A Semantic-Based Approach to Attain Reproducibility of Computational Environments in Scientic Work ows: A Case Study

Reproducible research in scientic work ows is often addressed by tracking the provenance of the produced results. While this approach allows inspecting intermediate and nal results, improves understanding, and permits replaying a work ow execution, it does not ensure that the computational environment is available for subsequent executions to reproduce the experiment. In this work, we propose describing the resources involved in the execution of an experiment using a set of semantic vocabularies, so as to conserve the computational environment. We dene a process for documenting the work ow application, management system, and their dependencies based on 4 domain ontologies. We then conduct an experimental evaluation sing a real work ow application on an academic and a public Cloud platform. Results show that our approach can reproduce an equivalent execution environment of a predened virtual machine image on both computing platforms

3rd EGEE User Forum

We have organized this book in a sequence of chapters, each chapter associated with an application or technical theme introduced by an overview of the contents, and a summary of the main conclusions coming from the Forum for the chapter topic. The first chapter gathers all the plenary session keynote addresses, and following this there is a sequence of chapters covering the application flavoured sessions. These are followed by chapters with the flavour of Computer Science and Grid Technology. The final chapter covers the important number of practical demonstrations and posters exhibited at the Forum. Much of the work presented has a direct link to specific areas of Science, and so we have created a Science Index, presented below. In addition, at the end of this book, we provide a complete list of the institutes and countries involved in the User Forum

Universal History and the Emergence of Species Being

This paper seeks to recover the function of universal history, which was to place particulars into relation with universals. By the 20th century universal history was largely discredited because of an idealism that served to lend epistemic coherence to the overwhelming complexity arising from universal history's comprehensive scope. Idealism also attempted to account for history's being "open"--for the human ability to transcend circumstance. The paper attempts to recover these virtues without the idealism by defining universal history not by its scope but rather as a scientific method that provides an understanding of any kind of historical process, be it physical, biological or human. While this method is not new, it is in need of a development that offers a more robust historiography and warrant as a liberating historical consciousness. The first section constructs an ontology of process by defining matter as ontic probabilities rather than as closed entities. This is lent warrant in the next section through an appeal to contemporary physical science. The resulting conceptual frame and method is applied to the physical domain of existents, to the biological domain of social being and finally to the human domain of species being. It is then used to account for the emergence of human history's initial stage--the Archaic Socio-Economic Formation and for history' stadial trajectory--its alternation of evolution and revolution

A Semantic-Based Approach to Attain Reproducibility of Computational Environments in Scientific Workflows: A Case Study

Abstract. Reproducible research in scientific workflows is often addressed by tracking the provenance of the produced results. While this approach allows inspecting intermediate and final results, improves understanding, and permits replaying a workflow execution, it does not ensure that the computational environment is available for subsequent executions to reproduce the experiment. In this work, we propose describing the resources involved in the execution of an experiment using a set of semantic vocabularies, so as to conserve the computational environment. We define a process for documenting the workflow application, management system, and their dependencies based on 4 domain ontologies. We then conduct an experimental evaluation using a real workflow application on an academic and a public Cloud platform. Results show that our approach can reproduce an equivalent execution environment of a predefined virtual machine image on both computing platforms

A Semantic-Based Approach to Attain Reproducibility of Computational Environments in Scientific Workflows: A Case Study

Abstract. Reproducible research in scientific workflows is often addressed by tracking the provenance of the produced results. While this approach allows inspecting intermediate and final results, improves understanding, and permits replaying a workflow execution, it does not ensure that the computational environment is available for subsequent executions to reproduce the experiment. In this work, we propose describing the resources involved in the execution of an experiment using a set of semantic vocabularies, so as to conserve the computational environment. We define a process for documenting the workflow application, management system, and their dependencies based on 4 domain ontologies. We then conduct an experimental evaluation using a real workflow application on an academic and a public Cloud platform. Results show that our approach can reproduce an equivalent execution environment of a predefined virtual machine image on both computing platforms

Emerging Informatics

The book on emerging informatics brings together the new concepts and applications that will help define and outline problem solving methods and features in designing business and human systems. It covers international aspects of information systems design in which many relevant technologies are introduced for the welfare of human and business systems. This initiative can be viewed as an emergent area of informatics that helps better conceptualise and design new world-class solutions. The book provides four flexible sections that accommodate total of fourteen chapters. The section specifies learning contexts in emerging fields. Each chapter presents a clear basis through the problem conception and its applicable technological solutions. I hope this will help further exploration of knowledge in the informatics discipline

SciTech News Volume 70, No. 1 (2016)

Columns and Reports From the Editor 3 SciTech News Call for Articles 3 Assistant Editor wanted 4 Division News Science-Technology Division 5 Chemistry Division 7 Engineering Division 12 Aerospace Section of the Engineering Division 13 Call for Nominations & Applications Sparks Award for Professional Development11 Reviews Sci-Tech Book News Reviews 1

Governing data in modernity/coloniality: astronomy data in the Atacama Desert and the struggle for collective autonomy

In recent years, different actors in Chile have portrayed the vast volumes of astronomy data produced by international observatories in the Atacama Desert as a unique opportunity for scientific and economic development. Research, policy and corporate initiatives have been put into place to leverage this situation. In this thesis I examine the governance of this data by developing a framework based on collective autonomy. Unlike the paradigms of openness and sovereignty, collective autonomy speaks to long-standing concerns related to social justice in Latin America that took shape in parallel with European colonialism. This framework builds upon decolonial thinking and mobilised groups in the region, situating the analysis in the context of a capitalist modern/colonial world system. Collective autonomy also draws on post-Marxism, foregrounding dissenting voices and examining the changing positionalities of the parties involved. In analytical terms, I approach interviews, field notes and policy documents from a discursive-material perspective sensitive to the role of both meaning and matter. The empirical chapters explore three different spheres. First, I look at the implementation of dataintensive research and examine how the articulation of a new positionality by local actors favours an obedient stance in knowledge generation. After that, I turn to the economy and trace emerging meanings of development, extractivism and the state as actors make sense of what is going on with astronomy data. Finally, I connect the expansion of data infrastructure in Chile with the long-standing threat to Indigenous worlds cultivating balanced modes of existence in the territory. As this thesis shows, collective autonomy introduces previously ignored concerns and changes the actors, scales and aims at stake in the governance of data. Furthermore, this framework aims to depart from the precepts of capitalist modernity and, instead, supports decoloniality and the flourishing of multiple worlds

Science, labor and scientific progress

My dissertation introduces a new materialist theory of scientific progress built on a novel characterization of scientific work and an analysis of progress appropriate to it. Two questions, crucial for understanding scientific progress, are answered: a. Why is it possible for scientists at a given time to have more epistemic abilities than scientists at an earlier time? b. How can knowledge acquired in the past be used in on-going or future research? I argue that these questions are best answered by analyzing science as a form of labor. The elements of the labor process, involving both intellectual and material means, provide a starting-point for the systematic study of how scientific abilities evolve. As a unit of analysis, the labor process exposes features of the dynamics of knowledge accumulation that traditional analyses do not. I analyze historical cases from chemistry and the Scientific Revolution, attending carefully to how scientific work is conducted and conceived. First, I argue that scientific progress consists not just in the growth of theoretical or empirical knowledge, as in traditional philosophy of science, but also in the growth of know-how. The tools of science play a crucial role in determining the abilities scientists can and must have to do science. Tools also determine how scientists’ abilities change over time, by enabling, but also constraining, the incorporation of knowledge into the labor process. I argue that an extremely important mechanism of progress in science consists of a feedback loop between the production of new knowledge and instrument construction. This process requires the integration, and transformation into material form, of different kinds of knowledge. As the process is repeated over the long term, scientific work is transformed because it becomes less dependent on native human epistemic abilities. Second, the evolution of scientific abilities depends on ambient ideological conditions: Social attitudes towards different kinds of work are critical, as are notions about the proper object of science. What results is a picture of scientific change involving the interactions of different kinds of knowledge and in which internal and external factors, as well as instrumental rationality, play a significant role

Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv

Background: The automation of data analysis in the form of scientific workflows has become a widely adopted practice in many fields of research. Computationally driven data-intensive experiments using workflows enable Automation, Scaling, Adaption and Provenance support (ASAP). However, there are still several challenges associated with the effective sharing, publication and reproducibility of such workflows due to the incomplete capture of provenance and lack of interoperability between different technical (software) platforms. Results: Based on best practice recommendations identified from literature on workflow design, sharing and publishing, we define a hierarchical provenance framework to achieve uniformity in the provenance and support comprehensive and fully re-executable workflows equipped with domain-specific information. To realise this framework, we present CWLProv, a standard-based format to represent any workflow-based computational analysis to produce workflow output artefacts that satisfy the various levels of provenance. We utilise open source community-driven standards; interoperable workflow definitions in Common Workflow Language (CWL), structured provenance representation using the W3C PROV model, and resource aggregation and sharing as workflow-centric Research Objects (RO) generated along with the final outputs of a given workflow enactment. We demonstrate the utility of this approach through a practical implementation of CWLProv and evaluation using real-life genomic workflows developed by independent groups. Conclusions: The underlying principles of the standards utilised by CWLProv enable semantically-rich and executable Research Objects that capture computational workflows with retrospective provenance such that any platform supporting CWL will be able to understand the analysis, re-use the methods for partial re-runs, or reproduce the analysis to validate the published findings.Submitted to GigaScience (GIGA-D-18-00483