scholarly journals MEMOPS: Data modelling and automatic code generation

2010 ◽  
Vol 7 (3) ◽  
Author(s):  
Rasmus H. Fogh ◽  
Wayne Boucher ◽  
John M.C. Ionides ◽  
Wim F. Vranken ◽  
Tim J. Stevens ◽  
...  
Keyword(s):  
Data Storage ◽  
Code Generation ◽  
Data Access ◽  
Biological Data ◽  
Metadata Standards ◽  
Application Programming ◽  
Definition Of ◽  
The Individual ◽  
Automatic Code ◽  
Computational Analyses

SummaryIn recent years the amount of biological data has exploded to the point where much useful information can only be extracted by complex computational analyses. Such analyses are greatly facilitated by metadata standards, both in terms of the ability to compare data originating from different sources, and in terms of exchanging data in standard forms, e.g. when running processes on a distributed computing infrastructure. However, standards thrive on stability whereas science tends to constantly move, with new methods being developed and old ones modified. Therefore maintaining both metadata standards, and all the code that is required to make them useful, is a non-trivial problem. Memops is a framework that uses an abstract definition of the metadata (described in UML) to generate internal data structures and subroutine libraries for data access (application programming interfaces - APIs - currently in Python, C and Java) and data storage (in XML files or databases). For the individual project these libraries obviate the need for writing code for input parsing, validity checking or output. Memops also ensures that the code is always internally consistent, massively reducing the need for code reorganisation. Across a scientific domain a Memops-supported data model makes it easier to support complex standards that can capture all the data produced in a scientific area, share them among all programs in a complex software pipeline, and carry them forward to deposition in an archive. The principles behind the Memops generation code will be presented, along with example applications in Nuclear Magnetic Resonance (NMR) spectroscopy and structural biology.

scholarly journals A formal pattern of information system design

2021 ◽  
Vol 2094 (3) ◽  
pp. 032045
Author(s):  
A Y Unger
Keyword(s):  
Information Systems ◽  
Data Storage ◽  
Application Programming Interface ◽  
Data Access ◽  
Server Side ◽  
Data Access Control ◽  
Independent Information ◽  
Application Logic ◽  
Application Programming ◽  
Client Side

Abstract A new design pattern intended for distributed cloud-based information systems is proposed. Pattern is based on the traditional client-server architecture. The server side is divided into three principal components: data storage, application server and cache server. Each component can be used to deploy parts of several independent information systems, thus realizing shared-resource approach. A strategy of separation of competencies between the client and the server is proposed. The strategy assumes that the client side is responsible for application logic and the server side is responsible for data storage consistency and data access control. Data protection is ensured by means of two particular approaches: at the entity level and at the transaction level. The application programming interface to access data is presented at the level of identified transaction descriptors.

scholarly journals MUPIF WORKFLOW EDITOR AND AUTOMATIC CODE GENERATOR

2020 ◽  
Vol 26 ◽  
pp. 107-111
Author(s):  
Stanislav Šulc ◽  
Vít Šmilauer ◽  
Bořek Patzák
Keyword(s):  
Code Generation ◽  
Automatic Code Generation ◽  
Graphical Interface ◽  
Code Generator ◽  
Data Dependencies ◽  
Mechanical Simulation ◽  
Computational Code ◽  
Easy Integration ◽  
Definition Of ◽  
Automatic Code

Integrating applications or codes into MuPIF API Model enables easy integration of such APIs into any workflow representing complex multiphysical simulation. This concept of MuPIF also enables automatic code generation of the computational code for given workflow structure. This article describes a ’workflow generator’ tool for the code generation together with ’workflow editor’ graphical interface for interactive definition of the workflow structure and the inner data dependencies. The usage is explained on a thermo-mechanical simulation.

Adapting Reproducible Research Capabilities to Resilient Distributed Calculations

2016 ◽  
Vol 8 (1) ◽  
pp. 58-69
Author(s):  
Manuel Rodríguez-Pascual ◽  
Christos Kanellopoulos ◽  
Antonio Juan Rubio-Montero ◽  
Diego Darriba ◽  
Ognjen Prnjat ◽  
...  
Keyword(s):  
Open Access ◽  
Fault Tolerant ◽  
Data Access ◽  
Distributed Applications ◽  
Reproducible Research ◽  
Data Repositories ◽  
Metadata Standards ◽  
Definition Of ◽  
And Control ◽  
Application Developers

Nowadays, computing calculations are becoming more and more demanding due to the huge pool of resources available. This demand must be satisfied in terms of computational efficiency and resilience, which is compromised in distributed and heterogeneous platforms. Not only this, data obtained are often either reused by other researchers or recalculated. In this work, a set of tools to overcome the problem of creating and executing fault tolerant distributed applications on dynamic environments is presented. Such a set also ensures the reproducibility of the performed experiments providing a portable, unattended and resilient framework that encapsulates the infrastructure-dependent operations away from the application developers and users, allowing performing experiments based on Open Access data repositories. In this way, users can seamlessly search and lately access datasets that can be automatically retrieved as input data into a code already integrated in the proposed workflow. Such a search is based on metadata standards and relies on Persistent Identifiers (PID) to assign specific repositories. The applications profit from Distributed Toolbox, a framework devoted to the creation and execution of distributed applications and includes tools for unattended cluster and grid execution, where a total fault tolerance is provided. By decoupling the definition of the remote tasks from its execution and control, the development, execution and maintenance of distributed applications is significantly simplified with respect to previous solutions, increasing their robustness and allowing running them on different computational platforms with little effort. The integration with Open Access databases and employment of PIDs for long-lasting references ensures that the data related to the experiments will persist, closing a complete research circle of data access/processing/storage/dissemination of results.

Sample database of the Centre for Polar Ecology - Database design and data management

2014 ◽  
Vol 4 (2) ◽  
pp. 140-148 ◽  
Author(s):  
Jana Kvíderová
Keyword(s):  
Data Management ◽  
Data Storage ◽  
Data Entry ◽  
Data Access ◽  
Taxonomic Diversity ◽  
Diversity Indices ◽  
Culture Collection ◽  
Biological Data ◽  
Data Set ◽  
Data Tables

The increasing number of observations and samples led to development of systems for data storage and management. In this paper, design and experience with data manage-ment of the Sample database (SampleDTB) used in the Centre for Polar Ecology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic, is presented. The SampleDTB was designed for microbiological, phycological or hydro-biological data. The SampleDTB consists of data tables including defined lists of cli-matic zones, habitats, communities and taxons, specific queries for datasets determina-tion and searches, forms for filling in samples and reports. The data tables contain detailed information on site, its environment, types of habitats and communities, in-cluding data on taxonomic diversity. The queries provide source data for reports or serve for searches for specific taxon, sample etc. Forms are used primarily for data entry or modifications. The reports provide summaries and charts for export, either for whole data set or for specific datasets. Data management resulted in system of sample numbering, site specification, and system for photographs storage. Possible future development will be focused on on-line data access, biovolume and diversity indices calculation, laboratory sample processing, and connection to culture collection database.

The Autobiographical Subject and the Death Penalty

2013 ◽  
Vol 35 (2) ◽  
pp. 165-187
Author(s):  
E. S. Burt
Keyword(s):  
Death Penalty ◽  
First Person ◽  
Philosophical Investigation ◽  
The Subject ◽  
Definition Of ◽  
The Individual

Why does writing of the death penalty demand the first-person treatment that it also excludes? The article investigates the role played by the autobiographical subject in Derrida's The Death Penalty, Volume I, where the confessing ‘I’ doubly supplements the philosophical investigation into what Derrida sees as a trend toward the worldwide abolition of the death penalty: first, to bring out the harmonies or discrepancies between the individual subject's beliefs, anxieties, desires and interests with respect to the death penalty and the state's exercise of its sovereignty in applying it; and second, to provide a new definition of the subject as haunted, as one that has been, but is no longer, subject to the death penalty, in the light of the worldwide abolition currently underway.

ГЕРМЕНЕВТИКА ЛИЧНОСТИ КАК МЕТОД СОВРЕМЕННОЙ ПЕРСОНОЛОГИИ

1970 ◽  
Vol 6 (1) ◽  
pp. 32-42
Author(s):  
Елена Старовойтенко
Keyword(s):  
Text Setting ◽  
Research Setting ◽  
Textual Representations ◽  
General Scientific ◽  
Definition Of ◽  
The Individual ◽  
The Continuum

Персонологическая интерпретация текстов предполагает реализацию общенаучных, а также специфических для персонологии, герменевтических установок, к которым относятся: установка на интерпретацию текста как исследование, установка на разнообразие герменевтических действий с текстом, установка на выявление неисследованных содержаний текста, установка на творческое постижение тайн текста, установка на целостное отношение к личности и "Я" автора текста, установка на выявление способности автора быть "практикующим феноменологом", установка на определение места изучаемого текста в континууме текстовых репрезентаций "личности", установка на соотнесение своего понимания текста с другими интерпретациями и их интеграцию, установка на раскрытие сущности авторской "идеи личности", возможное только в единстве интерпретаций, установка на построение и применение герменевтической модели, определяющей процедуру интерпретации как исследования и творчества, установка на определение места проделанного герменевтического поиска в культуре познания и жизни личности, установка на интерпретацию различных видов "текстов личности". Personological interpretation of texts suggests the implementation of the general scientific and also hermeneutical settings specific for Personology which include the setting of the interpretation of the text as a research, setting of a variety of hermeneutical actions with the text, setting to identify unexplored contents of the text, setting of the creative comprehension of the mysteries of the text, setting of the integrity of the attitude of the individual and the "I" of the author of the text, setting to reveal the author's ability to be "practicing phenomenologist", setting of the definition of the place in the text in the continuum of textual representations of the "personality", setting in the correlation of the understanding of the text with other interpretations and their integration, setting of the disclosure of the author's "ideas person" is possible only in the unity of interpretation, setting of the construction and usage of hermeneutical models defining the procedure for the interpretation of both studies and work, the setting to determine the place of hermeneutical research in culture and knowledge of a person's life, setting of the interpretation of various types of "texts of the individual."

¿Quién soy yo? Reflexiones teórico sistémicas acerca de la indentidad individual

2017 ◽  
Vol 1 (1) ◽  
pp. 15-31
Author(s):  
Francisco Xavier Morales
Keyword(s):  
Identity Construction ◽  
Social Systems ◽  
Social Contexts ◽  
Individual Identity ◽  
Contemporary Society ◽  
Self Identity ◽  
Moral Communication ◽  
Identity Based ◽  
Definition Of ◽  
The Individual

The problem of identity is an issue of contemporary society that is not only expressed in daily life concerns but also in discourses of politics and social movements. Nevertheless, the I and the needs of self-fulfillment usually are taken for granted. This paper offers thoughts regarding individual identity based on Niklas Luhmann’s systems theory. From this perspective, identity is not observed as a thing or as a subject, but rather as a “selfillusion” of a system of consciousness, which differentiates itself from the world, event after event, in a contingent way. As concerns the definition  of contents of self-identity, the structures of social systems define who is a person, how he or she should act, and how much esteem he or she should receive. These structures are adopted by consciousness as its own identity structures; however, some social contexts are more relevant for self-identity construction than others. Moral communication increases the probability that structure appropriation takes place, since the emotional element of identity is linked to the esteem/misesteem received by the individual from the interactions in which he or she participates.

Public Service Motivation in Buffy the Vampire Slayer

Public Voices ◽  
2016 ◽  
Vol 12 (1) ◽  
pp. 67 ◽  
Author(s):  
Sharon Mastracci
Keyword(s):  
Popular Culture ◽  
Public Service ◽  
Public Service Motivation ◽  
Public Servants ◽  
Buffy The Vampire Slayer ◽  
The Public ◽  
American Popular Culture ◽  
Public Servant ◽  
Definition Of ◽  
The Individual

In this paper, the author examines public service as depicted in the television series Buffy the Vampire Slayer (BtVS). First, she shows how slaying meets the economist’s definition of a public good, using the BtVS episode “Flooded” (6.04). Second, she discusses public service motivation (PSM) to determine whether or not Buffy, a public servant, operates from a public service ethic. Relying on established measures and evidence from shooting scripts and episode transcripts, the author concludes Buffy is a public servant motivated by a public service ethic. In this way, BtVS informs scholarship on public service by broadening the concept of PSM beyond the public sector; prompting one to wonder whether it is located in a sector, an occupation, or in the individual. These conclusions allow the author to situate Buffy alongside other idealized public servants in American popular culture.

The Concept of the Individual and Its Scope

2018 ◽  
Author(s):  
Ursula Renz
Keyword(s):  
Strict Sense ◽  
Physical Concept ◽  
Individual Group ◽  
Group Minds ◽  
Definition Of ◽  
The Individual

This chapter discusses the implications of Spinoza’s concept of individual bodies, as introduced in the definition of individuum in the physical digression. It begins by showing that this definition allows for an extremely wide application of the term; accordingly, very different sorts of physical entities can be described as Spinozistic individuals. Given the quite distinct use of the terms divisibilis and indivisibilis in his metaphysics, however, the chapter argues that the physical concept of individuality is not universally applied in the Ethics but reserved for physical or natural-philosophical considerations. The chapter concludes with a discussion of the problem of collective individuals. It is argued that, while societies or states are described as individual bodies, they do not constitute individual group minds in the strict sense of the term for Spinoza. This in turn indicates that minds are not individuated in the same way as bodies.

scholarly journals Validity of the Gender Dysphoria diagnosis and incidence trends in Sweden: a nationwide register study

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Malin Indremo ◽  
Richard White ◽  
Thomas Frisell ◽  
Sven Cnattingius ◽  
Alkistis Skalkidou ◽  
...  
Keyword(s):  
Gender Dysphoria ◽  
Age Groups ◽  
Medical Intervention ◽  
Future Research ◽  
Advantages And Disadvantages ◽  
Incidence Trends ◽  
Interaction Terms ◽  
Definition Of ◽  
The Individual ◽  
Nationwide Register Study

AbstractThe aim of this study was to examine the validity of the Gender Dysphoria (GD) diagnoses in the Swedish National Patient Register (NPR), to discuss different register-based definitions of GD and to investigate incidence trends. We collected data on all individuals with registered GD diagnoses between 2001 and 2016 as well as data on the coverage in the NPR. We regarded gender confirming medical intervention (GCMI) as one proxy for a clinically valid diagnosis and calculated the positive predictive value (PPV) for receiving GCMI for increasing number of registered GD diagnoses. We assessed crude and coverage-adjusted time trends of GD during 2004–2015 with a Poisson regression, using assigned sex and age as interaction terms. The PPV for receiving GCMI was 68% for ≥ 1 and 79% for ≥ 4 GD-diagnoses. The incidence of GD was on average 35% higher with the definition of ≥ 1 compared to the definition of ≥ 4 diagnoses. The incidence of GD, defined as ≥ 4 diagnoses increased significantly during the study period and mostly in the age categories 10–17 and 18–30 years, even after adjusting for register coverage. We concluded that the validity of a single ICD code denoting clinical GD in the Swedish NPR can be questioned. For future research, we propose to carefully weight the advantages and disadvantages of different register-based definitions according to the individual study’s needs, the time periods involved and the age-groups under study.

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