Reuse Mechanisms Research Articles

COPO - Managing sample metadata for biodiversity: considerations from the Darwin Tree of Life project

Large-scale reference genome sequencing projects for all of biodiversity are underway and common standards have been in place for some years to enable the understanding and sharing of sequence data. However, the metadata that describes the collection, processing and management of samples, and link to the associated sequencing and genome data, are not yet adequately developed and standardised for these projects. At the time of writing, the Darwin Tree of Life (DToL) Project is over two years into its ten-year ambition to sequence all described eukaryotic species in Britain and Ireland. We have sought consensus from a wide range of scientists across taxonomic domains to determine the minimal set of metadata that we collectively deem as critically important to accompany each sequenced specimen. These metadata are made available throughout the subsequent laboratory processes, and once collected, need to be adequately managed to fulfil the requirements of good data management practice. Due to the size and scale of management required, software tools are needed. These tools need to implement rigorous development pathways and change management procedures to ensure that effective research data management of key project and sample metadata is maintained. Tracking of sample properties through the sequencing process is handled by Lab Information Management Systems (LIMS), so publication of the sequenced data is achieved via technical integration of LIMS and data management tools. Discussions with community members on how metadata standards need to be managed within large-scale programmes is a priority in the planning process. Here we report on the standards we developed with respect to a robust and reusable mechanism of metadata collection, in the hopes that other projects forthcoming or underway will adopt these practices for metadata.

Traceability and reuse mechanisms, the most important properties of model transformation languages

ContextDedicated model transformation languages are claimed to provide many benefits over the use of general purpose languages for developing model transformations. However, the actual advantages and disadvantages associated with the use of model transformation languages are poorly understood empirically. There is little knowledge and even less empirical assessment about what advantages and disadvantages hold in which cases and where they originate from. In a prior interview study, we elicited expert opinions on what advantages result from what factors surrounding model transformation languages as well as a number of moderating factors that moderate the influence.ObjectiveWe aim to quantitatively asses the interview results to confirm or reject the influences and moderation effects posed by different factors. We further intend to gain insights into how valuable different factors are to the discussion so that future studies can draw on these data for designing targeted and relevant studies.MethodWe gather data on the factors and quality attributes using an online survey. To analyse the data and examine the hypothesised influences and moderations, we use universal structure modelling based on a structural equation model. Universal structure modelling produces significance values and path coefficients for each hypothesised and modelled interdependence between factors and quality attributes that can be used to confirm or reject correlation and to weigh the strength of influence present.ResultsWe analyzed 113 responses. The results show that the MTL capabilities Tracing and Reuse Mechanisms are most important overall. Though the observed effects were generally 10 times lower than anticipated. Furthermore, we found that moderation effects need to be individually assessed for each influence on a quality attribute. The moderation effects of a single moderating variable vary significantly for each influence, with the strongest effects being 1000 times higher than the weakest.ConclusionThe empirical assessment of MTLs is a complex topic that cannot be solved by looking at a single stand-alone factor. Our results provide clear indication that evaluation should consider transformations of different sizes and use-cases that go beyond mapping one elements attributes to another. Language development on the other hand should focus on providing practical, transformation specific reuse mechanisms that allow MTLs to excel in areas such as maintainability and productivity compared to GPLs.

On the adoption and effects of source code reuse on defect proneness and maintenance effort

Software reusability mechanisms, like inheritance and delegation in Object-Oriented programming, are widely recognized as key instruments of software design that reduce the risks of source code being affected by defects, other than to reduce the effort required to maintain and evolve source code. Previous work has traditionally employed source code reuse metrics for prediction purposes, e.g., in the context of defect prediction. However, our research identifies two noticeable limitations of the current literature. First, still little is known about the extent to which developers actually employ code reuse mechanisms over time. Second, it is still unclear how these mechanisms may contribute to explaining defect-proneness and mainten0ance effort during software evolution. We aim at bridging this gap of knowledge, as an improved understanding of these aspects might provide insights into the actual support provided by these mechanisms, e.g., by suggesting whether and how to use them for prediction purposes. We propose an exploratory study, conducted on 12 Java projects–over 44,900 commits–of the Defects4J dataset, aiming at (1) assessing how developers use inheritance and delegation during software evolution; and (2) statistically analyzing the impact of inheritance and delegation on fault proneness and maintenance effort. Our results let emerge various usage patterns that describe the way inheritance and delegation vary over time. In addition, we find out that inheritance and delegation are statistically significant factors that influence both source code defect-proneness and maintenance effort.

COPO - Managing sample metadata for biodiversity: considerations from the Darwin Tree of Life project.

Large-scale reference genome sequencing projects for all of biodiversity are underway and common standards have been in place for some years to enable the understanding and sharing of sequence data. However, the metadata that describes the collection, processing and management of samples, and link to the associated sequencing and genome data, are not yet adequately developed and standardised for these projects. At the time of writing, the Darwin Tree of Life (DToL) Project is over two years into its ten-year ambition to sequence all described eukaryotic species in Britain and Ireland. We have sought consensus from a wide range of scientists across taxonomic domains to determine the minimal set of metadata that we collectively deem as critically important to accompany each sequenced specimen. These metadata are made available throughout the subsequent laboratory processes, and once collected, need to be adequately managed to fulfil the requirements of good data management practice. Due to the size and scale of management required, software tools are needed. These tools need to implement rigorous development pathways and change management procedures to ensure that effective research data management of key project and sample metadata is maintained. Tracking of sample properties through the sequencing process is handled by Lab Information Management Systems (LIMS), so publication of the sequenced data is achieved via technical integration of LIMS and data management tools. Discussions with community members on how metadata standards need to be managed within large-scale programmes is a priority in the planning process. Here we report on the standards we developed with respect to a robust and reusable mechanism of metadata collection, in the hopes that other projects forthcoming or underway will adopt these practices for metadata.

Code Cloning in Smart Contracts on the Ethereum Platform: An Extended Replication Study

Smart contracts are programs deployed on blockchains that run upon meeting predetermined conditions. Once deployed, smart contracts are immutable, thus, defects in the deployed code cannot be fixed. As a consequence, software engineering anti-patterns, such as code cloning, pose a threat to code quality and security if unnoticed before deployment. In this paper, we report on the cloning practices of the Ethereum blockchain platform by analyzing 33,073 smart contracts amounting to over 4MLOC. Prior work reported an unusually high 79.2% of code clones in Ethereum smart contracts. We replicate this study at the conceptual level, i.e., we answer the same research questions by employing different methods. In particular, we analyze clones at the granularity of functions instead of code files, thereby providing a more fine-grained estimate of the clone ratio. Furthermore, we analyze more complex clone types, allowing for a richer analysis of cloning cases. To achieve this finer granularity of cloning analysis, we rely on the NiCad clone detection tool and extend it with support for Solidity, the programming language of the Ethereum platform. Our analysis shows that most findings of the original study hold at the finer granularity of our study as well; but also sheds light on some differences, and contributes new findings. Most notably, we report a 30.13% overall clone ratio, out of which 27.03% are exact duplicates. Our findings motivate improving the reuse mechanisms of Solidity, and in a broader context, of programming languages used for the development of smart contracts. Tool builders and language engineers can use this paper in the design and development of such reuse mechanisms. Business stakeholders can use this paper to better assess the security risks and technical outlooks of blockchain platforms.

Managing sample metadata for biodiversity: considerations from the Darwin Tree of Life project

Large-scale reference genome sequencing projects for all of biodiversity are underway and common standards have been in place for some years to enable the understanding and sharing of sequence data. However, the metadata that describes the collection, processing and management of samples, and link to the associated sequencing and genome data, are not yet adequately developed and standardised for these projects. At the time of writing, the Darwin Tree of Life (DToL) Project is over two years into its ten-year ambition to sequence all described eukaryotic species in Britain and Ireland. We have sought consensus from a wide range of scientists across taxonomic domains to determine the minimal set of metadata that we collectively deem as critically important to accompany each sequenced specimen. These metadata are made available throughout the subsequent laboratory processes, and once collected, need to be adequately managed to fulfil the requirements of good data management practice. Due to the size and scale of management required, software tools are needed. These tools need to implement rigorous development pathways and change management procedures to ensure that effective research data management of key project and sample metadata is maintained. Tracking of sample properties through the sequencing process is handled by Lab Information Management Systems (LIMS), so publication of the sequenced data is achieved via technical integration of LIMS and data management tools. Discussions with community members on how metadata standards need to be managed within large-scale programmes is a priority in the planning process. Here we report on the standards we developed with respect to a robust and reusable mechanism of metadata collection, in the hopes that other projects forthcoming or underway will adopt these practices for metadata.

Method of increasing the reliability of knowledge-oriented systems software through code reuse mechanisms

The issues of possibility of application of the code reuse mechanism in the process of designing and developing software of knowledge-oriented systems have been considered. The necessity of an individual research on the development of software for analytical and information resources that provide support to all participants in the process of knowledge-oriented systems software development has been proved. The necessity of using the mechanisms of reuse of previously developed and verified program code as an element of the information resource has been shown. In frame of the developed method of improving the reliability of knowledge-oriented systems software through the of code reuse mechanisms, a new visual form of function libraries representation in the shape of a single software shell has been proposed. As a basic framework for solving the problem of information resource development, usage of Unified Modeling Language (UML), which is based on the paradigm of object-oriented programming has been proposed. Mentioned choice is justified by the fact that UML is an integral part of a unified software development process and is essentially an open standard that uses graphical notation to create an abstract model of the system. The obtained theoretical provisions are imaged into a running example, which shows one of the possible options for organizing libraries of functions as an element of the information resource. The use case diagrams, interaction diagrams, sequence diagrams, class diagrams have been developed and justified. Based on the obtained practical results, a block diagram of the method, which, in contrast to existing solutions, includes a procedure for generating of proofreads for basic UML-diagrams in accordance with requirements of the programming environments has been proposed.

A Methodology for Generating Systems Architectural Glimpse Statements Using the 5W1H Maxim

Attempts to facilitate and streamline systems architecting have resulted in a great number of reusable principles, practices, mechanisms, frameworks, and tools. Such a practice is the use of architectural viewpoints and views. However, as systems change, these practices should also evolve. The increasing scale and complexity of systems resulting from an ever-growing pool of human needs and breakthroughs may lead, in some cases, to an increased gap between the abstraction activities attempting to capture the whole of a system, and the instantiation activities that produce concrete and detailed descriptions of a system’s architecture. To address this issue, this article introduces a new notion, that of architectural glimpse statements, fundamental questions acting as the building blocks for architectural views and products. This notion can help architects ask the right questions in the right manner to create fundamental statements, the elaboration on which can lead directly to concrete architectural products. Working on top of standardized and common approaches, the article introduces a language for the creation of architectural glimpse statements using the 5W1H maxim. Based on this language, a tool and guidelines are also provided to facilitate the usage of glimpses. Finally, the overall methodology is demonstrated in two case studies.

Simulation Testbed for Evaluating Distributed Querying and Searching of Mass Spectrometry Big Data in a Network-based Infrastructure.

Advance access and reuse mechanisms for large-scale Mass Spectrometry (MS) data are essential for democratizing data for the omics research community and making it adhere to FAIR (Findable, Accessible, Interoperable, Reusable) principles. Although a number of centralized data repositories have been established, they have been limited to search mechanisms that depend on the meta-data associated with these MS datasets. Furthermore, they require constant influx of resources for maintenance. In this paper, we proposed an alternative novel distributed infrastructure for direct MS/MS spectral search. We designed and developed a simulation testbed using concepts from computer networks, queuing theory, and stochastic simulation methods. Results show that a distributed MS search based on raw MS/MS spectra can scale gracefully for up-to 2000 participating nodes, while simultaneously processing queries using the proposed networked infrastructure on the order of milliseconds to a few seconds for up-to a total of fifty billion MS/MS spectra.

Dynamic service provisioning of hybrid advanced and immediate requests in SDM-EONs

Hybrid immediate request (IR) and advanced reservation (AR) is an inevitable traffic model for future SDM-EONs to accommodate uncertainty and abundance of services. Different from the traditional IR handling instant services like chat messaging, AR can balance the traffic load by postponing allocation to delay-tolerant requests such as cloud computing, e-science, IPTV etc. Although IR/AR mixed traffics are essential in future SDM-EONs, several problems arise especially when solving dynamic RSCA problems. Most importantly, inter-core crosstalk (XT) and resource fairness need to be considered to satisfy high-quality transmission and to avoid unnecessary resource occupation of formerly arriving AR requests.We propose a dynamic HTA-RSCA algorithm that combines time recycling and reuse mechanisms in the time domain with routing, spectrum and core assignment (RSCA) in the spatial-spectrum domain. Specially, pretreatment techniques include super-channel (Sp-Ch) order pre-definition and time-spectrum partition. These appropriate operations are ready for efficient resource searching and requests assignment. Taking transmission quality into consideration, XT-avoid principle is involved in Sp-Ch order pre-definition and dynamic time domain mechanisms to realize the fair and flexible provisioning. XT-awareness is included in the final allocation step to rank available resources options. Simulation results confirm that the dynamic HTA-RSCA can reduce network blocking probability (BP) than comparison algorithms. To the best of our knowledge, this is the first attempt applying time mechanisms to address dynamic provisioning of hybrid IR and AR requests in SDM-EONs.

Water reuse and growth inhibition mechanisms for cultivation of microalga Euglena gracilis

BackgroundMicroalgae can contribute to more than 40% of global primary biomass production and are suitable candidates for various biotechnology applications such as food, feed products, drugs, fuels, and wastewater treatment. However, the primary limitation for large-scale algae production is the fact that algae requires large amounts of fresh water for cultivation. To address this issue, scientists around the world are working on ways to reuse the water to grow microalgae so that it can be grown in successive cycles without the need for fresh water.ResultsIn this study, we present the results when we cultivate microalgae with cultivation water that is purified and reused. Specifically, we purify the cultivation water using an ultrafiltration membrane (UFM) treatment and investigate how this treatment affects: the biomass and biochemical components of the microalgae; characteristics of microalgae growth inhibitors; the mechanism whereby potential growth inhibitors are secreted (followed using metabolomics analysis); the effect of activated carbon (AC) treatment and advanced oxidation processes (AOPs) on the removal of growth inhibitors of Euglena gracilis. Firstly, the results show that E. gracilis can be only cultivated through two growth cycles with water that has been filtered and reused, and the growth of E. gracilis is significantly inhibited when the water is used a third time. Secondly, as the number of reused water cycles increases, the Cl− concentration gradually increases in the cultivation water. When the Cl− concentration accumulates to a level of fivefold higher than that of the control, growth of E. gracilis is inhibited as the osmolality tolerance range is exceeded. Interestingly, the osmolality of the reused water can be reduced by replacing NH4Cl with urea as the source of nitrogen in the cultivation water. Thirdly, E. gracilis secretes humic acid (HA)—which is produced by the metabolic pathways for valine, leucine, and isoleucine biosynthesis and by linoleic acid metabolism—into the cultivation water. Because HA contains large fluorescent functional groups, specifically extended π(pi)-systems containing C=C and C=O groups and aromatic rings, we were able to observe a positive correlation between HA concentration and the rate of inhibition of E. gracilis growth using fluorescence spectroscopy. Moreover, photosynthetic efficiency is adversely interfered by HA, thereby reductions in the synthetic efficiency of paramylon and lipid in E. gracilis. In this way, we are able to confirm that HA is the main growth inhibitor of E. gracilis. Finally, we verify that all the HA is removed or converted into nutrients efficiently by AC or UV/H2O2/O3 treatments, respectively. As a result of these treatments, growth of E. gracilis is restored (AC treatment) and the amount of biomass is promoted (UV/H2O2/O3 treatment).ConclusionsThese studies have important practical and theoretical significance for the cyclic cultivation of E. gracilis and for saving water resources. Our work may also provide a useful reference for other microalgae cultivation.

Analysis of Mechanical Characteristics of a Mechanical Reusable Hold-down and Release Mechanism

Analysis of Mechanical Characteristics of a Mechanical Reusable Hold-down and Release Mechanism

Comparing and classifying model transformation reuse approaches across metamodels

Model transformations are essential elements of model-driven engineering (MDE) solutions, as they enable the automatic manipulation of models. MDE promotes the creation of domain-specific metamodels, but without proper reuse mechanisms, model transformations need to be developed from scratch for each new metamodel. In this paper, our goal is to understand whether transformation reuse across metamodels is needed by the community, evaluate its current state, identify practical needs and propose promising lines for further research. For this purpose, we first report on a survey to understand the reuse approaches used currently in practice and the needs of the community. Then, we propose a classification of reuse techniques based on a feature model and compare a sample of specific approaches—model types, concepts, a-posteriori typing, multilevel modeling, typing requirement models, facet-oriented modeling, mapping operators, constraint-based model types, and design patterns for model transformations—based on this feature model and a common example. We discuss strengths and weaknesses of each approach, provide a reading grid used to compare their features, compare with community needs, identify gaps in current transformation reuse approaches in relation to these needs and propose future research directions.

INDIeAuthor: A Metamodel-Based Textual Language for Authoring Educational Courses

This paper presents the INDIeAuthor authoring tool, which has been developed at the Digital Content Production Center, Polytechnic University of Cartagena (UPCT). INDIeAuthor has been developed in order for the university to have its own tool that supports all the desired features, in addition to a platform with which to investigate innovative features. When building INDIeAuthor, we have overcome some limitations identified for existing authoring tools: 1) Lack of two essential content reuse mechanisms: defined-user templates and course-independent units; 2) No support to sequence the units on a course; 3) Gamification feature is either very limited or does not exist. Two new aspects of the proposal are: providing a family of four textual domain-specific languages rather than a graphical user interface and applying model-based software engineering techniques during the implementation of the languages. Four essential aspects in the course definition can be specified to the language family: content, assessment, gamification, and sequencing. We discuss the benefits of representing courses as models and present two utilities developed as a proof of concept. This paper also contributes with the definition of a feature model that establishes a conceptual framework in which to compare authoring tools. An evaluation of INDIeAuthor is also presented: a case study was carried to evaluate the language characteristics, and the tool is contrasted with eight widely-used authoring tools. This paper presented here is the baseline of INDIe Erasmus+ European project that is currently ongoing.

Automatic service abstraction through data, information and knowledge prioritisation

Web service is a popular solution to integrate components when building a software system, or to allow communication between a system and third-party users, providing a flexible and reusable mechanism to access its functionalities. Scientists have been proposing numerous models for defining anything 'as a service (aaS)', including discussions of products, processes, data and information management, and security as a service. Various web service-based systems are prevailing in health service, personalised recommendation provision. We propose a framework towards constructing and searching typed resources in terms of data, information and knowledge through a hierarchy composing data graph, information graph and knowledge graph in order to improve performance in accessing and processing resources. We use cases to illustrate the mechanism of the framework.

Adaptive and Non Adaptive LTE Fractional Frequency Reuse Mechanisms Mobility Performance

Adaptive and Non Adaptive LTE Fractional Frequency Reuse Mechanisms Mobility Performance

ReSpecTX: Programming interaction made easy

In this paper we present the ReSpecTX language, toolchain, and standard library as a first step of a path aimed at closing the gap between coordination languages ? mostly a prerogative of the academic realm until now ? and their industrial counterparts. Since the limited adoption of coordination languages within the industrial realm is also due to the lack of suitable toolchains and libraries of reusable mechanisms, ReSpecTX equips a core coordination language (ReSpecT) with tools and features commonly found in mainstream programming languages. In particular, ReSpecTX makes it possible to provide a reference library of reusable and composable interaction patterns.

A modular reasoning system using uninterpreted predicates for code reuse

This paper proposes a modular proof system based on uninterpreted predicates. The proposed proof system allows modular reasoning about programs with an open-world assumption, which goes beyond behavioral subtyping. The proof system enables modular reasoning about languages with very flexible code reuse mechanisms, such as traits and deltas in the context of object-oriented programming. Whereas related work on incremental proof systems prove soundness in terms of internal consistency, this paper establishes both soundness and relative completeness of the proposed proof system by relating it to a standard proof system for a simple object-oriented language. The applicability of the approach is demonstrated on different code reuse mechanisms: unrestricted class inheritance, delta-oriented programming, and trait-based programming.

Soap production: A green prospective

A green prospective based on the reuse of waste materials such as almond shells, orange peel and used cooking oil to manufacture soap is presented.In Portugal, thousands of tons of waste are generated from used cooking oil and production of nut shells’ residues is growing every year. In addition, the high consumption of citrus fruits, oranges in particular, generates large amounts of citrus peel. Therefore, it is necessary to diversify reuse mechanisms of these wastes, in order to make them back into raw materials. Complying with this trend, this work was carried out by processing and grinding almond shells, treating used oil, processing orange peels and extracting limonene, formulating and producing soap, and performing an acceptance study of the final product. Results validated a high potential of the idea in the field of environmental education, so it can be replicated in practical classes. It can also be useful for waste management, and it can support the development of community projects on an ecological approach.

Combine and conquer: an evolutionary hyper-heuristic approach for solving constraint satisfaction problems

Selection hyper-heuristics are a technology for optimization in which a high-level mechanism controls low-level heuristics, so as to be capable of solving a wide range of problem instances efficiently. Hyper-heuristics are used to generate a solution process rather than producing an immediate solution to a given problem. This process is a re-usable mechanism that can be applied both to seen and unseen problem instances. In this paper, we propose a selection hyper-heuristic process with the intention to rise the level of generality and solve consistently well a wide range of constraint satisfaction problems. The hyper-heuristic technique is based on a messy genetic algorithm that generates high-level heuristics formed by rules (condition $$\rightarrow $$ź heuristic). The high-level heuristics produced are seen to be good at solving instances from certain parts of the parameterized space of problems, producing results using effort comparable to the best single heuristic per instance. This is beneficial, as the choice of best heuristic varies from instance to instance, so the high-level heuristics are definitely preferable to selecting any one low-level heuristic for all instances. The results confirm the robustness of the proposed approach and how high-level heuristics trained for some specific classes of instances can also be applied to unseen classes without significant lost of efficiency. This paper contributes to the understanding of heuristics and the way they can be used in a collaborative way to benefit from their combined strengths.