows can hide resources and services as a virtualization layer providing a user interface that e-scientists can use. There are many workflow systems used by research communities but they are not interoperable. To learn a workflow system and create workflows in this workflow system may require significant efforts from e-scientists. Considering these efforts it is not reasonable to expect that research communities will learn new workflow systems if they want to run workflows developed in other workflow systems. The solution is to create workflow interoperability solutions to allow workflow sharing. The FP7 Sharing Interoperable Workflow for Large-Scale Scientific Simulation on Available DCIs (SHIWA) project developed two interoperability solutions to support workflow sharing: Coarse-Grained Interoperability (CGI) and Fine-Grained Interoperability (FGI). The project created the SHIWA Simulation Platform (SSP) to implement the Coarse-Grained Interoperability approach as a production-level service for research communities. The paper describes the CGI approach and how it enables sharing and combining existing workflows into complex applications and run them on Distributed Computing Infrastructures. The paper also outlines the architecture, components and usage scenarios of the simulation platform.

Common motifs in scientific workflows: An empirical analysis

While workflow technology has gained momentum in the last decade as a means for specifying and enacting computational experiments in modern science, reusing and repurposing existing workflows to build new scientific experiments is still a daunting task. This is partly due to the difficulty that scientists experience when attempting to understand existing workflows, which contain several data preparation and adaptation steps in addition to the scientifically significant analysis steps. One way to tackle the understandability problem is through providing abstractions that give a high-level view of activities undertaken within workflows. As a first step towards abstractions, we report in this paper on the results of a manual analysis performed over a set of real-world scientific workflows from Taverna and Wings systems. Our analysis has resulted in a set of scientific workflow motifs that outline i) the kinds of data intensive activities that are observed in workflows (data oriented motifs), and ii) the different manners in which activities are implemented within workflows (workflow oriented motifs). These motifs can be useful to inform workflow designers on the good and bad practices for workflow development, to inform the design of automated tools for the generation of workflow abstractions, etc.

Mining Abstractions in Scientific Workows

Los flujos de trabajo científicos han sido adoptados durante la última década para representar los métodos computacionales utilizados en experimentos in silico, así como para dar soporte a sus publicaciones asociadas. Dichos flujos de trabajo han demostrado ser útiles para compartir y reproducir experimentos científicos, permitiendo a investigadores visualizar, depurar y ahorrar tiempo a la hora de re-ejecutar un trabajo realizado con anterioridad. Sin embargo, los flujos de trabajo científicos pueden ser en ocasiones difíciles de entender y reutilizar. Esto es debido a impedimentos como el gran número de flujos de trabajo existentes en repositorios, su heterogeneidad o la falta generalizada de documentación y ejemplos de uso. Además, dado que normalmente es posible implementar un mismo método utilizando algoritmos o técnicas distintas, flujos de trabajo aparentemente distintos pueden estar relacionados a un determinado nivel de abstracción, basándose, por ejemplo, en su funcionalidad común. Esta tesis se centra en la reutilización de flujos de trabajo y su abstracción mediante la exploración de relaciones entre los flujos de trabajo de un repositorio y la extracción de abstracciones que podrían ayudar a la hora de reutilizar otros flujos de trabajo existentes. Para ello, se propone un modelo simple de representación de flujos de trabajo y sus ejecuciones, se analizan las abstracciones típicas que se pueden encontrar en los repositorios de flujos de trabajo, se exploran las prácticas habituales de los usuarios a la hora de reutilizar flujos de trabajo existentes y se describe un método para descubrir abstracciones útiles para usuarios, basadas en técnicas existentes de teoría de grafos. Los resultados obtenidos exponen las abstracciones y prácticas comunes de usuarios en términos de reutilización de flujos de trabajo, y muestran cómo las abstracciones que se extraen automáticamente tienen potencial para ser reutilizadas por usuarios que buscan diseñar nuevos flujos de trabajo. Abstract Scientific workflows have been adopted in the last decade to represent the computational methods used in in silico scientific experiments and their associated research products. Scientific workflows have demonstrated to be useful for sharing and reproducing scientific experiments, allowing scientists to visualize, debug and save time when re-executing previous work. However, scientific workflows may be difficult to understand and reuse. The large amount of available workflows in repositories, together with their heterogeneity and lack of documentation and usage examples may become an obstacle for a scientist aiming to reuse the work from other scientists. Furthermore, given that it is often possible to implement a method using different algorithms or techniques, seemingly disparate workflows may be related at a higher level of abstraction, based on their common functionality. In this thesis we address the issue of reusability and abstraction by exploring how workflows relate to one another in a workflow repository, mining abstractions that may be helpful for workflow reuse. In order to do so, we propose a simple model for representing and relating workflows and their executions, we analyze the typical common abstractions that can be found in workflow repositories, we explore the current practices of users regarding workflow reuse and we describe a method for discovering useful abstractions for workflows based on existing graph mining techniques. Our results expose the common abstractions and practices of users in terms of workflow reuse, and show how our proposed abstractions have potential to become useful for users designing new workflows.

Patterns

In recent years there has been widespread interest in patterns, perhaps provoked by a realisation that they constitute a fundamental brain activity and underpin many artificial intelligence systems. Theorised concepts of spatial patterns including scale, proportion, and symmetry, as well as social and psychological understandings are being revived through digital/parametric means of visualisation and production. The effect of pattern as an ornamental device has also changed from applied styling to mediated dynamic effect. The interior has also seen patterned motifs applied to wall coverings, linen, furniture and artefacts with the effect of enhancing aesthetic appreciation, or in some cases causing psychological and/or perceptual distress (Rodemann 1999). ----- ----- While much of this work concerns a repeating array of surface treatment, Philip Ball’s The Self- Made Tapestry: Pattern Formation in Nature (1999) suggests a number of ways that patterns are present at the macro and micro level, both in their formation and disposition. Unlike the conventional notion of a pattern being the regular repetition of a motif (geometrical or pictorial) he suggests that in nature they are not necessarily restricted to a repeating array of identical units, but also include those that are similar rather than identical (Ball 1999, 9). From his observations Ball argues that they need not necessarily all be the same size, but do share similar features that we recognise as typical. Examples include self-organized patterns on a grand scale such as sand dunes, or fractal networks caused by rivers on hills and mountains, through to patterns of flow observed in both scientific experiments and the drawings of Leonardo da Vinci.

Technology transfer evaluation in the high technology industry : an interdisciplinary perspective

The underlying objective of this study was to develop a novel approach to evaluate the potential for commercialisation of a new technology. More specifically, this study examined the 'ex-ante'. evaluation of the technology transfer process. For this purpose, a technology originating from the high technology sector was used. The technology relates to the application of software for the detection of weak signals from space, which is an established method of signal processing in the field of radio astronomy. This technology has the potential to be used in commercial and industrial areas other than astronomy, such as detecting water leakages in pipes. Its applicability to detecting water leakage was chosen owing to several problems with detection in the industry as well as the impact it can have on saving water in the environment. This study, therefore, will demonstrate the importance of interdisciplinary technology transfer. The study employed both technical and business evaluation methods including laboratory experiments and the Delphi technique to address the research questions. There are several findings from this study. Firstly, scientific experiments were conducted and these resulted in a proof of concept stage of the chosen technology. Secondly, validation as well as refinement of criteria from literature that can be used for „ex-ante. evaluation of technology transfer has been undertaken. Additionally, after testing the chosen technology.s overall transfer potential using the modified set of criteria, it was found that the technology is still in its early stages and will require further development for it to be commercialised. Furthermore, a final evaluation framework was developed encompassing all the criteria found to be important. This framework can help in assessing the overall readiness of the technology for transfer as well as in recommending a viable mechanism for commercialisation. On the whole, the commercial potential of the chosen technology was tested through expert opinion, thereby focusing on the impact of a new technology and the feasibility of alternate applications and potential future applications.

Quantification of the inevitable: the influence of soil macrofauna on soil water movement in rehabilitated open-cut mined lands

Recolonisation of soil by macrofauna (especially ants, termites and earthworms) in rehabilitated open-cut mine sites is inevitable and, in terms of habitat restoration and function, typically of great value. In these highly disturbed landscapes, soil invertebrates play a major role in soil development (macropore configuration, nutrient cycling, bioturbation, etc.) and can influence hydrological processes such as infiltration, seepage, runoff generation and soil erosion. Understanding and quantifying these ecosystem processes is important in rehabilitation design, establishment and subsequent management to ensure progress to the desired end goal, especially in waste cover systems designed to prevent water reaching and transporting underlying hazardous waste materials. However, the soil macrofauna is typically overlooked during hydrological modelling, possibly due to uncertainties on the extent of their influence, which can lead to failure of waste cover systems or rehabilitation activities. We propose that scientific experiments under controlled conditions and field trials on post-mining lands are required to quantify (i) macrofauna–soil structure interactions, (ii) functional dynamics of macrofauna taxa,and (iii) their effects on macrofauna and soil development over time. Such knowledge would provide crucial information for soil water models, which would increase confidence in mine waste cover design recommendations and eventually lead to higher likelihood of rehabilitation success of open-cut mining land.

Onko eläimillä oikeuksia? : Eläinkoelainsäädännön kehitys ja nykytila

The use of animals in scientific experiments tends to arouse strong emotional reactions among the general public, the most essential concern being the pain and suffering they cause. It is felt that suffering inflicted on other beings, including animals, is not morally acceptable. Is the function of a researcher who uses animals morally acceptable and beneficial for humans and animals? May such a researcher him/herself decide what animal experiments he/she can perform or should some outsider have the right to decide what kind of experiments a researcher can or cannot perform? The research material comprises the legislation of Finland and that of some member and non-member states of the European Union, together with European Union directives and pertinent preparatory parliamentary documents. The author has likewise studied the vast literature on animal rights, both pro and contra writings and opinions. The opinions of philosophers on the moral and legal rights of animals are markedly conflicting. Some strongly support the existence of rights, while others totally refute such an opinion, claiming that the question is only of the moral principles of man himself which imply that animals must be treated in a human manner. Speaking of animal rights only tends to muddle ideas on the one hand in philosophical considerations and in legal analyses on the other. The development of legislation in Finland and some other member states of the European Union has in principle been similar. In Finland, the positive laws on animal experiments nowadays comply with the EU directive 86/609/EEC. However, there are marked differences between member states in respect of the way they have in practice implemented the principles of the EU directive. No essential alterations have in practice been discernible in the actual performance of animal experiments during the decades when legislation has been developed in different countries. Self-regulation within the scientific community has been markedly more effectual than legislative procedures. Legal regulation has nevertheless clearly influenced the quality of breeding and life conditions of experimental laboratory animals, cages for example being nowadays larger than hitherto. EU parliament and council have now accepted in September 2010 a new directive on animal experiments which must be implemented in the national legislations by January 1, 2013.

FIN-CLARIN: A Framework for Depositing and Disseminating Language Resources for R&D

Researchers and developers in academia and industry would benefit from a facility that enables them to easily locate, licence and use the kind of empirical data they need for testing and refining their hypotheses and to deposit and disseminate their data e.g. to support replication and validation of reported scientific experiments. To answer these needs initially in Finland, there is an ongoing project at University of Helsinki and its collaborators to create a user-friendly web service for researchers and developers in Finland and other countries. In our talk, we describe ongoing work to create a palette of extensive but easily available Finnish language resources and technologies for the research community, including lexical resources, wordnets, morphologically tagged corpora, dependency syntactic treebanks and parsebanks, open-source finite state toolkits and libraries and language models to support text analysis and processing at customer site. Also first publicly available results are presented.