Integration Of Software Tools Research Articles

Resilience to Cope with Climate Change in Urban Areas—A Multisectorial Approach Focusing on Water—The RESCCUE Project

The RESCCUE Project is an H2020 research project that aims to help cities around the world to become more resilient to physical, social, and economic challenges, using the water sector as the central point of the approach. RESCCUE will generate models and tools to bring this objective to practice, while delivering a framework enabling city resilience assessment, planning and management. This will be achieved by integrating software tools, methods, and new knowledge related to the detailed urban services performance into novel and promising loosely coupled models (integrated models), multi-risk assessment method, and a comprehensive resilience platform. These tools will allow urban resilience assessment from a multisectorial approach, for current and future climate change scenarios, including multiple hazards and cascading effects. The RESCCUE approach will be implemented in three EU cities (Barcelona, Bristol, and Lisbon) and, with the support of UN-Habitat, disseminate their results among other cities belonging to major international networks. The aim of this paper is to present the main goals of this project, as well as the approach followed and the main expected results after the four years of implementation, so other cities around the world can use the RESCCUE approach to increase their resilience.

Probabilistic evaluation of the long-term power system resource adequacy: The Greek case

This paper deals with the probabilistic evaluation of the long-term resource adequacy of an interconnected power system. An integrated software tool that solves the long-term scheduling problem using a sophisticated unit commitment model is employed, while both traditional capacity and flexibility adequacy concepts are addressed. A novel methodology to assess the flexibility adequacy using the operational power system schedule is presented. Multi-year simulations of the Greek interconnected power system on an hour-by-hour basis for the forthcoming 10-year study horizon (period 2018–2027) under a set of scenarios regarding the future operating conditions have been performed, providing the key operational data for the calculation of all probabilistic indicators. Test results indicate that the existence of all currently available thermal generating units as well as the timely realization of all scheduled construction plans is of utmost importance for the long-term secure and reliable operation of the Greek interconnected power system. In a more generalized framework, the ambitious EU goals regarding decarbonization and increasing RES shares in electricity generation should be accompanied by detailed studies in order to ensure that no resource adequacy problems will arise in the near future due to the massive withdrawal of conventional base-load and, possibly, flexible generating units.

Implementation of a software platform to support an eco-design methodology within a manufacturing firm

The paper aims to explore the implementation of an eco-design methodology and the related software platform (G.EN.ESI – Green ENgineering dESIgn) within technical departments of a manufacturing firm. The G.EN.ESI eco-design methodology is based on the life cycle thinking concept and the software platform is conceived as a set of inter-operable software tools able to efficiently exchange data among them and with the traditional design systems (i.e. CAD, PDM and PLM). A multinational company, designing and producing household appliances, adopted the proposed methodology and related software platform for redesigning two cooker hood models with the aim to improve their environmental performances. Design and engineering departments evaluated the methodology and platform impact on the product development process, as well as the platform inter-operability with traditional design tools. The results indicate that methodology and software platform satisfy the requirements of the enterprise in terms of: (i) degree of expertise and training requirement on this subject, (ii) low impact in a consolidated design process and, (ii) good level of inter-operability among heterogeneous tools. However, the testing results highlight the necessity of a further platform optimisations in terms of software integration (single workbench made by integrated software tools with the same graphical user interface).

PHAROS: An Integrated Planning Tool for Meeting the Energy and Water Needs of Remote Islands using RES-based Hybrid Solutions

There is a significant number of Greek islands in the Aegean Sea that still meet their electricity demand on the basis of the local autonomous thermal power stations, using considerable amounts of imported oil. In addition, many of these islands suffer from water scarcity, covering their potable water needs with water imports at extremely high costs. Under the framework of PHAROS research project, and in an effort to support energy and water self-sufficiency, an integrated software tool has been developed for the optimal planning of hybrid renewable energy systems (HRES), capable of investigating the energy balance of autonomous island regions. In this context, a planning methodology for HRES combined with a sizing algorithm for desalination plants were devised and integrated in the advanced software tool named Energy System Analysis (ESA). ESA enables the detailed analysis of systems that include components such as wind, PV and desalination plants, energy storage devices and diesel engines. To this end, the long-lasting problems of the Aegean Sea islands, mainly stemming from their state of remoteness and isolation, require the examination of long-term energy strategies, which ESA can support in an efficient manner. In this context, the current work provides a short presentation of the ESA tool main features, using two discrete case studies that correspond to a North and a South Aegean Sea island respectively.

Challenges in operationalizing the water–energy–food nexus

ABSTRACTConcerns about the water–energy–food (WEF) nexus have motivated many discussions regarding new approaches for managing water, energy and food resources. Despite the progress in recent years, there remain many challenges in scientific research on the WEF nexus, while implementation as a management tool is just beginning. The scientific challenges are primarily related to data, information and knowledge gaps in our understanding of the WEF inter-linkages. Our ability to untangle the WEF nexus is also limited by the lack of systematic tools that could address all the trade-offs involved in the nexus. Future research needs to strengthen the pool of information. It is also important to develop integrated software platforms and tools for systematic analysis of the WEF nexus. The experience made in integrated water resources management in the hydrological community, especially in the framework of Panta Rhei, is particularly well suited to take a lead in these advances.

SAXS4COLL: an integrated software tool for analysing fibrous collagen-based tissues.

This article provides an overview of a new integrated software tool for reduction and analysis of small-angle X-ray scattering (SAXS) data from fibrous collagen tissues, with some wider applicability to other cylindrically symmetric scattering systems. SAXS4COLL combines interactive features for data pre-processing, bespoke background subtraction, semi-automated peak detection and calibration. Both equatorial and meridional SAXS peak parameters can be measured, and the former can be deconstructed into cylinder and lattice contributions. Finally, the software combines functionality for determination of collagen spatial order parameters with a rudimentary orientation plot capability.

NaviSE: superenhancer navigator integrating epigenomics signal algebra

BackgroundSuperenhancers are crucial structural genomic elements determining cell fate, and they are also involved in the determination of several diseases, such as cancer or neurodegeneration. Although there are pipelines which use independent pieces of software to predict the presence of superenhancers from genome-wide chromatin marks or DNA-interaction protein binding sites, there is not yet an integrated software tool that processes automatically algebra combinations of raw data sequencing into a comprehensive final annotated report of predicted superenhancers.ResultsWe have developed NaviSE, a user-friendly streamlined tool which performs a fully-automated parallel processing of genome-wide epigenomics data from sequencing files into a final report, built with a comprehensive set of annotated files that are navigated through a graphic user interface dynamically generated by NaviSE. NaviSE also implements an ‘epigenomics signal algebra’ that allows the combination of multiple activation and repression epigenomics signals. NaviSE provides an interactive chromosomal landscaping of the locations of superenhancers, which can be navigated to obtain annotated information about superenhancer signal profile, associated genes, gene ontology enrichment analysis, motifs of transcription factor binding sites enriched in superenhancers, graphs of the metrics evaluating the superenhancers quality, protein-protein interaction networks and enriched metabolic pathways among other features. We have parallelised the most time-consuming tasks achieving a reduction up to 30% for a 15 CPUs machine. We have optimized the default parameters of NaviSE to facilitate its use. NaviSE allows different entry levels of data processing, from sra-fastq files to bed files; and unifies the processing of multiple replicates. NaviSE outperforms the more time-consuming processes required in a non-integrated pipeline. Alongside its high performance, NaviSE is able to provide biological insights, predicting cell type specific markers, such as SOX2 and ZIC3 in embryonic stem cells, CDK5R1 and REST in neurons and CD86 and TLR2 in monocytes.ConclusionsNaviSE is a user-friendly streamlined solution for superenhancer analysis, annotation and navigation, requiring only basic computer and next generation sequencing knowledge. NaviSE binaries and documentation are available at: https://sourceforge.net/projects/navise-superenhancer/.

Development of a fuzzy integrated software tool to prioritise technical requirements for effective design of online shopping websites

Recently, there has been a tremendous growth in the online shopping; nevertheless the users' satisfaction rate has dropped largely due to poor design of websites. Thus, there is a pressing need of well-designed websites. Decision making plays a significant role in effective design of websites. Quality function deployment (QFD) being a decision making tool, can be employed for the design of online shopping websites. However, QFD uses linguistic expressions and follows crisp approach generating uncertainty and vagueness which leads to inconsistency in results. This requires fuzzy integration with QFD to address the issue. In QFD, the customer needs (CNs) and technical requirements (TRs) are prioritised. However, the paper considers TRs prioritisation only and in this regard it aims to develop a fuzzy integrated technical requirements prioritisation software tool for effective design of online shopping websites. The tool is developed using VB.Net and MS-Access and symmetrical triangular fuzzy numbers (STFNs) are proposed to deal with the uncertainty and vagueness.

Development of a fuzzy integrated software tool to prioritise technical requirements for effective design of online shopping websites

Recently, there has been a tremendous growth in the online shopping; nevertheless the users' satisfaction rate has dropped largely due to poor design of websites. Thus, there is a pressing need of well-designed websites. Decision making plays a significant role in effective design of websites. Quality function deployment (QFD) being a decision making tool, can be employed for the design of online shopping websites. However, QFD uses linguistic expressions and follows crisp approach generating uncertainty and vagueness which leads to inconsistency in results. This requires fuzzy integration with QFD to address the issue. In QFD, the customer needs (CNs) and technical requirements (TRs) are prioritised. However, the paper considers TRs prioritisation only and in this regard it aims to develop a fuzzy integrated technical requirements prioritisation software tool for effective design of online shopping websites. The tool is developed using VB.Net and MS-Access and symmetrical triangular fuzzy numbers (STFNs) are proposed to deal with the uncertainty and vagueness.

Using a ‘network of practice’ approach to match grazing decision-support system design with farmer practice

The use of pasture measurement tools and decision-support systems (DSS) for grazing management remains limited on New Zealand dairy farms. However, effective use of such tools provides opportunities to optimise pasture grown and pasture harvested. The present study used a mixed-method qualitative research approach to investigate pasture data and technology use for grazing decision making, through interviews and workshops with farmers, rural professionals, commercial software developers and a panel of farming-system specialists. Results suggest that different drivers for use of pasture data and DSS exist between farm owner-operators and corporate farming operations. Larger multi-farm businesses are collecting pasture data for use at a governance level as well as for operational decision making. Understanding the seasonal influences on decision making, and incorporating major regional differences such as pasture growth rates and impact of irrigation use, provides guidance on how to better match DSS to farmer practice. Study participants identified a need for greater integration of software tools to connect in-paddock data capture with real-time feedback. Also, data integration is needed to enable the transfer of information across different platforms for corporate farming operations. Rural professionals used commercial grazing DSS products, but also constructed their own spreadsheets to enable functionality and reporting not available in the DSS products. The research highlighted a need for farmer-orientated tools that are flexible to incorporate differences in user goals, decision making, mobility and desired outputs. Key attributes identified were seasonality, simplicity, ability to trial before purchase, flexibility in application, scalability to match farm systems, and integration with other tools. Future research and design of DSS tools requires a focus on co-creation with farmers, to merge scientific and practical knowledge.

The Identification and Application of Human System Integration Software Tools to Support the Systems Engineering Lifecycle and the Acquisition Process

This paper discusses the challenges associated with ensuring Human System Integration (HSI) efforts are performed throughout long-duration projects, including the systems engineering lifecycle and the acquisition process. It describes an approach to support this process by identifying relevant software tools that can be used across the lifecycle. The paper also discusses a project to develop a catalog of relevant HSI software tools and to map these tools to the acquisition process and systems engineering lifecycle at the Department of Homeland Security.

A Flipped Lab Experience for Mechatronics Education

This article discusses different lab experiences for mechatronics education. Integrated software tools like MATLAB and Simulink and the availability of low-cost hardware are enabling technologies for the development of innovative laboratory and curriculum paradigms. An example of this is the laboratory curriculum developed for the Mechatronics course at Rensselaer, consisting of the Rensselaer Mechatronics Hardware Kit and the associated RASPLib software package, which allow the students to take the laboratory experience out of the classroom and into their dorm rooms. This has created unique opportunities for learning and pedagogy. The Mini Inverted Pendulum project provides students a complete Mechatronics design experience. The end objective is clear: use the motor and sensors in the Mechatronics Kit to balance the pendulum.

SCell: integrated analysis of single-cell RNA-seq data.

Analysis of the composition of heterogeneous tissue has been greatly enabled by recent developments in single-cell transcriptomics. We present SCell, an integrated software tool for quality filtering, normalization, feature selection, iterative dimensionality reduction, clustering and the estimation of gene-expression gradients from large ensembles of single-cell RNA-seq datasets. SCell is open source, and implemented with an intuitive graphical interface. Scripts and protocols for the high-throughput pre-processing of large ensembles of single-cell, RNA-seq datasets are provided as an additional resource. Binary executables for Windows, MacOS and Linux are available at http://sourceforge.net/projects/scell, source code and pre-processing scripts are available from https://github.com/diazlab/SCellSupplementary information: Supplementary data are available at Bioinformatics online. aaron.diaz@ucsf.edu.

ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research.

BackgroundTraditional Sanger sequencing has been used as a gold standard method for genetic testing in clinic to perform single gene test, which has been a cumbersome and expensive method to test several genes in heterogeneous disease such as cancer. With the advent of Next Generation Sequencing technologies, which produce data on unprecedented speed in a cost effective manner have overcome the limitation of Sanger sequencing. Therefore, for the efficient and affordable genetic testing, Next Generation Sequencing has been used as a complementary method with Sanger sequencing for disease causing mutation identification and confirmation in clinical research. However, in order to identify the potential disease causing mutations with great sensitivity and specificity it is essential to ensure high quality sequencing data. Therefore, integrated software tools are lacking which can analyze Sanger and NGS data together and eliminate platform specific sequencing errors, low quality reads and support the analysis of several sample/patients data set in a single run.ResultsWe have developed ClinQC, a flexible and user-friendly pipeline for format conversion, quality control, trimming and filtering of raw sequencing data generated from Sanger sequencing and three NGS sequencing platforms including Illumina, 454 and Ion Torrent. First, ClinQC convert input read files from their native formats to a common FASTQ format and remove adapters, and PCR primers. Next, it split bar-coded samples, filter duplicates, contamination and low quality sequences and generates a QC report. ClinQC output high quality reads in FASTQ format with Sanger quality encoding, which can be directly used in down-stream analysis. It can analyze hundreds of sample/patients data in a single run and generate unified output files for both Sanger and NGS sequencing data. Our tool is expected to be very useful for quality control and format conversion of Sanger and NGS data to facilitate improved downstream analysis and mutation screening.ConclusionsClinQC is a powerful and easy to handle pipeline for quality control and trimming in clinical research. ClinQC is written in Python with multiprocessing capability, run on all major operating systems and is available at https://sourceforge.net/projects/clinqc.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-0915-y) contains supplementary material, which is available to authorized users.

FITPix COMBO—Timepix detector with integrated analog signal spectrometric readout

The hybrid semiconductor pixel detector Timepix has proven a powerful tool in radiation detection and imaging. Energy loss and directional sensitivity as well as particle type resolving power are possible by high resolution particle tracking and per-pixel energy and quantum-counting capability. The spectrometric resolving power of the detector can be further enhanced by analyzing the analog signal of the detector common sensor electrode (also called back-side pulse). In this work we present a new compact readout interface, based on the FITPix readout architecture, extended with integrated analog electronics for the detector's common sensor signal. Integrating simultaneous operation of the digital per-pixel information with the common sensor (called also back-side electrode) analog pulse processing circuitry into one device enhances the detector capabilities and opens new applications. Thanks to noise suppression and built-in electromagnetic interference shielding the common hardware platform enables parallel analog signal spectroscopy on the back side pulse signal with full operation and read-out of the pixelated digital part, the noise level is 600 keV and spectrometric resolution around 100 keV for 5.5 MeV alpha particles. Self-triggering is implemented with delay of few tens of ns making use of adjustable low-energy threshold of the particle analog signal amplitude. The digital pixelated full frame can be thus triggered and recorded together with the common sensor analog signal. The waveform, which is sampled with frequency 100 MHz, can be recorded in adjustable time window including time prior to the trigger level. An integrated software tool provides control, on-line display and read-out of both analog and digital channels. Both the pixelated digital record and the analog waveform are synchronized and written out by common time stamp.

An efficient channel selection and power allocation scheme for TVWS based on interference analysis in smart metering infrastructure

Nowadays, smart meter (SM) technology is widely effectively used. In addition, power allocation (PA) and channel selection (CS) are considered problems with many proposed approaches. In this paper, we will suggest a specific scenario for an SM configuration system and show how to solve the optimization problem for transmission between SMs and the data concentrator unit (DCU), the center that collects the data from several SMs, via simulation. An efficient CS with PA scheme is proposed in the TV white space system, which uses the TV band spectrum. On the basic of the optimal configuration requirements, SMs can have a transmission schedule and channel selection to obtain the optimal efficiency of using spectrum resources when transmitting data to the DCU. The optimal goals discussed in this paper are the maximum capacity or maximum channel efficiency and the maximum allowable power of the SMs used to satisfy the quality of service without harm to another wireless system. In addition, minimization of the interference to the digital television system and other SMs is also important and needs to be considered when the solving coexistence scenario. Further, we propose a process that performs an interference analysis scheme by using the spectrum engineering advanced Monte Carlo analysis tool (SEAMCAT), which is an integrated software tool based on a Monte-Carlo simulation method. Briefly, the process is as follows: The optimization process implemented by genetic evolution optimization engines, i.e., a genetic algorithm, will calculate the best configuration for the SM system on the basis of the interference limitation for each SM by SEAMCAT in a specific configuration, which reaches the solution with the best defined optimal goal satisfaction.

Modeling of complex gas distribution systems operating under any vacuum conditions: Simulations of the ITER divertor pumping system

An integrated software tool for modeling and simulation of complex gas distribution systems operating under any vacuum conditions is presented and validated. The algorithm structure includes (a) the input geometrical and operational data of the network, (b) the definition of the fundamental set of network loops and pseudoloops, (c) the formulation and solution of the mass and energy conservation equations, (d) the kinetic data base of the flow rates for channels of any length in the whole range of the Knudsen number, supporting, in an explicit manner, the solution of the conservation equations and (e) the network output data (mainly node pressures and channel flow rates/conductance). The code validity is benchmarked under rough vacuum conditions by comparison with hydrodynamic solutions in the slip regime. Then, its feasibility, effectiveness and potential are demonstrated by simulating the ITER torus vacuum system with the six direct pumps based on the 2012 design of the ITER divertor. Detailed results of the flow patterns and paths in the cassettes, in the gaps between the cassettes and along the divertor ring, as well as of the total throughput for various pumping scenarios and dome pressures are provided. A comparison with previous results available in the literature is included.

Optimal operation of insular electricity grids under high RES penetration

This paper presents a scenario-based simulation analysis of the operation of the insular power system of Crete, Greece, on an hour-by-hour basis aiming at the evaluation of the impact of high Renewable Energy Sources (RES) penetration on the short-term power system scheduling. The possibility of introducing a pumped-storage plant as a storage facility to alleviate the negative effects of increased RES generation on the short-term operation is also investigated. The renewable generation impact is evaluated in terms of specific system indicators. An integrated software tool that performs annual simulation of the insular power system with hourly granularity aiming at the minimization of the total production cost while respecting the system and various generating unit operating constraints is used. Simulation results for the year 2015 provide quantitative assessment of the insular power system performance regarding its short-term operation under large-scale RES penetration and valuable conclusions are drawn.

The information systems' security level assessment model based on an ontology and evidential reasoning approach

In the area of information technology an amount of security issues persists through time. Ongoing activities on security solutions aim to integrate existing security guidelines, best practices, security standards and existing solutions, but they often lack a knowledge base or do not involve all security issues, particularly human influence.In this paper, we presented a model that can be the basis for a novel information systems security evaluation solution. This solution should be able to cover a wide range of all possible information security issues. Our model is based on an OWL ontology for knowledge base, uses an enhanced Evidential Reasoning algorithm for mathematical calculations and possesses a simple reflex intelligent agent's algorithm as a decision supporting element.Properties for this model supervene from properties of its constructing elements. Knowledge base being built on OWL ontology is a major element of the model. It can provide high flexibility and applicability to different information systems and business organizations; upgradeability to be up to date regarding current security issues and new threats; and high versatility, taking into evaluation all possible aspects regarding security issues, e.g., network security, software and hardware issues, human influence, security policies and disaster recovery plans. Enhanced Evidential Reasoning algorithm is based on the Dumpster–Shafer theory and is well suited for calculations with expert's subjective judgements combining qualitative with quantitative evaluation grades. We designed an algorithm for back coupling based on a simple reflex intelligent agent for results presentation and decision support.In our work, we explained how to connect and use each of the model's constructive elements to obtain information security evaluation results. In addition, we conducted a case study with the proposed model on a small business organization. To test our model, we also used the standard qualitative risk assessment method on the same business organization in order to compare both qualitative results.Preliminary testing results have shown that the presented model could achieve its goal if it would be developed into an integrated software tool with a well-defined and up-to-date ontological knowledge base.

DSSR: an integrated software tool for dissecting the spatial structure of RNA.

Insight into the three-dimensional architecture of RNA is essential for understanding its cellular functions. However, even the classic transfer RNA structure contains features that are overlooked by existing bioinformatics tools. Here we present DSSR (Dissecting the Spatial Structure of RNA), an integrated and automated tool for analyzing and annotating RNA tertiary structures. The software identifies canonical and noncanonical base pairs, including those with modified nucleotides, in any tautomeric or protonation state. DSSR detects higher-order coplanar base associations, termed multiplets. It finds arrays of stacked pairs, classifies them by base-pair identity and backbone connectivity, and distinguishes a stem of covalently connected canonical pairs from a helix of stacked pairs of arbitrary type/linkage. DSSR identifies coaxial stacking of multiple stems within a single helix and lists isolated canonical pairs that lie outside of a stem. The program characterizes ‘closed’ loops of various types (hairpin, bulge, internal, and junction loops) and pseudoknots of arbitrary complexity. Notably, DSSR employs isolated pairs and the ends of stems, whether pseudoknotted or not, to define junction loops. This new, inclusive definition provides a novel perspective on the spatial organization of RNA. Tests on all nucleic acid structures in the Protein Data Bank confirm the efficiency and robustness of the software, and applications to representative RNA molecules illustrate its unique features. DSSR and related materials are freely available at http://x3dna.org/.