scholarly journals An algorithm to detect and communicate the differences in computational models describing biological systems

2014 ◽  
Author(s):  
Martin Scharm ◽  
Olaf Wolkenhauer ◽  
Dagmar Waltemath
Keyword(s):  
Biological Networks ◽  
Computational Models ◽  
Biological Systems ◽  
Biomodels Database ◽  
Difference Detection ◽  
Model Repository ◽  
Mathematical Expressions ◽  
Collaborative Modelling ◽  
History Of ◽  
Over Time

Repositories, such as the BioModels Database and the Physiome Model Repository support the reuse of models and ensure transparency about results in publications linked to those models. With thousands of models available, a framework to track the differences between models and their versions is essential to compare and combine models. Difference detection allows users to study the history of models but also helps in the detection of errors and inconsistencies. However, current repositories lack suitable methods to track a model’s development over time. Consequently, researchers have problems to grasp the differences between models and their versions. Focusing on SBML and CellML, we developed an algorithm to accurately detect and describe differences between versions of a model with respect to (i) the models’ encoding, (ii) the structure of biological networks, and (iii) mathematical expressions. Our method is implemented in a comprehensive and open library called BiVeS. Our work facilitates the reuse and extension of existing models. It also supports collaborative modelling. Finally, it contributes to better reproducibility of modelling results and to the challenge of model provenance. Our algorithm is the first tailor-made detector of differences between versions of computational models in standard formats.

scholarly journals An algorithm to detect and communicate the differences in computational models describing biological systems

2014 ◽  
Author(s):  
Martin Scharm ◽  
Olaf Wolkenhauer ◽  
Dagmar Waltemath
Keyword(s):  
Biological Networks ◽  
Computational Models ◽  
Biological Systems ◽  
Biomodels Database ◽  
Difference Detection ◽  
Model Repository ◽  
Mathematical Expressions ◽  
Collaborative Modelling ◽  
History Of ◽  
Over Time

Repositories, such as the BioModels Database and the Physiome Model Repository support the reuse of models and ensure transparency about results in publications linked to those models. With thousands of models available, a framework to track the differences between models and their versions is essential to compare and combine models. Difference detection allows users to study the history of models but also helps in the detection of errors and inconsistencies. However, current repositories lack suitable methods to track a model’s development over time. Consequently, researchers have problems to grasp the differences between models and their versions. Focusing on SBML and CellML, we developed an algorithm to accurately detect and describe differences between versions of a model with respect to (i) the models’ encoding, (ii) the structure of biological networks, and (iii) mathematical expressions. Our method is implemented in a comprehensive and open library called BiVeS. Our work facilitates the reuse and extension of existing models. It also supports collaborative modelling. Finally, it contributes to better reproducibility of modelling results and to the challenge of model provenance. Our algorithm is the first tailor-made detector of differences between versions of computational models in standard formats.

scholarly journals COMODI: An ontology to characterise differences in versions of computational models in biology

2016 ◽  
Author(s):  
Martin Scharm ◽  
Dagmar Waltemath ◽  
Pedro Mendes ◽  
Olaf Wolkenhauer
Keyword(s):  
Computational Biology ◽  
Simulation Study ◽  
Computational Models ◽  
Open Model ◽  
Semantic Level ◽  
Difference Detection ◽  
Model Repository ◽  
Error Corrections ◽  
Systems Models ◽  
Over Time

Motivation: Open model repositories provide ready-to-reuse computational models of biological systems. Models within those repositories evolve over time, leading to many alternative and subsequent versions. Taken together, the underlying changes reflect a model’s provenance and thus can give valuable insights into the studied biology. Currently, however, changes cannot be semantically interpreted. To improve this situation, we developed an ontology of terms describing changes in computational biology models. The ontology can be used by scientists and within software to characterise model updates at the level of single changes. When studying or reusing a model, these annotations help with determining the relevance of a change in a given context. Methods: We manually studied changes in selected models from BioModels and the Physiome Model Repository. Using the BiVeS tool for difference detection, we then performed an automatic analysis of changes in all models published in these repositories. The resulting set of concepts led us to define candidate terms for the ontology. In a final step, we aggregated and classified these terms and built the first version of the ontology. Results: We present COMODI, an ontology needed because COmputational MOdels DIffer. It empowers users and software to describe changes in a model on the semantic level. COMODI also enables software to implement user-specific filter options for the display of model changes. Finally, COMODI is the next step towards predicting how a change in a model influences the simulation study. Conclusion: COMODI, coupled with our algorithm for difference detection, ensures the transparency of a model’s evolution and it enhances the traceability of updates and error corrections. Availability: COMODI is encoded in OWL. It is openly available at http://comodi.sems.uni-rostock.de/.

scholarly journals COMODI: An ontology to characterise differences in versions of computational models in biology

2016 ◽  
Author(s):  
Martin Scharm ◽  
Dagmar Waltemath ◽  
Pedro Mendes ◽  
Olaf Wolkenhauer
Keyword(s):  
Computational Biology ◽  
Simulation Study ◽  
Computational Models ◽  
Open Model ◽  
Semantic Level ◽  
Difference Detection ◽  
Model Repository ◽  
Error Corrections ◽  
Systems Models ◽  
Over Time

Motivation: Open model repositories provide ready-to-reuse computational models of biological systems. Models within those repositories evolve over time, leading to many alternative and subsequent versions. Taken together, the underlying changes reflect a model’s provenance and thus can give valuable insights into the studied biology. Currently, however, changes cannot be semantically interpreted. To improve this situation, we developed an ontology of terms describing changes in computational biology models. The ontology can be used by scientists and within software to characterise model updates at the level of single changes. When studying or reusing a model, these annotations help with determining the relevance of a change in a given context. Methods: We manually studied changes in selected models from BioModels and the Physiome Model Repository. Using the BiVeS tool for difference detection, we then performed an automatic analysis of changes in all models published in these repositories. The resulting set of concepts led us to define candidate terms for the ontology. In a final step, we aggregated and classified these terms and built the first version of the ontology. Results: We present COMODI, an ontology needed because COmputational MOdels DIffer. It empowers users and software to describe changes in a model on the semantic level. COMODI also enables software to implement user-specific filter options for the display of model changes. Finally, COMODI is the next step towards predicting how a change in a model influences the simulation study. Conclusion: COMODI, coupled with our algorithm for difference detection, ensures the transparency of a model’s evolution and it enhances the traceability of updates and error corrections. Availability: COMODI is encoded in OWL. It is openly available at http://comodi.sems.uni-rostock.de/.

scholarly journals Evolution of computational models in BioModels Database and the Physiome Model Repository

2018 ◽  
Vol 12 (1) ◽  
Author(s):  
Martin Scharm ◽  
Tom Gebhardt ◽  
Vasundra Touré ◽  
Andrea Bagnacani ◽  
Ali Salehzadeh-Yazdi ◽  
...  
Keyword(s):  
Computational Models ◽  
Biomodels Database ◽  
Model Repository

The Path of Standard Albanian Language Formation

2018 ◽  
Vol 5 (2) ◽  
pp. 106-115
Author(s):  
Sindorela Doli Kryeziu
Keyword(s):  
Single Unit ◽  
Cultural Factors ◽  
Language History ◽  
Whole Process ◽  
History Of ◽  
Social And Cultural Factors ◽  
Cultural Body ◽  
Over Time ◽  
Language Literature

Abstract In our paper we will talk about the whole process of standardization of the Albanian language, where it has gone through a long historical route, for almost a century.When talking about standard Albanian language history and according to Albanian language literature, it is often thought that the Albanian language was standardized in the Albanian Language Orthography Congress, held in Tirana in 1972, or after the publication of the Orthographic Rules (which was a project at that time) of 1967 and the decisions of the Linguistic Conference, a conference of great importance that took place in Pristina, in 1968. All of these have influenced chronologically during a very difficult historical journey, until the standardization of the Albanian language.Considering a slightly wider and more complex view than what is often presented in Albanian language literature, we will try to describe the path (history) of the standard Albanian formation under the influence of many historical, political, social and cultural factors that are known in the history of the Albanian people. These factors have contributed to the formation of a common state, which would have, over time, a common standard language.It is fair to think that "all activity in the development of writing and the Albanian language, in the field of standardization and linguistic planning, should be seen as a single unit of Albanian culture, of course with frequent manifestations of specific polycentric organization, either because of divisions within the cultural body itself, or because of the external imposition"(Rexhep Ismajli," In Language and for Language ", Dukagjini, Peja, 1998, pp. 15-18.)

Transocean and the History of Tax Inversions

2018 ◽  
Vol 34 (1) ◽  
pp. 1-12
Author(s):  
Susan M. Albring ◽  
Randal J. Elder ◽  
Mitchell A. Franklin
Keyword(s):  
Multinational Corporations ◽  
Economic Impacts ◽  
Income Taxes ◽  
Tax Rates ◽  
Corporate Tax ◽  
Corporate Income Taxes ◽  
History Of ◽  
Jobs Act ◽  
The U.S ◽  
Over Time

ABSTRACT The first tax inversion in 1983 was followed by small waves of subsequent inversion activity, including two inversions completed by Transocean. Significant media and political attention focused on transactions made by U.S. multinational corporations that were primarily designed to reduce U.S. corporate income taxes. As a result, the U.S. government took several actions to limit inversion activity. The Tax Cuts and Jobs Act of 2017 (TCJA) significantly lowered U.S. corporate tax rates and one expected impact of TCJA is a reduction of inversion activity. Students use the Transocean inversions to understand the reasons why companies complete a tax inversion and how the U.S. tax code affects inversion activity. Students also learn about the structure of inversion transactions and how they have changed over time as the U.S. government attempted to limit them. Students also assess the tax and economic impacts of inversion transactions to evaluate tax policy.

Historical Representations and Recent Changes

2018 ◽  
Author(s):  
Jürgen Schaflechner
Keyword(s):  
Comparative Analysis ◽  
South Asia ◽  
Oral Histories ◽  
Detailed History ◽  
Modern Times ◽  
History Of ◽  
Historical Representations ◽  
The Rich ◽  
Many Sources ◽  
Over Time

Chapter 3 introduces the tradition of ritual journeys and sacred geographies in South Asia, then hones in on a detailed history of the grueling and elaborate pilgrimage attached to the shrine of Hinglaj. Before the construction of the Makran Coastal Highway the journey to the Goddess’s remote abode in the desert of Balochistan frequently presented a lethally dangerous undertaking for her devotees, the hardships of which have been described by many sources in Bengali, Gujarati, Hindi, Sindhi, and Urdu. This chapter draws heavily from original sources, including travelogues and novels, which are supplanted with local oral histories in order to weave a historical tapestry that displays the rich array of practices and beliefs surrounding the pilgrimage and how they have changed over time. The comparative analysis demonstrates how certain motifs, such as austerity (Skt. tapasyā), remain important themes within the whole Hinglaj genre even in modern times while others have been lost in the contemporary era.

Introduction

2018 ◽  
Author(s):  
Marko Geslani
Keyword(s):  
Comparative Study ◽  
Royal Power ◽  
History Of ◽  
Historical Developments ◽  
The Comparative Study ◽  
The Relationship ◽  
Over Time ◽  
Indian Religion

The introduction reviews the historiographic problem of the relation between fire sacrifice (yajña) and image worship (pūjā), which have traditionally been seen as opposing ritual structures serving to undergird the distinction of “Vedic” and “Hindu.” Against such an icono- and theocentric approach, it proposes a history of the priesthood in relation to royal power, centering on the relationship between the royal chaplain (purohita) and astrologer (sāṃvatsara) as a crucial, unexplored development in early Indian religion. In order to capture these historical developments, it outlines a method for the comparative study of ritual forms over time.

The Growth of Historical Method in Tang China

2018 ◽  
Author(s):  
Charles Hartman ◽  
Anthony DeBlasi
Keyword(s):  
Eleventh Century ◽  
Seventh Century ◽  
Daily Production ◽  
Successor State ◽  
Historical Method ◽  
Official History ◽  
History Of ◽  
Over Time

This chapter discusses how the full emergence of the centralized, aristocratic state in the seventh century brought about an official historiography that was part of the bureaucracy of that state. Beginning in the Tang, each dynastic court maintained an office of historiography. Over time, a regularized process evolved that, in theory and often in reality, turned the daily production of court bureaucratic documents into an official history of the dynasty. Although this process was ongoing throughout the dynasty, the final, standard ‘dynastic history’ was usually completed after the dynasty's demise by its successor state. Indeed, the very concept of a series of dynastic histories that, taken together, would present an official history of successive, legitimate Chinese states, dates from the eleventh century.

scholarly journals TIME THROUGH TIME: ITS EVOLUTION THROUGH WESTERN PHILOSOPHY IN SEVEN IDEAS

Think ◽  
2021 ◽  
Vol 20 (58) ◽  
pp. 23-38
Author(s):  
Emily Thomas
Keyword(s):  
Western Philosophy ◽  
The World ◽  
History Of ◽  
Over Time

ABSTRACTWhat is time? Just like everything else in the world, our understanding of time has changed continually over time. This article tracks this question through the history of Western philosophy and looks at major answers from the likes of Aristotle, Kant, and McTaggart.

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