Object-oriented design

Holland, Ian M.; Lieberherr, Karl

doi:10.1145/234313.234421

Cited by 12 publications

(6 citation statements)

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“…Our goal was to create a flexible software architecture for modeling membrane proteins; we therefore used object-oriented design principles [ 35 ] to encapsulate individual scientific concepts for membrane protein modeling into a set of software ‘building blocks’, or objects. Each object includes information (data) and actions (methods) required to represent a given scientific concept.…”

Section: Methodsmentioning

confidence: 99%

An Integrated Framework Advancing Membrane Protein Modeling and Design

et al. 2015

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Membrane proteins are critical functional molecules in the human body, constituting more than 30% of open reading frames in the human genome. Unfortunately, a myriad of difficulties in overexpression and reconstitution into membrane mimetics severely limit our ability to determine their structures. Computational tools are therefore instrumental to membrane protein structure prediction, consequently increasing our understanding of membrane protein function and their role in disease. Here, we describe a general framework facilitating membrane protein modeling and design that combines the scientific principles for membrane protein modeling with the flexible software architecture of Rosetta3. This new framework, called RosettaMP, provides a general membrane representation that interfaces with scoring, conformational sampling, and mutation routines that can be easily combined to create new protocols. To demonstrate the capabilities of this implementation, we developed four proof-of-concept applications for (1) prediction of free energy changes upon mutation; (2) high-resolution structural refinement; (3) protein-protein docking; and (4) assembly of symmetric protein complexes, all in the membrane environment. Preliminary data show that these algorithms can produce meaningful scores and structures. The data also suggest needed improvements to both sampling routines and score functions. Importantly, the applications collectively demonstrate the potential of combining the flexible nature of RosettaMP with the power of Rosetta algorithms to facilitate membrane protein modeling and design.

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Section: Methodsmentioning

confidence: 99%

An Integrated Framework Advancing Membrane Protein Modeling and Design

et al. 2015

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“…The important classic software engineering guidelines developed especially for structured design are also important in object-oriented design. These software engineering guidelines or characteristics are: modularity, low module coupling and high module cohesion, data hiding [19].…”

Section: Design Characteristicsmentioning

confidence: 99%

Facilitating Software Reuse Through Design Characteristics in Object-Oriented Paradigm

Aljedebi

Al-Mutawa

2022

Comm. Math. Appl.

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Software are used to increases quality as well as productivity that could be associated with lower costs. Implementing software with capability for reuse is difficult without sufficient support. This paper includes tutorial represents four important design characteristics in objectoriented paradigm for facilitating the production of more reusable software. It reviews the concepts of modularity, cohesion, coupling and information hiding and provides a discussion about their effect on software reuse. Object-oriented approach is having wide attention both in research environments and in industry. This tutorial is prepared for newbie developers of reusable software assets and for everyone else interested in the subject.

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“…Generically, it involves several decisions that can not be made by a method or a tool, due to the natural discontinuity between functional and structural models. Holland and Lieberherr consider that the identification of objects and the description of the relationships between them are two of the three challenges of object oriented design in the construction of object oriented models [20].…”

Section: Requirements Transformationmentioning

confidence: 99%

Specification of Requirements Models

Machado¹,

Ramos²,

Fernandes³

Engineering and Managing Software Requirements

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The main aim of this chapter is to present and discuss a set of modeling and specification techniques, in what concerns their ontology and support in the requirements representation of computer-based systems. A systematic classification of meta-models, also called models of computation, is presented. This topic is highly relevant since it supports the definition of sound specification methodologies in relation to the semantic definition of the modeling views to adopt for a given system. The usage and applicability of Unified Modeling Language (UML) diagrams is also related to their corresponding meta-models. A set of desirable characteristics for the specification methodologies is presented and justified to allow system designers and requirements engineers to more consciously define or choose a particular specification methodology. A heuristic-based approach to support the transformation of user into system requirements is suggested, with some graphical examples in UML notation.Computer-based systems integrate, as information processing sub-systems, one or more computing systems able to capture, store, process, transfer, present and manage information. Within the design of computer-based systems, this justifies the need for the incorporation of several technological entities: (1) software, firmware, and (analog and digital) hardware, to process and store information; (2) communication network services to transport information; (3) sensors and actuators to interact with the physical environment; and (4) human-machine interfaces to exchange information with human operators. Although computer-based systems can be strictly based on computer technologies, they normally include other entities such as human operators, organizational subsystems, documentation, and manuals.Since computer-based systems are, by nature, heterogeneous, modeling and specifying their requirements demands a holistic approach.A requirement can be defined as "something that a client needs." From the point of view of the system designer or the requirements engineer, a requirement could also be defined as "something that must be designed." The IEEE 610 standard [21] defines a requirement as: (1) a condition or capability needed by a user to solve a problem or achieve an objective; (2) a condition or capability that must be met or possessed by a system or system component to satisfy a contract, standard, specification or other formally imposed documents; (3) a documented representation of a condition or capability as in (1) or (2).

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Object-oriented design

Cited by 12 publications

References 1 publication

An Integrated Framework Advancing Membrane Protein Modeling and Design

An Integrated Framework Advancing Membrane Protein Modeling and Design

Facilitating Software Reuse Through Design Characteristics in Object-Oriented Paradigm

Specification of Requirements Models

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