scholarly journals A fully computational and reasonable representation for karyotypes

2019 ◽  
Vol 35 (24) ◽  
pp. 5264-5270
Author(s):  
Jennifer D Warrender ◽  
Anthony V Moorman ◽  
Phillip Lord
Keyword(s):  
Source Code ◽  
Significant Advance ◽  
Ontology Development ◽  
Development Environment ◽  
Tawny Owl ◽  
Causes Of Disease ◽  
Search Data ◽  
Computational Representation

Abstract Summary The human karyotype has been used as a mechanism for describing and detecting gross abnormalities in the genome for many decades. It is used both for routine diagnostic purposes and for research to further our understanding of the causes of disease. Despite these important applications there has been no rigorous computational representation of the karyotype; rather an informal, string-based representation is used, making it hard to check, organize and search data of this form. In this article, we describe our use of OWL, the Ontology Web Language, to generate a fully computational representation of the karyotype; the development of this ontology represents a significant advance from the traditional bioinformatics use for tagging and navigation and has necessitated the development of a new ontology development environment called Tawny-OWL. Availability and implementation The Karyotype Ontology and associated Tawny-OWL source code is available on GitHub at https://github.com/jaydchan/tawny-karyotype, under a LGPL License, Version 3.0.

Replication of Quantum Computing towards an Unconventional Environment using QuIDE

2019 ◽  
Vol 8 (4) ◽  
pp. 9461-9464
Keyword(s):  
Quantum Computer ◽  
Source Code ◽  
Circuit Diagram ◽  
Quantum Computers ◽  
Coordinated Development ◽  
Development Environment ◽  
Integrated Development ◽  
Complexity Of Algorithms ◽  
Performance Results ◽  
Exponential Complexity

Current quantum computer simulation strategies are inefficient in simulation and their realizations are also failed to minimize those impacts of the exponential complexity for simulated quantum computations. We proposed a Quantum computer simulator model in this paper which is a coordinated Development Environment – QuIDE (Quantum Integrated Development Environment) to support the improvement of algorithm for future quantum computers. The development environment provides the circuit diagram of graphical building and flexibility of source code. Analyze the complexity of algorithms shows the performance results of the simulator and used for simulation as well as result of its deployment during simulation

scholarly journals Means of integrating static source security analysis technology into the software development environment

2020 ◽  
Author(s):  
N. V. Goryuk ◽  
Keyword(s):  
Software Development ◽  
Static Analysis ◽  
Software Security ◽  
Source Code ◽  
Security Analysis ◽  
Development Environment ◽  
Static Source ◽  
Software Development Environment ◽  
Further Development ◽  
Code Development

The article investigates automation methods and means of integration of static source security analysis technology. The process of software security analysis, which is implemented by the technology of static analysis of the source code, is studied, and the methods of solving the problem of automation and integration of the technology into the source code development environment are offered. The perspective direction of further development of the technology of static analysis of the source code is established.

SeaLion: An eclipse-based IDE for answer-set programming with advanced debugging support

2013 ◽  
Vol 13 (4-5) ◽  
pp. 657-673 ◽  
Author(s):  
PAULA-ANDRA BUSONIU ◽  
JOHANNES OETSCH ◽  
JÖRG PÜHRER ◽  
PETER SKOČOVSKÝ ◽  
HANS TOMPITS
Keyword(s):  
Source Code ◽  
Answer Set Programming ◽  
Model Driven Engineering ◽  
Development Environment ◽  
Integrated Development ◽  
Model Driven ◽  
Class Diagrams ◽  
The Rich ◽  
Answer Sets ◽  
Answer Set

AbstractIn this paper, we present SeaLion, an integrated development environment (IDE) for answer-set programming (ASP).SeaLionprovides source-code editors for the languages ofGringoandDLVand offers popular amenities like syntax highlighting, syntax checking, code completion, visual program outline, and refactoring functionality. The tool has been realised in the context of a research project whose goal is the development of techniques to support the practical coding process of answer-set programs. In this respect,SeaLionis the first IDE for ASP that provides debugging features that work for real-world answer-set programs and supports the rich languages of modern answer-set solvers. Indeed,SeaLionimplements a stepping-based debugging approach that allows the developer to quickly track down programming errors by simply following his or her intuitions on the intended semantics. Besides that,SeaLionsupports ASP development using model-driven engineering techniques including domain modelling with extended UML class diagrams and visualisation of answer sets in corresponding instance diagrams. Moreover, customised visualisation as well as visual editing of answer sets is realised by the Kara plugin ofSeaLion. Further implemented features are a documentation generator based on the Lana annotation language, support for external solvers, and interoperability with external tools.SeaLioncomes as a plugin of the popular Eclipse platform and provides interfaces for future extensions of the IDE.

scholarly journals Towards a Modern Ontology Development Environment

2020 ◽  
Vol 176 ◽  
pp. 753-762
Author(s):  
Adrian Stadnicki ◽  
Filip Filip Pietroń ◽  
Patryk Burek
Keyword(s):  
Ontology Development ◽  
Development Environment

scholarly journals Ontologies for Supporting Engineering Design Optimization

2006 ◽  
Author(s):  
Paul Witherell ◽  
Sundar Krishnamurty ◽  
Ian R. Grosse
Keyword(s):  
Design Optimization ◽  
Knowledge Base ◽  
Engineering Design ◽  
Formal Method ◽  
Left Ventricular ◽  
Ontology Development ◽  
Development Environment ◽  
First Case ◽  
Engineering Design Optimization

This paper presents an optimization ontology and its implementation into a prototype computational knowledge base tool dubbed ONTOP (ONTology for OPtimization). Salient features of ONTOP include a knowledge base which incorporates both standardized optimization terminology, formal method definitions, and often unrecorded optimization details, such as any idealizations and assumptions that may be made when creating an optimization model, as well as the model developer’s rationale and justification behind these idealizations and assumptions. ONTOP was developed using Prote´ge´, a Java-based, free open-source ontology development environment created by Stanford University. Two engineering design optimization case studies are presented. The first case study consists of the optimization of a structural beam element and demonstrates ONTOP’s ability to address the variations in an optimal solution that may arise when different techniques and approaches are used. A second case study, a more complex design problem which deals with the optimization of an impeller of a pediatric left ventricular heart assist device, demonstrates the wealth of knowledge ONTOP is able to capture. Together, these test beds help illustrate the potential value of an ontology in representing application-specific knowledge while facilitating both the sharing and exchanging of this knowledge in engineering design optimization.

TOWARD A UNIFIED ENGLISH-LIKE REPRESENTATION OF SEMANTIC MODELS, DATA, AND GRAPH PATTERNS FOR SUBJECT MATTER EXPERTS

2013 ◽  
Vol 07 (03) ◽  
pp. 215-236 ◽  
Author(s):  
ANDREW CRAPO ◽  
ABHA MOITRA
Keyword(s):  
Open Source ◽  
English Language ◽  
Query Language ◽  
Source Code ◽  
Language Models ◽  
Modeling Languages ◽  
Development Environment ◽  
Ontology Language ◽  
Declarative Modeling ◽  
Graph Query Language

The Semantic Application Design Language (SADL) combines advances in standardized declarative modeling languages based on formal logic with advances in domain-specific language (DSL) development environments to create a controlled-English language that translates directly into the Web Ontology Language (OWL), the SPARQL graph query language, and a compatible if/then rule language. Models in the SADL language can be authored, tested, and maintained in an Eclipse-based integrated development environment (IDE). This environment offers semantic highlighting, statement completion, expression templates, hyperlinking of concepts to their definition, model validation, automatic error correction, and other advanced authoring features to enhance the ease and productivity of the modeling environment. In addition, the SADL language offers the ability to build in validation tests and test suites that can be used for regression testing. Through common Eclipse functionality, the models can be easily placed under source code control, versioned, and managed throughout the life of the model. Differences between versions can be compared side-by-side. Finally, the SADL-IDE offers an explanation capability that is useful in understanding what was inferred by the reasoner/rule engine and why those conclusions were reached. Perhaps more importantly, explanation is available of why an expected inference failed to occur. The objective of the language and the IDE is to enable domain experts to play a more active and productive role in capturing their knowledge and making it available as computable artifacts useful for automation where appropriate and for decision support systems in applications that benefit from a collaborative human-computer approach. SADL is built entirely on open source code and most of SADL is itself released to open source. This paper explores the concepts behind the language and provides details and examples of the authoring and model lifecycle support facilities.

scholarly journals Pembangunan Perangkat Lunak PuniEdit (Perangkat Lunak Editor untuk Multi Language Programming)

2019 ◽  
Author(s):  
Budiman
Keyword(s):  
Programming Languages ◽  
Programming Language ◽  
Source Code ◽  
Computer Software ◽  
Object Oriented ◽  
Object Oriented Programming ◽  
Text Editor ◽  
Development Environment ◽  
Integrated Development ◽  
High Level

During this period continued to develop computer software, programming language was no exception. At the start of the era of low level programming languages, then developed a high level programming language. It is characterized by the appearance of a method of programming offered by a programming language, that is, object-oriented programming (OOP). IDE (Integrated Development Environment) is a computer program that has some facilities that are required in the development of the software. The purpose of the IDEA is to provide all the necessary utilities in building software. As for the type of software text editor that can be used to manipulate the source code hereinafter referred to as the source code of programming languages such as Ultraedit, JediEdit, ClearEdit, cEdit, the Golden Pen, and so on. PuniEdit software is a text-based editor software that can simplify the user through correction, insertion, and modification of the source code. PuniEdit software is built using Borland Delphi 7.0 and SynEdit component. This software can be used for the Pascal programming language, C++ and HTML. In addition, the software PuniEdit can perform management of the token. This PuniEdit software, the user can clearly see every occurrence of the type of token as keywords (reserved word), identifier, operator, and so on.Keywords: Source code, programming language, source code is scanned.

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