WorldWideScience

Sample records for biology driven software

  1. Software engineering architecture-driven software development

    CERN Document Server

    Schmidt, Richard F

    2013-01-01

    Software Engineering: Architecture-driven Software Development is the first comprehensive guide to the underlying skills embodied in the IEEE's Software Engineering Body of Knowledge (SWEBOK) standard. Standards expert Richard Schmidt explains the traditional software engineering practices recognized for developing projects for government or corporate systems. Software engineering education often lacks standardization, with many institutions focusing on implementation rather than design as it impacts product architecture. Many graduates join the workforce with incomplete skil

  2. Chaste: A test-driven approach to software development for biological modelling

    KAUST Repository

    Pitt-Francis, Joe

    2009-12-01

    Chaste (\\'Cancer, heart and soft-tissue environment\\') is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence. Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling. Program summary: Program title: Chaste. Catalogue identifier: AEFD_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEFD_v1_0.html. Program obtainable from: CPC Program Library, Queen\\'s University, Belfast, N. Ireland. Licensing provisions: LGPL 2.1. No. of lines in distributed program, including test data, etc.: 5 407 321. No. of bytes in distributed program, including test data, etc.: 42 004 554. Distribution format: tar.gz. Programming language: C++. Operating system: Unix. Has the code been vectorised or parallelized?: Yes. Parallelized using MPI. RAM:< 90   Megabytes for two of the scenarios described in Section 6 of the manuscript (Monodomain re-entry on a slab or Cylindrical crypt simulation). Up to 16 Gigabytes (distributed across processors) for full resolution bidomain cardiac simulation. Classification: 3. External routines: Boost, CodeSynthesis XSD, CxxTest, HDF5, METIS, MPI, PETSc, Triangle, Xerces. Nature of problem: Chaste may be used for solving coupled ODE and PDE systems arising from modelling biological systems. Use of Chaste in two application areas are described in this paper: cardiac

  3. Economics-driven software architecture

    CERN Document Server

    Mistrik, Ivan; Kazman, Rick; Zhang, Yuanyuan

    2014-01-01

    Economics-driven Software Architecture presents a guide for engineers and architects who need to understand the economic impact of architecture design decisions: the long term and strategic viability, cost-effectiveness, and sustainability of applications and systems. Economics-driven software development can increase quality, productivity, and profitability, but comprehensive knowledge is needed to understand the architectural challenges involved in dealing with the development of large, architecturally challenging systems in an economic way. This book covers how to apply economic consider

  4. Empirically Driven Software Engineering Research

    Science.gov (United States)

    Rombach, Dieter

    Software engineering is a design discipline. As such, its engineering methods are based on cognitive instead of physical laws, and their effectiveness depends highly on context. Empirical methods can be used to observe the effects of software engineering methods in vivo and in vitro, to identify improvement potentials, and to validate new research results. This paper summarizes both the current body of knowledge and further challenges wrt. empirical methods in software engineering as well as empirically derived evidence regarding software typical engineering methods. Finally, future challenges wrt. education, research, and technology transfer will be outlined.

  5. Model-driven software migration a methodology

    CERN Document Server

    Wagner, Christian

    2014-01-01

    Today, reliable software systems are the basis of any business or company. The continuous further development of those systems is the central component in software evolution. It requires a huge amount of time- man power- as well as financial resources. The challenges are size, seniority and heterogeneity of those software systems. Christian Wagner addresses software evolution: the inherent problems and uncertainties in the process. He presents a model-driven method which leads to a synchronization between source code and design. As a result the model layer will be the central part in further e

  6. Model Driven Software Development for Agricultural Robotics

    DEFF Research Database (Denmark)

    Larsen, Morten

    2016-01-01

    The design and development of agricultural robots, consists of both mechan- ical, electrical and software components. All these components must be de- signed and combined such that the overall goal of the robot is fulfilled. The design and development of these systems require collaboration between...... processing, control engineering, etc. This thesis proposes a Model-Driven Software Develop- ment based approach to model, analyse and partially generate the software implementation of a agricultural robot. Furthermore, Guidelines for mod- elling the architecture of an agricultural robots are provided......, assisting with bridging the different engineering disciplines. Timing play an important role in agricultural robotic applications, synchronisation of robot movement and implement actions is important in order to achieve precision spraying, me- chanical weeding, individual feeding, etc. Discovering...

  7. Static Checking of Interrupt-driven Software

    DEFF Research Database (Denmark)

    Brylow, Dennis; Damgaard, Niels; Palsberg, Jens

    2001-01-01

    in a few seconds on a standard PC. Our tool is one of the first to give an efficient and useful static analysis of assembly code. It enables increased confidence in correctness, significantly reduced testing requirements, and support for maintenance throughout the system life-cycle....... require extensive brute-force testing, making development and maintenance costly. This is particularly true for system components that are written in assembly language. Static checking has the potential of alleviating these problems, but until now there has been little tool support for programming...... at the assembly level. In this paper we present the design and implementation of a static checker for interrupt-driven Z86-based software with hard real-time requirements. For six commercial microcontrollers, our checker has produced upper bounds on interrupt latencies and stack sizes, as well as verified...

  8. Model-driven and software product line engineering

    CERN Document Server

    Royer, Jean-Claude

    2013-01-01

    Many approaches to creating Software Product Lines have emerged that are based on Model-Driven Engineering. This book introduces both Software Product Lines and Model-Driven Engineering, which have separate success stories in industry, and focuses on the practical combination of them. It describes the challenges and benefits of merging these two software development trends and provides the reader with a novel approach and practical mechanisms to improve software development productivity.The book is aimed at engineers and students who wish to understand and apply software product lines

  9. An ontology-driven software development framework

    OpenAIRE

    Mavetera, Nehemiah; Kroeze, Jan H

    2010-01-01

    The software development process has been curtailed by the lack of a methodology that can capture and maintain the softer, humanist characteristics of organizational systems into the software product. This is attributed to the absence of a software model that can capture and maintain these characteristics at analysis through to design and implementation phases of the development life cycle. Using grounded theory method, the authors investigated issues that limit the usability of software s...

  10. SOA-Driven Business-Software Alignment

    NARCIS (Netherlands)

    Shishkov, Boris; Sinderen, van Marten; Quartel, Dick

    2006-01-01

    The alignment of business processes and their supporting application software is a major concern during the initial software design phases. This paper proposes a design approach addressing this problem of business-software alignment. The approach takes an initial business model as a basis in derivin

  11. Model-driven evolution of software architectures

    NARCIS (Netherlands)

    Graaf, B.S.

    2007-01-01

    Software evolves continuously. As a consequence, software systems tend to become increasingly complex and, as such, more difficult to change. A software system's complexity is for a large part determined by its structure, or architecture. In this thesis we investigate how to reduce the risks and cos

  12. Test driven software development with Java EE

    OpenAIRE

    Balantič, Matija

    2013-01-01

    Test driven development (TDD) is a technique with the main idea of writing a failing test first, which is then made to pass by implementing a particular snippet of code. Development is done in short iterations which consist of three basic steps, namely test-code-refactor. The thesis shows the development of Java EE web applications FerApp using test driven development and continuous integration. The application development was driven with unit tests and complemented with integration and f...

  13. A model-driven traceability framework for software product lines

    OpenAIRE

    Anquetil, Nicolas; Kulesza, Uirá; Mitschke, Ralf; Moreira, Ana; Royer, Jean-Claude; Rummler, Andreas; Sousa, André

    2010-01-01

    Software product line (SPL) engineering is a recent approach to software development where a set of software products are derived for a well defined target application domain, from a common set of core assets using analogous means of production (for instance, through Model Driven Engineering). Therefore, such family of products are built from reuse, instead of developed individually from scratch. SPL promise to lower the costs of development, increase the quality of software, give clients mor...

  14. Small is beautiful: customer driven software development

    OpenAIRE

    Hansen, Henrik A.B.; Koch, Christian; Pleman, Allan

    1999-01-01

    Summary form only given. The topics addressed in this paper is how networking can be used as a way for small software houses to enhances their innovative capabilities by using different kinds of collaboration in order to overcome the problems of lacking knowledge as well as resources in order to develop their software. In small software houses operating in markets with complex products such as ERP (enterprise resource planning) systems, networking is necessary in order to gain the needed know...

  15. Architecture for interoperable software in biology.

    Science.gov (United States)

    Bare, James Christopher; Baliga, Nitin S

    2014-07-01

    Understanding biological complexity demands a combination of high-throughput data and interdisciplinary skills. One way to bring to bear the necessary combination of data types and expertise is by encapsulating domain knowledge in software and composing that software to create a customized data analysis environment. To this end, simple flexible strategies are needed for interconnecting heterogeneous software tools and enabling data exchange between them. Drawing on our own work and that of others, we present several strategies for interoperability and their consequences, in particular, a set of simple data structures--list, matrix, network, table and tuple--that have proven sufficient to achieve a high degree of interoperability. We provide a few guidelines for the development of future software that will function as part of an interoperable community of software tools for biological data analysis and visualization.

  16. Software Project Management A Process-Driven Approach

    CERN Document Server

    Ahmed, Ashfaque

    2011-01-01

    To build reliable, industry-applicable software products, large-scale software project groups must continuously improve software engineering processes to increase product quality, facilitate cost reductions, and adhere to tight schedules. Emphasizing the critical components of successful large-scale software projects, Software Project Management: A Process-Driven Approach discusses human resources, software engineering, and technology to a level that exceeds most university-level courses on the subject. The book is organized into five parts. Part I defines project management with information o

  17. Model-driven software development approaches in robotics research

    OpenAIRE

    Ramaswamy, Arun Kumar; Monsuez, Bruno; Tapus, Adriana

    2014-01-01

    Recently, there is an encouraging trend in adopting model-driven engineering approaches for software development in robotics research. In this paper, currently available model-driven techniques in robotics are analyzed with respect to the domain-specific requirements. A conceptual overview of our software development approach called 'Self Adaptive Framework for Robotic Systems (SafeRobots)' is explained and we also try to position our approach within this model ecosystem.

  18. Small is beautiful: customer driven software development

    DEFF Research Database (Denmark)

    Hansen, Henrik A.B.; Koch, Christian; Pleman, Allan

    1999-01-01

    Summary form only given. The topics addressed in this paper is how networking can be used as a way for small software houses to enhances their innovative capabilities by using different kinds of collaboration in order to overcome the problems of lacking knowledge as well as resources in order...... to develop their software. In small software houses operating in markets with complex products such as ERP (enterprise resource planning) systems, networking is necessary in order to gain the needed knowledge and resources in the production development process. Network is not seen as a magic word but leads...... to different benefits and short comings for the collaborative companies depending on the specific context. In this paper we discuss three types of networks: collaboration between users and producer(s), collaboration between a software house and third party suppliers, and a collaboration between academics...

  19. Model-driven dependability assessment of software systems

    CERN Document Server

    Bernardi, Simona; Petriu, Dorina C

    2013-01-01

    In this book, the authors present cutting-edge model-driven techniques for modeling and analysis of software dependability. Most of them are based on the use of UML as software specification language. From the software system specification point of view, such techniques exploit the standard extension mechanisms of UML (i.e., UML profiling). UML profiles enable software engineers to add non-functional properties to the software model, in addition to the functional ones. The authors detail the state of the art on UML profile proposals for dependability specification and rigorously describe the t

  20. Model-Driven Development of Complex Software: A Research Roadmap

    OpenAIRE

    France, Robert; Rumpe, Bernhard

    2014-01-01

    The term Model-Driven Engineering (MDE) is typically used to describe software development approaches in which abstract models of software systems are created and systematically transformed to concrete implementations. In this paper we give an overview of current research in MDE and discuss some of the major challenges that must be tackled in order to realize the MDE vision of software development. We argue that full realizations of the MDE vision may not be possible in the near to medium-ter...

  1. EDUTAINMENT SOFTWARE EVALUATION PREPARED FOR BIOLOGY INSTRUCTION

    Directory of Open Access Journals (Sweden)

    Yılmaz KARA

    2009-05-01

    Full Text Available The aim of this study is to determine whether an edutainment software program, called “Biyoskop” prepared for computer assisted biology instruction, has educational quality according to the criteria which have to be taken into consideration during the evaluation process of an educational software program. The subjects of the study consist of a group of 48 biology teachers. In this research, “educational software evaluation scale”, which lists the criteria necessary for courseware programs used in computer assisted instruction, has been used in order to attain teachers’ evaluations regarding the appropriateness of content, ease-of-use, technical and educational adequacy of the software. As a result of the analysis of the gathered data, it has been evaluated that the software ranks “average” in terms of adequacy due to the lack of sufficient qualifications, such as the relation of the content to the target behavior, compatibility with the curriculum, providing opportunities of progress for the students asking for further information, providing additional activities and containing an achievement test.

  2. Suitability of Modern Software Development Methodologies for Model Driven Development

    Directory of Open Access Journals (Sweden)

    Ruben Picek

    2009-12-01

    Full Text Available As an answer to today’s growing challenges in software industry, wide spectrum of new approaches of software development has occurred. One prominent direction is currently most promising software development paradigm called Model Driven Development (MDD. Despite a lot of skepticism and problems, MDD paradigm is being used and improved to accomplish many inherent potential benefits. In the methodological approach of software development it is necessary to use some kind of development process. Modern methodologies can be classified into two main categories: formal or heavyweight and agile or lightweight. But when it is a question about MDD and development process for MDD, currently known methodologies are very poor or better said they don't have any explanation of MDD process. As the result of research, in this paper, author examines the possibilities of using existing modern software methodologies in context of MDD paradigm.

  3. On environment-driven software model for Internetware

    Institute of Scientific and Technical Information of China (English)

    LU Jian; MA XiaoXing; TAO XianPing; CAO Chun; HUANG Yu; YU Ping

    2008-01-01

    Internetware is envisioned as a general software paradigm for the application style of resources integration and sharing in the open, dynamic and uncertain platforms such as the Internet. Continuing the agent-based Internetware model presented in a previous paper, in this paper, after an analysis of the behavioral patterns and the technical challenges of environment-driven applications, a software-structuring model is proposed for environment-driven Internetware applications. A series of explorations on the enabling techniques for the model, especially the modeling, management and utilization of context information are presented. Several proto-typical systems have also been built to prove the concepts and evaluate the tech-niques. These research efforts make a further step toward the Internetware para-digm by providing an initial framework for the construction of context-aware and self-adaptive software application systems in the open network environment.

  4. Chaste: using agile programming techniques to develop computational biology software.

    Science.gov (United States)

    Pitt-Francis, Joe; Bernabeu, Miguel O; Cooper, Jonathan; Garny, Alan; Momtahan, Lee; Osborne, James; Pathmanathan, Pras; Rodriguez, Blanca; Whiteley, Jonathan P; Gavaghan, David J

    2008-09-13

    Cardiac modelling is the area of physiome modelling where the available simulation software is perhaps most mature, and it therefore provides an excellent starting point for considering the software requirements for the wider physiome community. In this paper, we will begin by introducing some of the most advanced existing software packages for simulating cardiac electrical activity. We consider the software development methods used in producing codes of this type, and discuss their use of numerical algorithms, relative computational efficiency, usability, robustness and extensibility. We then go on to describe a class of software development methodologies known as test-driven agile methods and argue that such methods are more suitable for scientific software development than the traditional academic approaches. A case study is a project of our own, Cancer, Heart and Soft Tissue Environment, which is a library of computational biology software that began as an experiment in the use of agile programming methods. We present our experiences with a review of our progress thus far, focusing on the advantages and disadvantages of this new approach compared with the development methods used in some existing packages. We conclude by considering whether the likely wider needs of the cardiac modelling community are currently being met and suggest that, in order to respond effectively to changing requirements, it is essential that these codes should be more malleable. Such codes will allow for reliable extensions to include both detailed mathematical models--of the heart and other organs--and more efficient numerical techniques that are currently being developed by many research groups worldwide. PMID:18565813

  5. Aspects across Software Life Cycle: A Goal-Driven Approach

    Science.gov (United States)

    Niu, Nan; Yu, Yijun; González-Baixauli, Bruno; Ernst, Neil; Sampaio Do Prado Leite, Julio Cesar; Mylopoulos, John

    Goal modeling fits model-driven engineering (MDE) in that it captures stakeholder concerns and the interdependencies using concepts that are much less bound to the underlying implementation technology and are much closer to the problem languages. Aspect-oriented software development (AOSD) provides language constructs to facilitate the representation of multiple perceptions and to alleviate tangling and scattering concerns. Synthesis of AOSD and MDE not only manages software complexity but also improves productivity, as well as model quality and longevity. In this paper, we propose a model-driven framework for tracing aspects from requirements to implementation and testing, where goal models become engineering assets and straightforward model-to-code transformation bridges the gap between domain concepts and implementation technologies. We test our hypotheses and evaluate the framework’s applicability and usefulness with a case study of an open-source e-commerce platform written in PHP.

  6. Model-driven prototyping for corporate software specification

    OpenAIRE

    Memmel, Thomas; Bock, Carsten; Reiterer, Harald

    2007-01-01

    Corporate software development faces very demanding challenges, especially concerning the design of user interfaces. Collaborative design with stakeholders demands modeling methods that everybody can understand and apply. But when using traditional, paper-based methods to gather and document requirements, an IT organization often experiences frustrating communication issues between the business and development teams. We present ways of implementing model-driven prototyping for corporate softw...

  7. Data driven computing for Biological Systems

    Energy Technology Data Exchange (ETDEWEB)

    Samatova, Nagiza F.; Gorin, Andrey; Uberbacher, Edward; Karpinets, Tatiana V.; Park, Byung H.; Pan, Chongle; Straatsma, TP; Cannon, William R.; Resat, Haluk; Lins, Roberto D.; Oehmen, Christopher S.

    2007-11-01

    Biological breakthroughs that can lead to improved diagnosis and treatment of diseases, generation of clean energy, and solutions to other critical societal problems require high performance, data-intensive computational tools that have the ability to process, analyze and cohesively integrate massive amounts of data and information in real time. Biological computing problems are typically data-intensive and must share very large sets of data effectively across many processors. However, the various components of biological systems, composed of complex networks and pathways, must be integrated to gain a coherent understanding of the system. The more different types of data that can be integrated, the deeper the insights into the biology of the system being studied. Conventional analysis software, however, hasn’t been able to efficiently deal with such massive data set. The goal of the Data-Intensive Computing for Complex Biological Systems (BioPilot) project, a multiyear project funded by the U.S. Department of Energy’s Office of Advanced Scientific Computing Research (ASCR), is to create an integrated suite of highly flexible, highly adaptable pipelines of computational tools for analyzing large-scale data sets that will be used to address specific challenges facing the U.S. Department of Energy (DOE) and our society.

  8. The Systems Biology Research Tool: evolvable open-source software

    OpenAIRE

    Wright Jeremiah; Wagner Andreas

    2008-01-01

    Abstract Background Research in the field of systems biology requires software for a variety of purposes. Software must be used to store, retrieve, analyze, and sometimes even to collect the data obtained from system-level (often high-throughput) experiments. Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level. Results We introduce a free, easy-to-use, open-source, integrated software platform calle...

  9. Development of the software generation method using model driven software engineering tool

    Energy Technology Data Exchange (ETDEWEB)

    Jang, H. S.; Jeong, J. C.; Kim, J. H.; Han, H. W.; Kim, D. Y.; Jang, Y. W. [KOPEC, Taejon (Korea, Republic of); Moon, W. S. [NEXTech Inc., Seoul (Korea, Republic of)

    2003-10-01

    The methodologies to generate the automated software design specification and source code for the nuclear I and C systems software using model driven language is developed in this work. For qualitative analysis of the algorithm, the activity diagram is modeled and generated using Unified Modeling Language (UML), and then the sequence diagram is designed for automated source code generation. For validation of the generated code, the code audits and module test is performed using Test and QA tool. The code coverage and complexities of example code are examined in this stage. The low pressure pressurizer reactor trip module of the Plant Protection System was programmed as subject for this task. The test result using the test tool shows that errors were easily detected from the generated source codes that have been generated using test tool. The accuracy of input/output processing by the execution modules was clearly identified.

  10. Bioconductor: open software development for computational biology and bioinformatics

    DEFF Research Database (Denmark)

    Gentleman, R.C.; Carey, V.J.; Bates, D.M.;

    2004-01-01

    The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisci......The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry...... into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples....

  11. The Systems Biology Research Tool: evolvable open-source software

    Directory of Open Access Journals (Sweden)

    Wright Jeremiah

    2008-06-01

    Full Text Available Abstract Background Research in the field of systems biology requires software for a variety of purposes. Software must be used to store, retrieve, analyze, and sometimes even to collect the data obtained from system-level (often high-throughput experiments. Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level. Results We introduce a free, easy-to-use, open-source, integrated software platform called the Systems Biology Research Tool (SBRT to facilitate the computational aspects of systems biology. The SBRT currently performs 35 methods for analyzing stoichiometric networks and 16 methods from fields such as graph theory, geometry, algebra, and combinatorics. New computational techniques can be added to the SBRT via process plug-ins, providing a high degree of evolvability and a unifying framework for software development in systems biology. Conclusion The Systems Biology Research Tool represents a technological advance for systems biology. This software can be used to make sophisticated computational techniques accessible to everyone (including those with no programming ability, to facilitate cooperation among researchers, and to expedite progress in the field of systems biology.

  12. PROJECT-DRIVEN SOFTWARE BUSINESS IN TRANSILVANIA - A CASE STUDY

    Directory of Open Access Journals (Sweden)

    Radu Marius

    2015-07-01

    Full Text Available The fairly low salaries of the IT workers compared to the Western countries, the skills and the location have supported outsourcing become one of the most competitive Romanian sectors. IT sector in Romania maintains a steady growth favoured by outsourcing companies. Moreover Romania is highly competitive when you take into account the level of technical proficiency and soft skills in the country. Romanian labour force can drive relevant projects even in small teams. This case study explores the realty of Romanian IT companies profiles. It presents in comparison two companies bases on organizational and strategic dimensions: project approach orientation, leadership, project value driven, and social responsibility. The corporate goal of the first company presented in the case study - Fortech - is to achieve the best adaptive organizational structure which can sustain its competitive advantage. This advantage results from combination of three main ingredients: scaled up human resource capital, versatile knowledge management and adaptability to customer needs. Fortech manages and administrates and execute their business activities using project management methodologies and practices in order to achieve the strategic goals. On the other hand Dolphin Kiss Company is a “Python boutique agency” created around a single contract and organized on a single project. The project was contracted with a top company from telecommunication industry. The company is a small team of creative software engineers focused on developing a very innovative software business solution. This case study is an empirical qualitative research intended to depict the main differences between two relevant company profiles present in the actual economic context: small team – results oriented – highly skilled VS large structure of outsourcing teams – matrix organized – customer oriented. The case study constructs a space for debates regarding the potential evolution of the

  13. Lessons Learned in Software Testing A Context-Driven Approach

    CERN Document Server

    Kaner, Cem; Pettichord, Bret

    2008-01-01

    Decades of software testing experience condensed into the most important lessons learned.The world's leading software testing experts lend you their wisdom and years of experience to help you avoid the most common mistakes in testing software. Each lesson is an assertion related to software testing, followed by an explanation or example that shows you the how, when, and why of the testing lesson. More than just tips, tricks, and pitfalls to avoid, Lessons Learned in Software Testing speeds you through the critical testing phase of the software development project without the extensive trial an

  14. Way of Working for Embedded Control Software using Model-Driven Development Techniques

    NARCIS (Netherlands)

    Bezemer, Maarten M.; Groothuis, Marcel A.; Broenink, Jan F.; Brugali, D.; Schlegel, C.; Broenink, J.F.

    2011-01-01

    Embedded targets normally do not have much resources to aid developing and debugging the software. So model-driven development (MDD) is used for designing embedded software with a `first time right' approach. For such an approach, a good way of working (WoW) is required for embedded software develop

  15. Beyond standardization : dynamic software infrastructures for systems biology

    NARCIS (Netherlands)

    Swertz, Morris A.; Jansen, Ritsert C.

    2007-01-01

    Progress in systems biology is seriously hindered by slow production of suitable software infrastructures. Biologists need infrastructure that easily connects to work that is done in other laboratories, for which standardization is helpful. However, the infrastructure must also accommodate the speci

  16. Experiences in Teaching a Graduate Course on Model-Driven Software Development

    Science.gov (United States)

    Tekinerdogan, Bedir

    2011-01-01

    Model-driven software development (MDSD) aims to support the development and evolution of software intensive systems using the basic concepts of model, metamodel, and model transformation. In parallel with the ongoing academic research, MDSD is more and more applied in industrial practices. After being accepted both by a broad community of…

  17. A Semantics and Data-Driven Biomedical Multimedia Software System

    Directory of Open Access Journals (Sweden)

    Shih-Hsi Liu

    2010-08-01

    Full Text Available Developing a large-scale biomedical multimedia software system is always a challenging task: Satisfaction of sundry and stringent biomedical multimedia related requirements and standards; Heterogeneous software deployment and communication environments; and tangling correlation between data/contents and software functionalities, among others. This paper introduces a novel biomedical multimedia software system developed under Service-Oriented Architecture (SOA. Such a system takes the advantage of interoperability of SOA to solve the heterogeneity and correlation problems. The paper also classifies the system into services, annotation, ontologies, semantics matching, and QoS optimization aspects which may potentially solve the requirements problem: By establishing data ontology with respect to data properties, contents, QoS, and biomedical regulations and expanding service ontology to describe more functional and QoS specifications supported by services, appropriate services for processing biomedical multimedia data may be discovered, performed, tuned up or replaced as needed. Lastly, a biomedical education project that improves the performance of feature extraction and classification processed afterwards is introduced to illustrate the advantages of our software system developed under SOA.

  18. Process-Driven Software Development Methodology for Enterprise Information System

    Directory of Open Access Journals (Sweden)

    Kwan Hee Han

    2014-02-01

    Full Text Available In today’s process-centered business organization, it is imperative that enterprise information system must be converted from task-centered to proc ess-centered system. Traditional software development methodology is function-oriented, in wh ich each function manages its own data and it results in redundancy because data that belo ngs to one object are stored by several functions. Proposed in this paper is a process-driv en software development methodology, in which business process is a major concern and workf low functionalities are identified and specified throughout the entire development life cy cle. In the proposed methodology, the development process, modeling tools and deliverable s are clarified explicitly. Proposed methodology can be a guideline to practitioners inv olved in enterprise software development, of which workflow is an essential part.

  19. Integrative systems biology for data-driven knowledge discovery.

    Science.gov (United States)

    Greene, Casey S; Troyanskaya, Olga G

    2010-09-01

    Integrative systems biology is an approach that brings together diverse high-throughput experiments and databases to gain new insights into biological processes or systems at molecular through physiological levels. These approaches rely on diverse high-throughput experimental techniques that generate heterogeneous data by assaying varying aspects of complex biological processes. Computational approaches are necessary to provide an integrative view of these experimental results and enable data-driven knowledge discovery. Hypotheses generated from these approaches can direct definitive molecular experiments in a cost-effective manner. By using integrative systems biology approaches, we can leverage existing biological knowledge and large-scale data to improve our understanding of as yet unknown components of a system of interest and how its malfunction leads to disease.

  20. Framework for Visualizing Model-Driven Software Evolution and its Application

    CERN Document Server

    Rao, Akepogu Anand

    2010-01-01

    Software Visualization encompasses the development and evaluation of methods for graphically representing different aspects of methods of software, including its structure, execution and evolution. Creating visualizations helps the user to better understand complex phenomena. It is also found by the software engineering community that visualization is essential and important. In order to visualize the evolution of the models in Model-Driven Software Evolution, authors have proposed a framework which consists of 7 key areas (views) and 22 key features for the assessment of Model Driven Software Evolution process and addresses a number of stakeholder concerns. The framework is derived by the application of the Goal Question Metric Paradigm. This paper aims to describe an application of the framework by considering different visualization tools/CASE tools which are used to visualize the models in different views and to capture the information of models during their evolution. Comparison of such tools is also pos...

  1. Biological impact of music and software-based auditory training

    OpenAIRE

    Kraus, Nina

    2012-01-01

    Auditory-based communication skills are developed at a young age and are maintained throughout our lives. However, some individuals – both young and old – encounter difficulties in achieving or maintaining communication proficiency. Biological signals arising from hearing sounds relate to real-life communication skills such as listening to speech in noisy environments and reading, pointing to an intersection between hearing and cognition. Musical experience, amplification, and software-based ...

  2. Model-driven software development with ACTIVECHARTS - a case study

    OpenAIRE

    Gessenharter, Dominik

    2012-01-01

    Modeling static structure by using UML class diagrams is well supported by many tools and a de facto standard in modern software development. But generating code is still in a rudimentary stage. Many tools comprise extensible code generators, but the initial implementations of tool vendors are on a very low level. Although the claim that code generation is beneficial with respect to e. g. code quality and development time is generally accepted, state-of-the-art tool support is still far away ...

  3. Requirements-driven design of autonomic application software

    OpenAIRE

    Lapouchnian, Alexei; Yu, Yijun; Liaskos, Sotirios; Mylopoulos, John

    2006-01-01

    Autonomic computing systems reduce software maintenance costs and management complexity by taking on the responsibility for their configuration, optimization, healing, and protection. These tasks are accomplished by switching at runtime to a different system behaviour - the one that is more efficient, more secure, more stable, etc. - while still fulfilling the main purpose of the system. Thus, identifying the objectives of the system, analyzing alternative ways of how these objectives can be ...

  4. A Domain Knowledge Driven Approach for User Interface Software Development

    Institute of Scientific and Technical Information of China (English)

    王海鹰; 刘慎权

    1991-01-01

    A domain knowledge driven user interface development approach is described.As a conceptual design of the user interface,the domain knowledge defines the user interface in terms of objects,actions and their relationships that the user would use to interact with the application system.It also serves as input to a user interface management system (UIMS) and is the kernel of the target user interface.The principal ideas and the implementation techniques of the approach is discussed.The user interface model,user interface designer oriented high-level specification notatiopn,and the transformation algorithms on domain knowledge are presented.

  5. State of arbitrary complexity and Model Driven Architecture in the software development in Cuba

    Directory of Open Access Journals (Sweden)

    Nemury Silega

    2014-01-01

    Full Text Available Informatic systems play an important role in the society because are used in the majority of fields. The community of software researchers and developers devotes substantial efforts to determine how software systems can increasingly improve the environment in which they are deployed, for example, in medicine, business management, education, among other domains. But paradoxically these efforts do not correspond to those devoted to improving the environment of software development itself. There are insufficient proposals to streamline the software development process. The authors conducted an analysis of several proposals to improve the software development process in Cuba, propose how to address the problem based on the paradigm of Model Driven Architecture and make an assessment of the impact this may have on Cuban software industry.

  6. iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis

    Directory of Open Access Journals (Sweden)

    McNally James

    2009-01-01

    Full Text Available Abstract Background In recent years, the genome biology community has expended considerable effort to confront the challenges of managing heterogeneous data in a structured and organized way and developed laboratory information management systems (LIMS for both raw and processed data. On the other hand, electronic notebooks were developed to record and manage scientific data, and facilitate data-sharing. Software which enables both, management of large datasets and digital recording of laboratory procedures would serve a real need in laboratories using medium and high-throughput techniques. Results We have developed iLAP (Laboratory data management, Analysis, and Protocol development, a workflow-driven information management system specifically designed to create and manage experimental protocols, and to analyze and share laboratory data. The system combines experimental protocol development, wizard-based data acquisition, and high-throughput data analysis into a single, integrated system. We demonstrate the power and the flexibility of the platform using a microscopy case study based on a combinatorial multiple fluorescence in situ hybridization (m-FISH protocol and 3D-image reconstruction. iLAP is freely available under the open source license AGPL from http://genome.tugraz.at/iLAP/. Conclusion iLAP is a flexible and versatile information management system, which has the potential to close the gap between electronic notebooks and LIMS and can therefore be of great value for a broad scientific community.

  7. Architecture-driven Migration of Legacy Systems to Cloud-enabled Software

    DEFF Research Database (Denmark)

    Ahmad, Aakash; Babar, Muhammad Ali

    2014-01-01

    of legacy systems to cloud computing. The framework leverages the software reengineering concepts that aim to recover the architecture from legacy source code. Then the framework exploits the software evolution concepts to support architecture-driven migration of legacy systems to cloud-based architectures....... The Legacy-to-Cloud Migration Horseshoe comprises of four processes: (i) architecture migration planning, (ii) architecture recovery and consistency, (iii) architecture transformation and (iv) architecture-based development of cloud-enabled software. We aim to discover, document and apply the migration...

  8. Project-Driven Learning-by-Doing Method for Teaching Software Engineering using Virtualization Technology

    Directory of Open Access Journals (Sweden)

    Kun Ma

    2014-10-01

    Full Text Available Many universities are now offering software engineering an undergraduate level emphasizing knowledge point. However, some enterprise managers reflected that education ignore hands-on ability training, and claimed that there is the isolation between teaching and practice. This paper presents the design of a Software Engineering course (sixth semester in network engineering at University of Jinan for undergraduate Software Engineering students that uses virtualization technology to teach them project-driven learning-by-doing software development process. We present our motivation, challenges encountered, pedagogical goals and approaches, findings (both positive experiences and negative lessons. Our motivation was to teach project-driven Software Engineering using virtualization technology. The course also aims to develop entrepreneurial skills needed for software engineering graduates to better prepare them for the software industry. Billing models of virtualization help pupils and instructors find the cost of the experiment. In pay-as-you-go manner, two labs and three step-by-step projects (single project, pair project, and team project are designed to help the students to complete the assignment excitedly. We conduct some detailed surveys and present the results of student responses. The assessment process designed for this course is illustrated. The paper also shows that learning-by-doing method correlates with the characteristics of different projects, which has resulted in a successful experience as reported by students in an end of a semester survey.

  9. A Health-care Application of Goal-driven Software Design

    Directory of Open Access Journals (Sweden)

    Maria-Eugenia IACOB

    2009-07-01

    Full Text Available In this paper we focus on goal engineering by addressing issues such as goal elicitation, specification, structuring and operationalisation. Specification of business goals is regarded as a means to raise the level of abstraction (and automation at which business logic is incorporated in model driven software design in the context of service oriented architectures. More specifically, the proposed goal modelling approach consists of an abstract syntax (metamodel and a concrete syntax (graphical notation for the specification of business goals. We also proposed a framework for the goal-driven design of service-oriented software applications. In particular, we illustrate our approach by means of a case study carried out in the healthcare sector and we explain the role business goals (operationalised in the form of business rules can play in software design. This research also outlines a number of areas that have significant research potential.

  10. Towards Quality of Service and Resource Aware Robotic Systems through Model-Driven Software Development

    CERN Document Server

    Steck, Andreas

    2010-01-01

    Engineering the software development process in robotics is one of the basic necessities towards industrial-strength service robotic systems. A major challenge is to make the step from code-driven to model-driven systems. This is essential to replace hand-crafted single-unit systems by systems composed out of components with explicitly stated properties. Furthermore, this fosters reuse by separating robotics knowledge from short-cycled implementational technologies. Altogether, this is one but important step towards "able" robots. This paper reports on a model-driven development process for robotic systems. The process consists of a robotics metamodel with first explications of non-functional properties. A model-driven toolchain based on Eclipse provides the model transformation and code generation steps. It also provides design time analysis of resource parameters (e.g. schedulability analysis of realtime tasks) as a first step towards overall resource awareness in the development of integrated robotic syste...

  11. Biological impact of music and software-based auditory training

    Science.gov (United States)

    Kraus, Nina

    2012-01-01

    Auditory-based communication skills are developed at a young age and are maintained throughout our lives. However, some individuals – both young and old – encounter difficulties in achieving or maintaining communication proficiency. Biological signals arising from hearing sounds relate to real-life communication skills such as listening to speech in noisy environments and reading, pointing to an intersection between hearing and cognition. Musical experience, amplification, and software-based training can improve these biological signals. These findings of biological plasticity, in a variety of subject populations, relate to attention and auditory memory, and represent an integrated auditory system influenced by both sensation and cognition. Learning outcomes The reader will (1) understand that the auditory system is malleable to experience and training, (2) learn the ingredients necessary for auditory learning to successfully be applied to communication, (3) learn that the auditory brainstem response to complex sounds (cABR) is a window into the integrated auditory system, and (4) see examples of how cABR can be used to track the outcome of experience and training. PMID:22789822

  12. Agile software development and its compatibility with a document-driven approach? A case study

    DEFF Research Database (Denmark)

    Heeager, Lise Tordrup; Nielsen, Peter Axel

    2009-01-01

    It is generally assumed among software developers and managers that a document-driven development process is incompatible with an agile development process. There are few reports on this issue and even less empirical research documenting the assumed incompatibility. More and more software companies...... however have a desire to adopt agile development processes while maintaining compliance with a quality assurance standard or even a process standard. We have studied the software development process of a Danish pharmaceutical company. For market reasons the company has to comply the US Food and Drug...... Administration’s standards for software development. The company has also successfully implemented significant parts of the agile methodology Scrum. We describe this case and we analyse using Soft Systems Methodology how well the development process combines these diverging sets of process requirements. We find...

  13. JColorGrid: software for the visualization of biological measurements

    Directory of Open Access Journals (Sweden)

    May Barnaby CH

    2006-04-01

    Full Text Available Abstract Background Two-dimensional data colourings are an effective medium by which to represent three-dimensional data in two dimensions. Such "color-grid" representations have found increasing use in the biological sciences (e.g. microarray 'heat maps' and bioactivity data as they are particularly suited to complex data sets and offer an alternative to the graphical representations included in traditional statistical software packages. The effectiveness of color-grids lies in their graphical design, which introduces a standard for customizable data representation. Currently, software applications capable of generating limited color-grid representations can be found only in advanced statistical packages or custom programs (e.g. micro-array analysis tools, often associated with steep learning curves and requiring expert knowledge. Results Here we describe JColorGrid, a Java library and platform independent application that renders color-grid graphics from data. The software can be used as a Java library, as a command-line application, and as a color-grid parameter interface and graphical viewer application. Data, titles, and data labels are input as tab-delimited text files or Microsoft Excel spreadsheets and the color-grid settings are specified through the graphical interface or a text configuration file. JColorGrid allows both user graphical data exploration as well as a means of automatically rendering color-grids from data as part of research pipelines. Conclusion The program has been tested on Windows, Mac, and Linux operating systems, and the binary executables and source files are available for download at http://jcolorgrid.ucsf.edu.

  14. A new practice-driven approach to develop software in a cyber-physical system environment

    Science.gov (United States)

    Jiang, Yiping; Chen, C. L. Philip; Duan, Junwei

    2016-02-01

    Cyber-physical system (CPS) is an emerging area, which cannot work efficiently without proper software handling of the data and business logic. Software and middleware is the soul of the CPS. The software development of CPS is a critical issue because of its complicity in a large scale realistic system. Furthermore, object-oriented approach (OOA) is often used to develop CPS software, which needs some improvements according to the characteristics of CPS. To develop software in a CPS environment, a new systematic approach is proposed in this paper. It comes from practice, and has been evolved from software companies. It consists of (A) Requirement analysis in event-oriented way, (B) architecture design in data-oriented way, (C) detailed design and coding in object-oriented way and (D) testing in event-oriented way. It is a new approach based on OOA; the difference when compared with OOA is that the proposed approach has different emphases and measures in every stage. It is more accord with the characteristics of event-driven CPS. In CPS software development, one should focus on the events more than the functions or objects. A case study of a smart home system is designed to reveal the effectiveness of the approach. It shows that the approach is also easy to be operated in the practice owing to some simplifications. The running result illustrates the validity of this approach.

  15. Pattern recognition software and techniques for biological image analysis.

    Directory of Open Access Journals (Sweden)

    Lior Shamir

    Full Text Available The increasing prevalence of automated image acquisition systems is enabling new types of microscopy experiments that generate large image datasets. However, there is a perceived lack of robust image analysis systems required to process these diverse datasets. Most automated image analysis systems are tailored for specific types of microscopy, contrast methods, probes, and even cell types. This imposes significant constraints on experimental design, limiting their application to the narrow set of imaging methods for which they were designed. One of the approaches to address these limitations is pattern recognition, which was originally developed for remote sensing, and is increasingly being applied to the biology domain. This approach relies on training a computer to recognize patterns in images rather than developing algorithms or tuning parameters for specific image processing tasks. The generality of this approach promises to enable data mining in extensive image repositories, and provide objective and quantitative imaging assays for routine use. Here, we provide a brief overview of the technologies behind pattern recognition and its use in computer vision for biological and biomedical imaging. We list available software tools that can be used by biologists and suggest practical experimental considerations to make the best use of pattern recognition techniques for imaging assays.

  16. Epithelioid Sarcoma: Opportunities for Biology-driven Targeted Therapy

    Directory of Open Access Journals (Sweden)

    Jonathan eNoujaim

    2015-08-01

    Full Text Available Epithelioid sarcoma is a soft tissue sarcoma of children and young adults for which the preferred treatment for localised disease is wide surgical resection. Medical management is to a great extent undefined, and therefore for patients with regional and distal metastases, the development of targeted therapies is greatly desired. In this review we will summarize clinically-relevant biomarkers (e.g., SMARCB1, CA125, dysadherin and others with respect to targeted therapeutic opportunities. We will also examine the role of EGFR, mTOR and polykinase inhibitors (e.g., sunitinib in the management of local and disseminated disease. Towards building a consortium of pharmaceutical, academic and non-profit collaborators, we will discuss the state of resources for investigating epithelioid sarcoma with respect to cell line resources, tissue banks, and registries so that a roadmap can be developed towards effective biology-driven therapies.

  17. A scalable architecture for the demand-driven deployment of location-neutral software services

    OpenAIRE

    MacInnis, Robert F.

    2010-01-01

    This thesis presents a scalable service-oriented architecture for the demand-driven deployment of location-neutral software services, using an end-to-end or ‘holistic’ approach to address identified shortcomings of the traditional Web Services model. The architecture presents a multi-endpoint Web Service environment which abstracts over Web Service location and technology and enables the dynamic provision of highly-available Web Services. The model describes mechanisms which provide a framewo...

  18. Using Transformation-Aspects in Model-Driven Software Product Lines

    OpenAIRE

    Arboleda, Hugo; Casallas, Rubby; Royer, Jean-Claude

    2009-01-01

    Model-Driven Software Product Lines (MD-SPL) are configured by using configuration models and Problem Space metamodels that capture product line scope. Products are derived by means of successive model transformations, starting from problem space models and based on the configuration models. Fine-variations of MD-SPLs correspond to characteristics that afect particular elements of models involved in the model transformations. In this paper, we present an approach to create MD-SPL including fi...

  19. A Health-care Application of Goal-driven Software Design

    OpenAIRE

    Iacob, Maria-Eugenia; Rothengatter, Diederik; Van Hillegersberg, Jos

    2009-01-01

    In this paper we focus on goal engineering by addressing issues such as goal elicitation, specification, structuring and operationalisation. Specification of business goals is regarded as a means to raise the level of abstraction (and automation) at which business logic is incorporated in model driven software design in the context of service oriented architectures. More specifically, the proposed goal modelling approach consists of an abstract syntax (metamodel) and a concrete syntax (graphi...

  20. On model-driven design of robot software using co-simulation

    OpenAIRE

    Jan F. Broenink; Ni, Yunyun; Groothuis, Marcel A.; Menegatti, E

    2010-01-01

    In this paper we show that using co-simulation for robot software design will be more efficient than without co-simulation. We will show an example of the plotter how the co-simulation is helping with the design process. We believe that a collaborative methodology based on model-driven design will improve the chances of closing the design loop early, improving cross-discipline design dialog, and reduce errors, saving cost and time.

  1. Balancing Plan-Driven and Agile Methods in Software Engineering Project Courses

    Science.gov (United States)

    Boehm, Barry; Port, Dan; Winsor Brown, A.

    2002-09-01

    For the past 6 years, we have been teaching a two-semester software engineering project course. The students organize into 5-person teams and develop largely web-based electronic services projects for real USC campus clients. We have been using and evolving a method called Model- Based (System) Architecting and Software Engineering (MBASE) for use in both the course and in industrial applications. The MBASE Guidelines include a lot of documents. We teach risk-driven documentation: if it is risky to document something, and not risky to leave it out (e.g., GUI screen placements), leave it out. Even so, students tend to associate more documentation with higher grades, although our grading eventually discourages this. We are always on the lookout for ways to have students learn best practices without having to produce excessive documentation. Thus, we were very interested in analyzing the various emerging agile methods. We found that agile methods and milestone plan-driven methods are part of a “how much planning is enough?” spectrum. Both agile and plan-driven methods have home grounds of project characteristics where they clearly work best, and where the other will have difficulties. Hybrid agile/plan-driven approaches are feasible, and necessary for projects having a mix of agile and plan-driven home ground characteristics. Information technology trends are going more toward the agile methods' home ground characteristics of emergent requirements and rapid change, although there is a concurrent increase in concern with dependability. As a result, we are currently experimenting with risk-driven combinations of MBASE and agile methods, such as integrating requirements, test plans, peer reviews, and pair programming into “agile quality management.”

  2. A Computational Systems Biology Software Platform for Multiscale Modeling and Simulation: Integrating Whole-Body Physiology, Disease Biology, and Molecular Reaction Networks

    Science.gov (United States)

    Eissing, Thomas; Kuepfer, Lars; Becker, Corina; Block, Michael; Coboeken, Katrin; Gaub, Thomas; Goerlitz, Linus; Jaeger, Juergen; Loosen, Roland; Ludewig, Bernd; Meyer, Michaela; Niederalt, Christoph; Sevestre, Michael; Siegmund, Hans-Ulrich; Solodenko, Juri; Thelen, Kirstin; Telle, Ulrich; Weiss, Wolfgang; Wendl, Thomas; Willmann, Stefan; Lippert, Joerg

    2011-01-01

    Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multiscale by nature, project work, and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform consisting of PK-Sim® and MoBi® capable of building and simulating models that integrate across biological scales. A prototypical multiscale model for the progression of a pancreatic tumor and its response to pharmacotherapy is constructed and virtual patients are treated with a prodrug activated by hepatic metabolization. Tumor growth is driven by signal transduction leading to cell cycle transition and proliferation. Free tumor concentrations of the active metabolite inhibit Raf kinase in the signaling cascade and thereby cell cycle progression. In a virtual clinical study, the individual therapeutic outcome of the chemotherapeutic intervention is simulated for a large population with heterogeneous genomic background. Thereby, the platform allows efficient model building and integration of biological knowledge and prior data from all biological scales. Experimental in vitro model systems can be linked with observations in animal experiments and clinical trials. The interplay between patients, diseases, and drugs and topics with high clinical relevance such as the role of pharmacogenomics, drug–drug, or drug–metabolite interactions can be addressed using this mechanistic, insight driven multiscale modeling approach. PMID:21483730

  3. A computational systems biology software platform for multiscale modeling and simulation: Integrating whole-body physiology, disease biology, and molecular reaction networks

    Directory of Open Access Journals (Sweden)

    Thomas eEissing

    2011-02-01

    Full Text Available Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multi-scale by nature, project work and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform consisting of PK-Sim® and MoBi® capable of building and simulating models that integrate across biological scales. A prototypical multiscale model for the progression of a pancreatic tumor and its response to pharmacotherapy is constructed and virtual patients are treated with a prodrug activated by hepatic metabolization. Tumor growth is driven by signal transduction leading to cell cycle transition and proliferation. Free tumor concentrations of the active metabolite inhibit Raf kinase in the signaling cascade and thereby cell cycle progression. In a virtual clinical study, the individual therapeutic outcome of the chemotherapeutic intervention is simulated for a large population with heterogeneous genomic background. Thereby, the platform allows efficient model building and integration of biological knowledge and prior data from all biological scales. Experimental in vitro model systems can be linked with observations in animal experiments and clinical trials. The interplay between patients, diseases, and drugs and topics with high clinical relevance such as the role of pharmacogenomics, drug-drug or drug-metabolite interactions can be addressed using this mechanistic, insight driven multiscale modeling approach.

  4. Toward a User-Driven Approach to Radiology Software Solutions: Putting the Wag Back in the Dog

    OpenAIRE

    Morgan, Matthew; Mates, Jonathan; Chang, Paul

    2006-01-01

    The relationship between healthcare providers and the software industry is evolving. In many cases, industry's traditional, market-driven model is failing to meet the increasingly sophisticated and appropriately individualized needs of providers. Advances in both technology infrastructure and development methodologies have set the stage for the transition from a vendor-driven to a more user-driven process of solution engineering. To make this transition, providers must take an active role in ...

  5. Athena: Modular CAM/CAD Software for Synthetic Biology

    OpenAIRE

    Chandran, Deepak; Bergmann, Frank T.; Sauro, Herbert M.

    2009-01-01

    Synthetic biology is the engineering of cellular networks. It combines principles of engineering and the knowledge of biological networks to program the behavior of cells. Computational modeling techniques in conjunction with molecular biology techniques have been successful in constructing biological devices such as switches, oscillators, and gates. The ambition of synthetic biology is to construct complex systems from such fundamental devices, much in the same way electronic circuits are bu...

  6. iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis

    OpenAIRE

    McNally James; Stocker Gernot; Fischer Maria; Rieder Dietmar; Bindea Gabriela; Kainz Simon; Oberstolz Michael; Trajanoski Zlatko

    2009-01-01

    Abstract Background In recent years, the genome biology community has expended considerable effort to confront the challenges of managing heterogeneous data in a structured and organized way and developed laboratory information management systems (LIMS) for both raw and processed data. On the other hand, electronic notebooks were developed to record and manage scientific data, and facilitate data-sharing. Software which enables both, management of large datasets and digital recording of labor...

  7. From Improving Processes To Improving Practice : Software Process Improvement in Transition from Plan-driven to Change-driven Development

    OpenAIRE

    Moe, Nils Brede

    2011-01-01

    As information technology’s role in the modern economy grows in importance, society makes exponentially greater demands on the diversity and quality of the software being produced. To develop high quality software, a good software development process is important. Software process improvement is about improving software quality and reliability, employee and client satisfaction, and return on investment. From the mid 1990s onwards, agile software development has been challenging the traditiona...

  8. Data-driven auto-configuration of the ATLAS reconstruction software

    CERN Document Server

    Boehler, M; The ATLAS collaboration

    2010-01-01

    The central data reconstruction of the ATLAS experiment of LHC is a very challenging task, involving large-scale computing and a wide variety of data formats, applications and software versions. In 2009-2010, the ATLAS detector has recorded hundreds of millions of collision, single beam and cosmic events, during an unstable commisioning period that gradually evolved to a stable operation mode aiming at physics. In parallel, the ATLAS Collaboration processed comparable amounts of simulated data, and also produced a collection of sophisticated derived datasets. To handle all this complexity, we have developed a powerful data-driven auto-configuration mechanism and a unified configuration interface that provides a lot of flexibility: "Reco_trf". The auto-configuration mechanism consists of inspecting the metadata of each job's input file to automatically derive the configuration parameters relevant for the input format and the requested tasks. This also simplifies considerably the configuration of jobs from ordi...

  9. Data-driven auto-configuration of the ATLAS reconstruction software

    CERN Document Server

    Boehler, M; The ATLAS collaboration

    2011-01-01

    The central data reconstruction of the ATLAS experiment of LHC is a very challenging task, involving large-scale computing and a wide variety of data formats, applications and software versions. In 2009-2010, the ATLAS detector has recorded hundreds of millions of collision, single beam and cosmic events, during the commissioning period with continuously changing conditons that gradually evolved to a stable operation mode aiming at physics. In parallel, the ATLAS Collaboration processed comparable amounts of simulated data, and also produced a collection of sophisticated derived datasets. To handle all this complexity, we have developed a powerful data-driven auto-configuration mechanism and a unified configuration interface that provides a lot of flexibility: "Reco\\_trf". The auto-configuration mechanism consists of inspecting the meta-data of each job's input file to automatically derive the configuration parameters relevant for the input format and the requested tasks. This also simplifies considerably the...

  10. V3CMM: a 3-view component meta-model for model-driven robotic software development

    OpenAIRE

    Alonso Cáceres, Diego; Vicente Chicote, Cristina; Ortiz Zaragoza, Francisco José; Pastor Franco, Juan Ángel; Álvarez Torres, María Bárbara

    2010-01-01

    There are many voices in the robotics community demanding a qualitative improvement in the robotics software development process and tools, in order to increase product flexibility, adaptability, and overall quality, while reducing its cost and time-to-market. This article describes a first step towards a model-driven approach to robotics software development, based on the definition of highly reusable and platform-independent component-based design models. The proposed approach revolves arou...

  11. Quality-driven multi-objective optimization of software architecture design : method, tool, and application

    NARCIS (Netherlands)

    Etemadi Idgahi (Etemaadi), Ramin

    2014-01-01

    Software architecting is a non-trivial and demanding task for software engineers to perform. The architecture is a key enabler for software systems. Besides being crucial for user functionality, the software architecture has deep impact on software qualities such as performance, safety, and cost.

  12. Rapid biological speciation driven by tectonic evolution in New Zealand

    Science.gov (United States)

    Craw, Dave; Upton, Phaedra; Burridge, Christopher P.; Wallis, Graham P.; Waters, Jonathan M.

    2016-02-01

    Collisions between tectonic plates lead to the rise of new mountain ranges that can separate biological populations and ultimately result in new species. However, the identification of links between tectonic mountain-building and biological speciation is confounded by environmental and ecological factors. Thus, there are surprisingly few well-documented examples of direct tectonic controls on terrestrial biological speciation. Here we present examples from New Zealand, where the rapid evolution of 18 species of freshwater fishes has resulted from parallel tectonic landscape evolution. We use numerical models to reconstruct changes in the deep crustal structure and surface drainage catchments of the southern island of New Zealand over the past 25 million years. We show that the island and mountain topography evolved in six principal tectonic zones, which have distinct drainage catchments that separated fish populations. We use new and existing phylogenetic analyses of freshwater fish populations, based on over 1,000 specimens from more than 400 localities, to show that fish genomes can retain evidence of this tectonic landscape development, with a clear correlation between geologic age and extent of DNA sequence divergence. We conclude that landscape evolution has controlled on-going biological diversification over the past 25 million years.

  13. Quality-driven multi-objective optimization of software architecture design: method, tool, and application

    OpenAIRE

    Etemadi Idgahi (Etemaadi), Ramin

    2014-01-01

    Software architecting is a non-trivial and demanding task for software engineers to perform. The architecture is a key enabler for software systems. Besides being crucial for user functionality, the software architecture has deep impact on software qualities such as performance, safety, and cost. In this dissertation, an automated approach for software architecture design is proposed that supports analysis and optimization of multiple quality attributes: First of all, we demonstrate an optimi...

  14. Biological effects and equivalent doses in radiotherapy: a software solution

    CERN Document Server

    Voyant, Cyril; Roustit, Rudy; Biffi, Katia; Marcovici, Celine Lantieri

    2013-01-01

    The limits of TDF (time, dose, and fractionation) and linear quadratic models have been known for a long time. Medical physicists and physicians are required to provide fast and reliable interpretations regarding the delivered doses or any future prescriptions relating to treatment changes. We therefore propose a calculation interface under the GNU license to be used for equivalent doses, biological doses, and normal tumor complication probability (Lyman model). The methodology used draws from several sources: the linear-quadratic-linear model of Astrahan, the repopulation effects of Dale, and the prediction of multi-fractionated treatments of Thames. The results are obtained from an algorithm that minimizes an ad-hoc cost function, and then compared to the equivalent dose computed using standard calculators in seven French radiotherapy centers.

  15. The Orion GN and C Data-Driven Flight Software Architecture for Automated Sequencing and Fault Recovery

    Science.gov (United States)

    King, Ellis; Hart, Jeremy; Odegard, Ryan

    2010-01-01

    The Orion Crew Exploration Vehicle (CET) is being designed to include significantly more automation capability than either the Space Shuttle or the International Space Station (ISS). In particular, the vehicle flight software has requirements to accommodate increasingly automated missions throughout all phases of flight. A data-driven flight software architecture will provide an evolvable automation capability to sequence through Guidance, Navigation & Control (GN&C) flight software modes and configurations while maintaining the required flexibility and human control over the automation. This flexibility is a key aspect needed to address the maturation of operational concepts, to permit ground and crew operators to gain trust in the system and mitigate unpredictability in human spaceflight. To allow for mission flexibility and reconfrgurability, a data driven approach is being taken to load the mission event plan as well cis the flight software artifacts associated with the GN&C subsystem. A database of GN&C level sequencing data is presented which manages and tracks the mission specific and algorithm parameters to provide a capability to schedule GN&C events within mission segments. The flight software data schema for performing automated mission sequencing is presented with a concept of operations for interactions with ground and onboard crew members. A prototype architecture for fault identification, isolation and recovery interactions with the automation software is presented and discussed as a forward work item.

  16. 'TISUCROMA': A Software for Color Processing of Biological Tissue's Images

    International Nuclear Information System (INIS)

    In this work a software intended to plot and analyze digital image RGB histograms from normal and abnormal regions of biological tissue. The obtained RGB histograms from each zone can be used to show the image in only one color or the mixture of some of them. The Software was developed in Lab View to process the images in a laptop. Some medical application examples are shown. (Author)

  17. A consumer/producer approach to risk-driven software reliability and testing

    OpenAIRE

    Schneidewind, Norman; Hinchey, Mike

    2009-01-01

    1. Introduction: We introduce the concept of using both consumer software and producer software in the analysis of risk as it relates to test criteria and strategies. There are two different versions of the software, one representing the consumer’s viewpoint, which requires reliable software at reasonable cost, and the other representing the producer’s viewpoint, trying to produce adequate software with the lowest effort. As a using organization, the consumer does not ...

  18. Electric Field Driven Torque in Biological Rotary Motors

    CERN Document Server

    Miller,, John H; Maric, Sladjana; Infante, Hans L; Claycomb, James R

    2013-01-01

    Ion driven rotary motors, such as Fo-ATP synthase (Fo) and the bacterial flagellar motor, act much like a battery-powered electric motor. They convert energy from ions as they move from high to low potential across a membrane into torque and rotary motion. Here we propose a mechanism whereby electric fields, emanating from channels in one or more stators, act on asymmetric charge distributions due to protonated and deprotonated sites in the rotor and drive it to rotate. The model predicts an ideal scaling law between torque and ion motive force, which can be hindered by mitochondrial mutations. The rotor of Fo drives the gamma-subunit to rotate within the ATP-producing complex (F1), working against an opposing torque that rises and falls periodically with angular position. Drawing an analogy with Brownian motion of a particle in a tilted washboard potential, we compute the highly nonlinear ATP production rate vs. proton motive force (pmf), showing a minimum pmf needed to drive ATP production with important me...

  19. Motility-driven glass and jamming transitions in biological tissues

    CERN Document Server

    Bi, Dapeng; Marchetti, M Cristina; Manning, M Lisa

    2015-01-01

    Cell motion inside dense tissues governs many biological processes, including embryonic development and cancer metastasis, and recent experiments suggest that these tissues exhibit collective glassy behavior. To make quantitative predictions about glass transitions in tissues, we study a self-propelled Voronoi (SPV) model that simultaneously captures polarized cell motility and multi-body cell-cell interactions in a confluent tissue, where there are no gaps between cells. We demonstrate that the model exhibits a jamming transition from a solid-like state to a fluid-like state that is controlled by three parameters: the single-cell motile speed, the persistence time of single-cell tracks, and a target shape index that characterizes the competition between cell-cell adhesion and cortical tension. In contrast to traditional particulate glasses, we are able to identify an experimentally accessible structural order parameter that specifies the entire jamming surface as a function of model parameters. We demonstrat...

  20. Motility-Driven Glass and Jamming Transitions in Biological Tissues

    Science.gov (United States)

    Bi, Dapeng; Yang, Xingbo; Marchetti, M. Cristina; Manning, M. Lisa

    2016-04-01

    Cell motion inside dense tissues governs many biological processes, including embryonic development and cancer metastasis, and recent experiments suggest that these tissues exhibit collective glassy behavior. To make quantitative predictions about glass transitions in tissues, we study a self-propelled Voronoi model that simultaneously captures polarized cell motility and multibody cell-cell interactions in a confluent tissue, where there are no gaps between cells. We demonstrate that the model exhibits a jamming transition from a solidlike state to a fluidlike state that is controlled by three parameters: the single-cell motile speed, the persistence time of single-cell tracks, and a target shape index that characterizes the competition between cell-cell adhesion and cortical tension. In contrast to traditional particulate glasses, we are able to identify an experimentally accessible structural order parameter that specifies the entire jamming surface as a function of model parameters. We demonstrate that a continuum soft glassy rheology model precisely captures this transition in the limit of small persistence times and explain how it fails in the limit of large persistence times. These results provide a framework for understanding the collective solid-to-liquid transitions that have been observed in embryonic development and cancer progression, which may be associated with epithelial-to-mesenchymal transition in these tissues.

  1. Component-Based QoS-Driven Synthesis of High Assurance Embedded Software Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Software is an integral part of many complex embedded systems, such as avionics, scientific exploration, and on-board systems. However, poor software reliability is...

  2. Model-Driven Robot-Software Design using integrated Models and Co-Simulation

    NARCIS (Netherlands)

    Broenink, Jan F.; Ni, Yunyun; McAllister, J.; Bhattacharyya, S.

    2012-01-01

    The work presented here is on a methodology for design of hard real-time embedded control software for robots, i.e. mechatronic products. The behavior of the total robot system (machine, control, software and I/O) is relevant, because the dynamics of the machine influences the robot software. Theref

  3. Data-Driven Decision Making as a Tool to Improve Software Development Productivity

    Science.gov (United States)

    Brown, Mary Erin

    2013-01-01

    The worldwide software project failure rate, based on a survey of information technology software manager's view of user satisfaction, product quality, and staff productivity, is estimated to be between 24% and 36% and software project success has not kept pace with the advances in hardware. The problem addressed by this study was the limited…

  4. Toward a user-driven approach to radiology software solutions: putting the wag back in the dog.

    Science.gov (United States)

    Morgan, Matthew; Mates, Jonathan; Chang, Paul

    2006-09-01

    The relationship between healthcare providers and the software industry is evolving. In many cases, industry's traditional, market-driven model is failing to meet the increasingly sophisticated and appropriately individualized needs of providers. Advances in both technology infrastructure and development methodologies have set the stage for the transition from a vendor-driven to a more user-driven process of solution engineering. To make this transition, providers must take an active role in the development process and vendors must provide flexible frameworks on which to build. Only then can the provider/vendor relationship mature from a purchaser/supplier to a codesigner/partner model, where true insight and innovation can occur. PMID:16741665

  5. Software educativo para la enseñanza de la Biología

    OpenAIRE

    Lorena Fuentes; Mayerling Villegas; Iván Mendoza

    2005-01-01

    El objetivo general de este estudio fue producir un software educativo para la enseñanza de la Biología en la tercera etapa de Educación Básica, basado en un ambiente interactivo y amigable con la incorporación de herramientas multimedia. Se fundamentó en las teorías conductista, cognitivista y constructivista del aprendizaje, así como también en los aspectos relativos a la producción de software educativos referidos por Gros. La investigación desarrollada fue de tipo docume...

  6. cPath: open source software for collecting, storing, and querying biological pathways

    Directory of Open Access Journals (Sweden)

    Gross Benjamin E

    2006-11-01

    Full Text Available Abstract Background Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. Results We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. Conclusion cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling.

  7. GRAPES: a software for parallel searching on biological graphs targeting multi-core architectures.

    Directory of Open Access Journals (Sweden)

    Rosalba Giugno

    Full Text Available Biological applications, from genomics to ecology, deal with graphs that represents the structure of interactions. Analyzing such data requires searching for subgraphs in collections of graphs. This task is computationally expensive. Even though multicore architectures, from commodity computers to more advanced symmetric multiprocessing (SMP, offer scalable computing power, currently published software implementations for indexing and graph matching are fundamentally sequential. As a consequence, such software implementations (i do not fully exploit available parallel computing power and (ii they do not scale with respect to the size of graphs in the database. We present GRAPES, software for parallel searching on databases of large biological graphs. GRAPES implements a parallel version of well-established graph searching algorithms, and introduces new strategies which naturally lead to a faster parallel searching system especially for large graphs. GRAPES decomposes graphs into subcomponents that can be efficiently searched in parallel. We show the performance of GRAPES on representative biological datasets containing antiviral chemical compounds, DNA, RNA, proteins, protein contact maps and protein interactions networks.

  8. Kinetic limits for pair-interaction driven master equations and biological swarm models

    CERN Document Server

    Carlen, Eric; Wennberg, Bernt

    2011-01-01

    We consider a class of stochastic processes modeling binary interactions in an N-particle system. Examples of such systems can be found in the modeling of biological swarms. They lead to the definition of a class of master equations that we call pair interaction driven master equations. We prove a propagation of chaos result for this class of master equations which generalizes Mark Kac's well know result for the Kac model in kinetic theory. We use this result to study kinetic limits for two biological swarm models. We show that propagation of chaos may be lost at large times and we exhibit an example where the invariant density is not chaotic.

  9. Event-Driven On-Board Software Using Priority-Based Communications Protocols

    Science.gov (United States)

    Fowell, S.; Ward, R.; Plummer, C.

    This paper describes current projects being performed by SciSys in the area of the use of software agents, built using CORBA middleware and SOIF communications protocols, to improve operations within autonomous satellite/ground systems. These concepts have been developed and demonstrated in a series of experiments variously funded by ESA's Technology Flight Opportunity Initiative (TFO) and Leading Edge Technology for SMEs (LET-SME), and the British National Space Centre's (BNSC) National Technology Programme. In [1] it is proposed that on-board software should evolve to one that uses an architecture of loosely -coupled software agents, integrated using minimum Real- Time CORBA ORBs such as the SciSys microORB. Building on that, this paper considers the requirements such an architecture and implementation place on the underlying communication protocols (software and hardware) and how these may be met by the emerging CCSDS SOIF recommendations. 2. TRENDS AND ISSUES 2.

  10. Real time acquisition, processing, and archiving of Doublet III diagram data employing table driven software

    International Nuclear Information System (INIS)

    This paper describes the diagnostic data acquisition, processing and archiving computer system for the Doublet III fusion research device. This paper's emphasis is mainly on the software, but provides a description of the hardware configuration

  11. Model-driven online capacity management for component-based software systems

    OpenAIRE

    Van Hoorn, André

    2014-01-01

    Capacity management is a core activity when designing and operating distributed software systems. It comprises the provisioning of data center resources and the deployment of software components to these resources. The goal is to continuously provide adequate capacity, i.e., service level agreements should be satisfied while keeping investment and operating costs reasonably low. Traditional capacity management strategies are rather static and pessimistic: resources are provisioned for anticip...

  12. Contribution to Quality-driven Evolutionary Software Development process for Service-Oriented Architectures

    OpenAIRE

    Arciniegas Herrera, Jose Luis

    2006-01-01

    The quality of software is a key element for the successful of a system. Currently, with the advance of the technology, consumers demand more and better services. Models for the development process have also to be adapted to new requirements. This is particular true in the case of service oriented systems (domain of this thesis), where an unpredictable number of users can access to one or several services. This work proposes an improvement in the models for the software development proces...

  13. A model-driven approach to broaden the detection of software performance antipatterns at runtime

    OpenAIRE

    Di Marco, Antinisca; Trubiani, Catia

    2014-01-01

    Performance antipatterns document bad design patterns that have negative influence on system performance. In our previous work we formalized such antipatterns as logical predicates that predicate on four views: (i) the static view that captures the software elements (e.g. classes, components) and the static relationships among them; (ii) the dynamic view that represents the interaction (e.g. messages) that occurs between the software entities elements to provide the system functionalities; (i...

  14. A document-driven method for certifying scientific computing software for use in nuclear safety analysis

    Energy Technology Data Exchange (ETDEWEB)

    Smith, W. Spencer; Koothoor, Mimitha [Computing and Software Department, McMaster University, Hamilton (Canada)

    2016-04-15

    This paper presents a documentation and development method to facilitate the certification of scientific computing software used in the safety analysis of nuclear facilities. To study the problems faced during quality assurance and certification activities, a case study was performed on legacy software used for thermal analysis of a fuel pin in a nuclear reactor. Although no errors were uncovered in the code, 27 issues of incompleteness and inconsistency were found with the documentation. This work proposes that software documentation follow a rational process, which includes a software requirements specification following a template that is reusable, maintainable, and understandable. To develop the design and implementation, this paper suggests literate programming as an alternative to traditional structured programming. Literate programming allows for documenting of numerical algorithms and code together in what is termed the literate programmer's manual. This manual is developed with explicit traceability to the software requirements specification. The traceability between the theory, numerical algorithms, and implementation facilitates achieving completeness and consistency, as well as simplifies the process of verification and the associated certification.

  15. Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data.

    Science.gov (United States)

    Robertson, Charles E; Harris, J Kirk; Wagner, Brandie D; Granger, David; Browne, Kathy; Tatem, Beth; Feazel, Leah M; Park, Kristin; Pace, Norman R; Frank, Daniel N

    2013-12-01

    Studies of the human microbiome, and microbial community ecology in general, have blossomed of late and are now a burgeoning source of exciting research findings. Along with the advent of next-generation sequencing platforms, which have dramatically increased the scope of microbiome-related projects, several high-performance sequence analysis pipelines (e.g. QIIME, MOTHUR, VAMPS) are now available to investigators for microbiome analysis. The subject of our manuscript, the graphical user interface-based Explicet software package, fills a previously unmet need for a robust, yet intuitive means of integrating the outputs of the software pipelines with user-specified metadata and then visualizing the combined data. PMID:24021386

  16. Architecture-Driven Integration of Modeling Languages for the Design of Software-Intensive Systems

    NARCIS (Netherlands)

    Dos Santos Soares, M.

    2010-01-01

    In the research that led to this thesis a multi-disciplinary approach, combining Traffic Engineering and Software Engineering, was used. Traffic engineers come up with new control strategies and algorithms for improving traffic. Once new solutions are defined from a Traffic Engineering point of view

  17. OpenStructure: an integrated software framework for computational structural biology

    Science.gov (United States)

    Biasini, M.; Schmidt, T.; Bienert, S.; Mariani, V.; Studer, G.; Haas, J.; Johner, N.; Schenk, A. D.; Philippsen, A.; Schwede, T.

    2013-01-01

    Research projects in structural biology increasingly rely on combinations of heterogeneous sources of information, e.g. evolutionary information from multiple sequence alignments, experimental evidence in the form of density maps and proximity constraints from proteomics experiments. The OpenStructure software framework, which allows the seamless integration of information of different origin, has previously been introduced. The software consists of C++ libraries which are fully accessible from the Python programming language. Additionally, the framework provides a sophisticated graphics module that interactively displays molecular structures and density maps in three dimensions. In this work, the latest developments in the OpenStructure framework are outlined. The extensive capabilities of the framework will be illustrated using short code examples that show how information from molecular-structure coordinates can be combined with sequence data and/or density maps. The framework has been released under the LGPL version 3 license and is available for download from http://www.openstructure.org. PMID:23633579

  18. OpenStructure: an integrated software framework for computational structural biology.

    Science.gov (United States)

    Biasini, M; Schmidt, T; Bienert, S; Mariani, V; Studer, G; Haas, J; Johner, N; Schenk, A D; Philippsen, A; Schwede, T

    2013-05-01

    Research projects in structural biology increasingly rely on combinations of heterogeneous sources of information, e.g. evolutionary information from multiple sequence alignments, experimental evidence in the form of density maps and proximity constraints from proteomics experiments. The OpenStructure software framework, which allows the seamless integration of information of different origin, has previously been introduced. The software consists of C++ libraries which are fully accessible from the Python programming language. Additionally, the framework provides a sophisticated graphics module that interactively displays molecular structures and density maps in three dimensions. In this work, the latest developments in the OpenStructure framework are outlined. The extensive capabilities of the framework will be illustrated using short code examples that show how information from molecular-structure coordinates can be combined with sequence data and/or density maps. The framework has been released under the LGPL version 3 license and is available for download from http://www.openstructure.org.

  19. Current trends and new challenges of databases and web applications for systems driven biological research

    Directory of Open Access Journals (Sweden)

    Pradeep Kumar eSreenivasaiah

    2010-12-01

    Full Text Available Dynamic and rapidly evolving nature of systems driven research imposes special requirements on the technology, approach, design and architecture of computational infrastructure including database and web application. Several solutions have been proposed to meet the expectations and novel methods have been developed to address the persisting problems of data integration. It is important for researchers to understand different technologies and approaches. Having familiarized with the pros and cons of the existing technologies, researchers can exploit its capabilities to the maximum potential for integrating data. In this review we discuss the architecture, design and key technologies underlying some of the prominent databases (DBs and web applications. We will mention their roles in integration of biological data and investigate some of the emerging design concepts and computational technologies that are likely to have a key role in the future of systems driven biomedical research.

  20. A Nomadicity-driven Negotiation Protocol, Tactics and Strategies for Interacting Software Agents.

    OpenAIRE

    Sameh, Abdel-Naby

    2010-01-01

    The rising integration of pocket computing devices in our daily life duties has taken the attention of researchers from different scientific backgrounds. Today's amount of software applications that bring together advanced mobile services and literature of Artificial Intelligence (AI) is quite remarkable and worth investigating. Cooperation, coordination and negotiation are some of AI's focal points wherein many of its related research efforts are strengthening the join between sophisticated ...

  1. A Generic Model Driven Approach for Safer Mission and Vehicle Management Software Design

    Science.gov (United States)

    Boudillet, O.; Person, T.; Genevoix, M.

    2012-01-01

    The purpose of a spacecraft, whether an observation or telecommunication satellite, a lander, a chaser as the ATV (Automated Transfer Vehicle) or a launcher is to perform a mission. A mission is composed of several modes, the number of modes being generally representative of the complexity of the mission assigned to the spacecraft. The Mission and Vehicle Management Software (MVMS) plays the role of an orchestra conductor that will internally control the proper behaviour of the spacecraft and all its avionics element inter-cooperation during its lifetime, and therefore the safety of the mission. The MVMS can either be one function of the main onboard software, or a fully piece of segregated software running on a dedicated processing unit or distributed on several hardware or functional nodes. This paper presents a generic design that can be used for low to medium complexity system, or, in case of highly complex systems, for the most critical MVMS functions. The design is model based oriented. SCADE Suite (from Esterel Technologies) has being selected for its very high adequacy for MVMS implementation and its capability to satisfy high safety requirements: The purpose is to make use of the autocoding facility offered by SCADE, knowing that a Criticality A (DO178B standard) certification kit is available for the generator.

  2. User Driven Development of Software Tools for Open Data Discovery and Exploration

    Science.gov (United States)

    Schlobinski, Sascha; Keppel, Frank; Dihe, Pascal; Boot, Gerben; Falkenroth, Esa

    2016-04-01

    The use of open data in research faces challenges not restricted to inherent properties such as data quality, resolution of open data sets. Often Open data is catalogued insufficiently or fragmented. Software tools that support the effective discovery including the assessment of the data's appropriateness for research have shortcomings such as the lack of essential functionalities like support for data provenance. We believe that one of the reasons is the neglect of real end users requirements in the development process of aforementioned software tools. In the context of the FP7 Switch-On project we have pro-actively engaged the relevant user user community to collaboratively develop a means to publish, find and bind open data relevant for hydrologic research. Implementing key concepts of data discovery and exploration we have used state of the art web technologies to provide an interactive software tool that is easy to use yet powerful enough to satisfy the data discovery and access requirements of the hydrological research community.

  3. Biana: a software framework for compiling biological interactions and analyzing networks

    Directory of Open Access Journals (Sweden)

    Planas-Iglesias Joan

    2010-01-01

    Full Text Available Abstract Background The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties. Results We introduce BIANA (Biologic Interactions and Network Analysis, a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i the integration of multiple sources of biological information, including biological entities and their relationships, and ii the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php. Conclusions BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

  4. Software Mutational Robustness: Bridging The Gap Between Mutation Testing and Evolutionary Biology

    CERN Document Server

    Schulte, Eric; Fast, Ethan; Forrest, Stephanie; Weimer, Westley

    2012-01-01

    In the mutation testing paradigm, test suite quality is measured by its ability to detect variant programs generated through application of random changes to an original program. In evolutionary biology however, neutral mutations that leave fitness unchanged are considered to be beneficial---improving the system's robustness and ability to discover evolutionary improvements. In this paper, we generate a population of variant programs from an original program by applying lightweight random mutations. We adopt biological terminology and refer to undetected variants as neutral, and the percentage of all variants that are neutral as mutational robustness. Although they are related to equivalent mutants in mutation testing, which are viewed as problematic, we show positive properties of neutral variants which are easily generated and can be used to protect software against unknown defects. Even when mutations are restricted to statements executed by the test suit, we find that mutational robustness is high: 36.75%...

  5. Kinetic limits for pair-interaction driven master equations and biological swarm models

    OpenAIRE

    Carlen, Eric; Degond, Pierre; Wennberg, Bernt

    2011-01-01

    We consider a class of stochastic processes modeling binary interactions in an N-particle system. Examples of such systems can be found in the modeling of biological swarms. They lead to the definition of a class of master equations that we call pair interaction driven master equations. We prove a propagation of chaos result for this class of master equations which generalizes Mark Kac's well know result for the Kac model in kinetic theory. We use this result to study kinetic limits for two b...

  6. Modeling density-driven flow in porous media principles, numerics, software

    CERN Document Server

    Holzbecher, Ekkehard O

    1998-01-01

    Modeling of flow and transport in groundwater has become an important focus of scientific research in recent years. Most contributions to this subject deal with flow situations, where density and viscosity changes in the fluid are neglected. This restriction may not always be justified. The models presented in the book demonstrate immpressingly that the flow pattern may be completely different when density changes are taken into account. The main applications of the models are: thermal and saline convection, geothermal flow, saltwater intrusion, flow through salt formations etc. This book not only presents basic theory, but the reader can also test his knowledge by applying the included software and can set up own models.

  7. MVC Architecture Driven Design and Agile Implementation of a Web-Based Software System

    Directory of Open Access Journals (Sweden)

    Sandhya Prakash

    2013-11-01

    Full Text Available This paper reports design and implementation of a web based software system for storing and managinginformation related to time management and productivity of employees working on a project.The systemhas been designed and implemented with best principles from model viewcontrollerand agile development.Such system has practical use for any organization in terms of ease of use, efficiency, and cost savings. Themanuscript describes design of the system as well as its database and user interface. Detailed snapshots ofthe working system are provided too

  8. HDBStat!: A platform-independent software suite for statistical analysis of high dimensional biology data

    Directory of Open Access Journals (Sweden)

    Brand Jacob PL

    2005-04-01

    Full Text Available Abstract Background Many efforts in microarray data analysis are focused on providing tools and methods for the qualitative analysis of microarray data. HDBStat! (High-Dimensional Biology-Statistics is a software package designed for analysis of high dimensional biology data such as microarray data. It was initially developed for the analysis of microarray gene expression data, but it can also be used for some applications in proteomics and other aspects of genomics. HDBStat! provides statisticians and biologists a flexible and easy-to-use interface to analyze complex microarray data using a variety of methods for data preprocessing, quality control analysis and hypothesis testing. Results Results generated from data preprocessing methods, quality control analysis and hypothesis testing methods are output in the form of Excel CSV tables, graphs and an Html report summarizing data analysis. Conclusion HDBStat! is a platform-independent software that is freely available to academic institutions and non-profit organizations. It can be downloaded from our website http://www.soph.uab.edu/ssg_content.asp?id=1164.

  9. Promoting Student Inquiry Using "Zea Mays" (Corn) Cultivars for Hypothesis-Driven Experimentation in a Majors Introductory Biology Course

    Science.gov (United States)

    Blair, Amy C.; Peters, Brenda J.; Bendixen, Conrad W.

    2014-01-01

    The AAAS Vision and Change report (2011) recommends incorporating student research experiences into the biology curriculum at the undergraduate level. This article describes, in detail, how "Zea mays" (corn) cultivars were used as a model for a hypothesis-driven short-term research project in an introductory biology course at a small…

  10. A Computational Systems Biology Software Platform for Multiscale Modeling and Simulation: Integrating Whole-Body Physiology, Disease Biology, and Molecular Reaction Networks

    OpenAIRE

    ThomasEissing

    2011-01-01

    Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multi-scale by nature, project work and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform co...

  11. Development and validation of evolutionary algorithm software as an optimization tool for biological and environmental applications.

    Science.gov (United States)

    Sys, K; Boon, N; Verstraete, W

    2004-06-01

    A flexible, extendable tool for the optimization of (micro)biological processes and protocols using evolutionary algorithms was developed. It has been tested using three different theoretical optimization problems: 2 two-dimensional problems, one with three maxima and one with five maxima and a river autopurification optimization problem with boundary conditions. For each problem, different evolutionary parameter settings were used for the optimization. For each combination of evolutionary parameters, 15 generations were run 20 times. It has been shown that in all cases, the evolutionary algorithm gave rise to valuable results. Generally, the algorithms were able to detect the more stable sub-maximum even if there existed less stable maxima. The latter is, from a practical point of view, generally more desired. The most important factors influencing the convergence process were the parameter value randomization rate and distribution. The developed software, described in this work, is available for free.

  12. Biological cell irradiation at ultrahigh dose rate employing laser driven protons

    Energy Technology Data Exchange (ETDEWEB)

    Doria, D.; Kakolee, K. F.; Kar, S. [Centre for Plasma Physics, Queen' s University Belfast, BT7 1NN (United Kingdom); School of Physics and Astronomy, University of Birmingham, B15 2TT (United Kingdom); and others

    2012-07-09

    The ultrashort duration of laser-driven multi-MeV ion bursts offers the possibility of radiobiological studies at extremely high dose rates. Employing the TARANIS Terawatt laser at Queen's University, the effect of proton irradiation at MeV-range energies on live cells has been investigated at dose rates exceeding 10{sup 9}Gy/s as a single exposure. A clonogenic assay showed consistent lethal effects on V-79 live cells, which, even at these dose rates, appear to be in line with previously published results employing conventional sources. A Relative Biological Effectiveness (RBE) of 1.4{+-}0.2 at 10% survival is estimated from a comparison with a 225 kVp X-ray source.

  13. Biological cell irradiation at ultrahigh dose rate employing laser driven protons

    Science.gov (United States)

    Doria, D.; Kakolee, K. F.; Kar, S.; Litt, S. K.; Fiorini, F.; Ahmed, H.; Green, S.; Jeynes, JC. G.; Kavanagh, J.; Kirby, D.; Kirkby, K. J.; Lewis, C. L.; Merchant, M. J.; Nersisyan, G.; Prasad, R.; Prise, K. M.; Schettino, G.; Zepf, M.; Borghesi, M.

    2012-07-01

    The ultrashort duration of laser-driven multi-MeV ion bursts offers the possibility of radiobiological studies at extremely high dose rates. Employing the TARANIS Terawatt laser at Queen's University, the effect of proton irradiation at MeV-range energies on live cells has been investigated at dose rates exceeding 109Gy/s as a single exposure. A clonogenic assay showed consistent lethal effects on V-79 live cells, which, even at these dose rates, appear to be in line with previously published results employing conventional sources. A Relative Biological Effectiveness (RBE) of 1.4±0.2 at 10% survival is estimated from a comparison with a 225 kVp X-ray source.

  14. GeneWeaver: data driven alignment of cross-species genomics in biology and disease.

    Science.gov (United States)

    Baker, Erich; Bubier, Jason A; Reynolds, Timothy; Langston, Michael A; Chesler, Elissa J

    2016-01-01

    The GeneWeaver data and analytics website (www.geneweaver.org) is a publically available resource for storing, curating and analyzing sets of genes from heterogeneous data sources. The system enables discovery of relationships among genes, variants, traits, drugs, environments, anatomical structures and diseases implicitly found through gene set intersections. Since the previous review in the 2012 Nucleic Acids Research Database issue, GeneWeaver's underlying analytics platform has been enhanced, its number and variety of publically available gene set data sources has been increased, and its advanced search mechanisms have been expanded. In addition, its interface has been redesigned to take advantage of flexible web services, programmatic data access, and a refined data model for handling gene network data in addition to its original emphasis on gene set data. By enumerating the common and distinct biological molecules associated with all subsets of curated or user submitted groups of gene sets and gene networks, GeneWeaver empowers users with the ability to construct data driven descriptions of shared and unique biological processes, diseases and traits within and across species. PMID:26656951

  15. Software engineering

    CERN Document Server

    Sommerville, Ian

    2010-01-01

    The ninth edition of Software Engineering presents a broad perspective of software engineering, focusing on the processes and techniques fundamental to the creation of reliable, software systems. Increased coverage of agile methods and software reuse, along with coverage of 'traditional' plan-driven software engineering, gives readers the most up-to-date view of the field currently available. Practical case studies, a full set of easy-to-access supplements, and extensive web resources make teaching the course easier than ever.

  16. Interactive Software for the study of membrane biology: lipid composition, solubilization and liposome reconstitution and characterization

    Directory of Open Access Journals (Sweden)

    I.A. Borin

    2006-07-01

    Full Text Available Biological  membranes define cellular boundaries, divide cells into discrete  compartments, organize complex reaction sequences, and act in signal reception and energy transformations. This topic is studied in all undergraduate biochemistry  courses.  Visualization  of  structures  generally  facilitates  the  understanding  of  many  related  topics  of membrane composition, structures, and protein interactions but they lack in many events that occurs in membranes. Also,  at  the  present  time,  animations  exploring  solubilization  and  reconstitution  of  membrane  proteins  in  vesicular systems are not available. Thus, we have developed a software  named  AnimaBio, in Macromedia  Flash 7.0, whose principal objective was the animation of some  processes  used  in the study  of membrane  biology and it was  didactically  divided  in:  (1 composition  and  physics  properties;  (2  construction  of  systems  mimetically  to  natural  membranes  and  (3 characterization of these biomimetic systems using experimental examples.The topics explained in each section were: (1 Membranes composition; lipids and proteins distribution; fluid mosaic  model;  the  basic  structural  unit  of  lipid  bilayer;  peripheral  proteins;  anchored  proteins;  integral  proteins; covalently attached oligosaccharides; solubilization of proteins and hemolytic effects; (2 construction of biomimetical systems using different techniques; sonication followed by direct insertion of proteins and co-solubilization methods; (3  Kinetic  properties  of  the  enzyme,  reconstituted  in  the  vesicular  system,  using  examples  of  actions  of  different agents such as: inhibitors, detergents, ionophores and photosensitive dyes. All topics were illustrated in the animation using  some  examples  such  as:  erythrocytes  membranes;  alkaline  phosphatase  (which

  17. Utilization of optical tracking to validate a software-driven isocentric approach to robotic couch movements for proton radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Hsi, Wen C., E-mail: Wen.Hsi@Mclaren.org, E-mail: Wenchien.hsi@sphic.org.cn; Zeidan, Omar A., E-mail: omar.zeidan@orlandohealth.com [ProCure Proton Therapy Center, Oklahoma City, Oklahoma 73142 (United States); Law, Aaron; Schreuder, Andreas N., E-mail: niek.schreuder@provisionhp.com [ProCure Training and Development Center, Bloomington, Indiana 47404 (United States)

    2014-08-15

    Purpose: An optical tracking and positioning system (OTPS) was developed to validate the software-driven isocentric (SDI) approach to control the six-degrees-of-freedom movement of a robotic couch. Methods: The SDI approach to movements rotating around a predefined isocenter, referred to as a GeoIso, instead of a mechanical pivot point was developed by the robot automation industry. With robotic couch-sag corrections for weight load in a traditional SDI approach, movements could be accurately executed for a GeoIso located within a 500 mm cubic volume on the couch for treatments. The accuracy of SDI movement was investigated using the OTPS. The GeoIso was assumed to align with the proton beam isocenter (RadIso) for gantry at the reference angle. However, the misalignment between GeoIso and RadIso was quantitatively investigated by measuring the displacements at various couch angles for a target placed at the RadIso at an initial couch angle. When circular target displacements occur on a plane, a relative isocenter shift (RIS) correction could be applied in the SDI movement to minimize target displacements. Target displacements at a fixed gantry angle without and with RIS correction were measured for 12 robotic couches. Target displacements for various gantry angles were performed on three couches in gantry rooms to study the gantry-induced RadIso shift. The RIS correction can also be applied for the RadIso shift. A new SDI approach incorporating the RIS correction with the couch sag is described in this study. In parallel, the accuracy of SDI translation movements for various weight loads of patients on the couch was investigated during positioning of patients for proton prostate treatments. Results: For a fixed gantry angle, measured target displacements without RIS correction for couch rotations in the horizontal plane varied from 4 to 20 mm. However, measured displacements perpendicular to couch rotation plane were about 2 mm for all couches. Extracted

  18. Utilization of optical tracking to validate a software-driven isocentric approach to robotic couch movements for proton radiotherapy

    International Nuclear Information System (INIS)

    Purpose: An optical tracking and positioning system (OTPS) was developed to validate the software-driven isocentric (SDI) approach to control the six-degrees-of-freedom movement of a robotic couch. Methods: The SDI approach to movements rotating around a predefined isocenter, referred to as a GeoIso, instead of a mechanical pivot point was developed by the robot automation industry. With robotic couch-sag corrections for weight load in a traditional SDI approach, movements could be accurately executed for a GeoIso located within a 500 mm cubic volume on the couch for treatments. The accuracy of SDI movement was investigated using the OTPS. The GeoIso was assumed to align with the proton beam isocenter (RadIso) for gantry at the reference angle. However, the misalignment between GeoIso and RadIso was quantitatively investigated by measuring the displacements at various couch angles for a target placed at the RadIso at an initial couch angle. When circular target displacements occur on a plane, a relative isocenter shift (RIS) correction could be applied in the SDI movement to minimize target displacements. Target displacements at a fixed gantry angle without and with RIS correction were measured for 12 robotic couches. Target displacements for various gantry angles were performed on three couches in gantry rooms to study the gantry-induced RadIso shift. The RIS correction can also be applied for the RadIso shift. A new SDI approach incorporating the RIS correction with the couch sag is described in this study. In parallel, the accuracy of SDI translation movements for various weight loads of patients on the couch was investigated during positioning of patients for proton prostate treatments. Results: For a fixed gantry angle, measured target displacements without RIS correction for couch rotations in the horizontal plane varied from 4 to 20 mm. However, measured displacements perpendicular to couch rotation plane were about 2 mm for all couches. Extracted

  19. Value Driven Outcomes (VDO): a pragmatic, modular, and extensible software framework for understanding and improving health care costs and outcomes

    Science.gov (United States)

    Kawamoto, Kensaku; Martin, Cary J; Williams, Kip; Tu, Ming-Chieh; Park, Charlton G; Hunter, Cheri; Staes, Catherine J; Bray, Bruce E; Deshmukh, Vikrant G; Holbrook, Reid A; Morris, Scott J; Fedderson, Matthew B; Sletta, Amy; Turnbull, James; Mulvihill, Sean J; Crabtree, Gordon L; Entwistle, David E; McKenna, Quinn L; Strong, Michael B; Pendleton, Robert C; Lee, Vivian S

    2015-01-01

    Objective To develop expeditiously a pragmatic, modular, and extensible software framework for understanding and improving healthcare value (costs relative to outcomes). Materials and methods In 2012, a multidisciplinary team was assembled by the leadership of the University of Utah Health Sciences Center and charged with rapidly developing a pragmatic and actionable analytics framework for understanding and enhancing healthcare value. Based on an analysis of relevant prior work, a value analytics framework known as Value Driven Outcomes (VDO) was developed using an agile methodology. Evaluation consisted of measurement against project objectives, including implementation timeliness, system performance, completeness, accuracy, extensibility, adoption, satisfaction, and the ability to support value improvement. Results A modular, extensible framework was developed to allocate clinical care costs to individual patient encounters. For example, labor costs in a hospital unit are allocated to patients based on the hours they spent in the unit; actual medication acquisition costs are allocated to patients based on utilization; and radiology costs are allocated based on the minutes required for study performance. Relevant process and outcome measures are also available. A visualization layer facilitates the identification of value improvement opportunities, such as high-volume, high-cost case types with high variability in costs across providers. Initial implementation was completed within 6 months, and all project objectives were fulfilled. The framework has been improved iteratively and is now a foundational tool for delivering high-value care. Conclusions The framework described can be expeditiously implemented to provide a pragmatic, modular, and extensible approach to understanding and improving healthcare value. PMID:25324556

  20. Biology Teacher and Expert Opinions about Computer Assisted Biology Instruction Materials: A Software Entitled Nucleic Acids and Protein Synthesis

    Science.gov (United States)

    Hasenekoglu, Ismet; Timucin, Melih

    2007-01-01

    The aim of this study is to collect and evaluate opinions of CAI experts and biology teachers about a high school level Computer Assisted Biology Instruction Material presenting computer-made modelling and simulations. It is a case study. A material covering "Nucleic Acids and Protein Synthesis" topic was developed as the "case". The goal of the…

  1. Arena3D: visualizing time-driven phenotypic differences in biological systems

    Directory of Open Access Journals (Sweden)

    Secrier Maria

    2012-03-01

    Full Text Available Abstract Background Elucidating the genotype-phenotype connection is one of the big challenges of modern molecular biology. To fully understand this connection, it is necessary to consider the underlying networks and the time factor. In this context of data deluge and heterogeneous information, visualization plays an essential role in interpreting complex and dynamic topologies. Thus, software that is able to bring the network, phenotypic and temporal information together is needed. Arena3D has been previously introduced as a tool that facilitates link discovery between processes. It uses a layered display to separate different levels of information while emphasizing the connections between them. We present novel developments of the tool for the visualization and analysis of dynamic genotype-phenotype landscapes. Results Version 2.0 introduces novel features that allow handling time course data in a phenotypic context. Gene expression levels or other measures can be loaded and visualized at different time points and phenotypic comparison is facilitated through clustering and correlation display or highlighting of impacting changes through time. Similarity scoring allows the identification of global patterns in dynamic heterogeneous data. In this paper we demonstrate the utility of the tool on two distinct biological problems of different scales. First, we analyze a medium scale dataset that looks at perturbation effects of the pluripotency regulator Nanog in murine embryonic stem cells. Dynamic cluster analysis suggests alternative indirect links between Nanog and other proteins in the core stem cell network. Moreover, recurrent correlations from the epigenetic to the translational level are identified. Second, we investigate a large scale dataset consisting of genome-wide knockdown screens for human genes essential in the mitotic process. Here, a potential new role for the gene lsm14a in cytokinesis is suggested. We also show how phenotypic

  2. Knowledge management for systems biology a general and visually driven framework applied to translational medicine

    Directory of Open Access Journals (Sweden)

    Falciani Francesco

    2011-03-01

    Full Text Available Abstract Background To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results To address this challenge we previously developed a generic knowledge management framework, BioXM™, which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the

  3. ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining

    OpenAIRE

    Sivachenko Andrey Y; Huan Tianxiao; Harrison Scott H; Chen Jake Y

    2008-01-01

    Abstract Background New systems biology studies require researchers to understand how interplay among myriads of biomolecular entities is orchestrated in order to achieve high-level cellular and physiological functions. Many software tools have been developed in the past decade to help researchers visually navigate large networks of biomolecular interactions with built-in template-based query capabilities. To further advance researchers' ability to interrogate global physiological states of c...

  4. SAmBA: an interactive software for optimizing the design of biological macromolecules crystallization experiments.

    Science.gov (United States)

    Audic, S; Lopez, F; Claverie, J M; Poirot, O; Abergel, C

    1997-10-01

    SAmBA is a new software for the design of minimal experimental protocols using the notion of orthogonal arrays of strength 2. The main application of SAmBA is the search of protein crystallization conditions. Given a user input defining the relevant effectors/variables (e.g., pH, temperature, salts) and states (e.g., pH: 5, 6, 7 and 8), this software proposes an optimal set of experiments in which all tested variables and the pairwise interactions between them are symmetrically sampled. No a priori restrictions on the number and range of experimental variables is imposed. SAmBA consists of two complementary programs, SAm and BA, using a simulated annealing approach and a backtracking algorithm, respectively. The software is freely available as C code or as an interactive JAVA applet at http:/(/)igs-server.cnrs-mrs.fr. PMID:9329089

  5. A Software Framework For the Detection and Classification of Biological Targets in Bio-Nano Sensing

    OpenAIRE

    Hafeez, Abdul

    2014-01-01

    Detection and identification of important biological targets, such as DNA, proteins, and diseased human cells are crucial for early diagnosis and prognosis. The key to discriminate healthy cells from the diseased cells is the biophysical properties that differ radically. Micro and nanosystems, such as solid-state micropores and nanopores can measure and translate these properties of biological targets into electrical spikes to decode useful insights. Nonetheless, such approaches result in siz...

  6. A Market-Driven Approach Based on Markov Decision Theory for Optimal Use of Resources in Software Development

    NARCIS (Netherlands)

    Noppen, Joost; Aksit, Mehmet; Nicola, Victor; Tekinerdogan, Bedir

    2004-01-01

    Changes in requirements may have a severe impact on development processes. For example, if requirements change during the course of a software development activity, it may be necessary to reschedule development activities so that the new requirements can be addressed in a timely manner. Unfortunatel

  7. Data-driven, data-intensive computing for modelling and analysis of biological networks: application to bioethanol production

    Science.gov (United States)

    Park, Byung-Hoon; Samatova, Nagiza F.; Karpinets, Tatiana; Jallouk, Andrew; Molony, Scott; Horton, Scott; Arcangeli, Steven

    2007-07-01

    Modelling biological networks is inherently data-driven and data-intensive. The combinatorial nature of this type of modelling, however, requires new methods capable of dealing with the enormous size and irregularity of the search. Searching via 'backtracking' is one possible solution that avoids exhaustive searches by constraining the search space to the subspace of feasible solutions. Despite its wide use in many combinatorial optimization problems, there are currently few parallel implementations of backtracking capable of effectively dealing with the memory-intensive nature of the process and the extremely unbalanced loads present. In this paper, a parallel, scalable, and memory-efficient backtracking algorithm within the context of maximal clique enumeration is presented, and its applicability to large-scale biological networks aimed at studying the mechanisms for efficient bioethanol production is discussed.

  8. Event driven software package for the database of Integrated Coastal and Marine Area Management (ICMAM) (Developed in 'C')

    Digital Repository Service at National Institute of Oceanography (India)

    Sadhuram, Y.; Murty, T.V.R.; Chandramouli, P.; Murthy, K.S.R.

    -biological, meteorological and climatilogical data. Data are stored as sequential access disk files for rapid access. Programs are interactive and have graphics capability. A wide range of display and analysis outputs are available. Routines are described from a user's point...

  9. Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.

    Science.gov (United States)

    Karp, Peter D; Latendresse, Mario; Paley, Suzanne M; Krummenacker, Markus; Ong, Quang D; Billington, Richard; Kothari, Anamika; Weaver, Daniel; Lee, Thomas; Subhraveti, Pallavi; Spaulding, Aaron; Fulcher, Carol; Keseler, Ingrid M; Caspi, Ron

    2016-09-01

    Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms.

  10. Integrative Biological Chemistry Program Includes The Use Of Informatics Tools, GIS And SAS Software Applications

    OpenAIRE

    Malcolm J. D’Souza; Kashmar, Richard J.; Hurst, Kent; Fiedler, Frank; Gross, Catherine E.; Deol, Jasbir K.; Wilson, Alora

    2015-01-01

    Wesley College is a private, primarily undergraduate minority-serving institution located in the historic district of Dover, Delaware (DE). The College recently revised its baccalaureate biological chemistry program requirements to include a one-semester Physical Chemistry for the Life Sciences course and project-based experiential learning courses using instrumentation, data-collection, data-storage, statistical-modeling analysis, visualization, and computational techniques...

  11. DOTcvpSB, a software toolbox for dynamic optimization in systems biology

    OpenAIRE

    Balsa-Canto Eva; Hirmajer Tomáš; Banga Julio R

    2009-01-01

    Abstract Background Mathematical optimization aims to make a system or design as effective or functional as possible, computing the quality of the different alternatives using a mathematical model. Most models in systems biology have a dynamic nature, usually described by sets of differential equations. Dynamic optimization addresses this class of systems, seeking the computation of the optimal time-varying conditions (control variables) to minimize or maximize a certain performance index. Dy...

  12. Application of model-driven techniques to the design of non-functional concerns of service-oriented software systems

    OpenAIRE

    Silva Gallino, Juan Pedro

    2012-01-01

    Internet se ha convertido en la herramienta por excelencia para el intercambio de servicios de negocio e información entre empresas. En este contexto, las arquitecturas orientadas a servicios (SOA) y los servicios web (WS) han surgido como la plataforma más apropiada para las interacciones aplicación-aplicación. Por otra parte, el desarrollo guiado por modelos (MDD), y Model-Driven Architecture (MDA) en particular, son nuevos paradigmas que promueven el uso de modelos del sistema como element...

  13. Patterns of HCI design and HCI design of patterns bridging HCI design and model-driven software engineering

    CERN Document Server

    Seffah, Ahmed

    2015-01-01

    As interactive systems are quickly becoming integral to our everyday lives, this book investigates how we can make these systems, from desktop and mobile apps to more wearable and immersive applications, more usable and maintainable by using HCI design patterns. It also examines how we can facilitate the reuse of design practices in the development lifecycle of multi-devices, multi-platforms and multi-contexts user interfaces. Effective design tools are provided for combining HCI design patterns and User Interface (UI) driven engineering to enhance design whilst differentiating between UI

  14. Agents, assemblers, and ANTS: scheduling assembly with market and biological software mechanisms

    Science.gov (United States)

    Toth-Fejel, Tihamer T.

    2000-06-01

    Nanoscale assemblers will need robust, scalable, flexible, and well-understood mechanisms such as software agents to control them. This paper discusses assemblers and agents, and proposes a taxonomy of their possible interaction. Molecular assembly is seen as a special case of general assembly, subject to many of the same issues, such as the advantages of convergent assembly, and the problem of scheduling. This paper discusses the contract net architecture of ANTS, an agent-based scheduling application under development. It also describes an algorithm for least commitment scheduling, which uses probabilistic committed capacity profiles of resources over time, along with realistic costs, to provide an abstract search space over which the agents can wander to quickly find optimal solutions.

  15. Quantitative, high-resolution proteomics for data-driven systems biology

    DEFF Research Database (Denmark)

    Cox, J.; Mann, M.

    2011-01-01

    Systems biology requires comprehensive data at all molecular levels. Mass spectrometry (MS)-based proteomics has emerged as a powerful and universal method for the global measurement of proteins. In the most widespread format, it uses liquid chromatography (LC) coupled to high-resolution tandem...... primary structure of proteins including posttranslational modifications, to localize proteins to organelles, and to determine protein interactions. Here, we describe the principles of analysis and the areas of biology where proteomics can make unique contributions. The large-scale nature of proteomics...... data and its high accuracy pose special opportunities as well as challenges in systems biology that have been largely untapped so far. © 2011 by Annual Reviews. All rights reserved....

  16. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

    Science.gov (United States)

    Galdzicki, Michal; Clancy, Kevin P; Oberortner, Ernst; Pocock, Matthew; Quinn, Jacqueline Y; Rodriguez, Cesar A; Roehner, Nicholas; Wilson, Mandy L; Adam, Laura; Anderson, J Christopher; Bartley, Bryan A; Beal, Jacob; Chandran, Deepak; Chen, Joanna; Densmore, Douglas; Endy, Drew; Grünberg, Raik; Hallinan, Jennifer; Hillson, Nathan J; Johnson, Jeffrey D; Kuchinsky, Allan; Lux, Matthew; Misirli, Goksel; Peccoud, Jean; Plahar, Hector A; Sirin, Evren; Stan, Guy-Bart; Villalobos, Alan; Wipat, Anil; Gennari, John H; Myers, Chris J; Sauro, Herbert M

    2014-06-01

    The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.

  17. Biological effectiveness on live cells of laser driven protons at dose rates exceeding 109 Gy/s

    Science.gov (United States)

    Doria, D.; Kakolee, K. F.; Kar, S.; Litt, S. K.; Fiorini, F.; Ahmed, H.; Green, S.; Jeynes, J. C. G.; Kavanagh, J.; Kirby, D.; Kirkby, K. J.; Lewis, C. L.; Merchant, M. J.; Nersisyan, G.; Prasad, R.; Prise, K. M.; Schettino, G.; Zepf, M.; Borghesi, M.

    2012-03-01

    The ultrashort duration of laser-driven multi-MeV ion bursts offers the possibility of radiobiological studies at extremely high dose rates. Employing the TARANIS Terawatt laser at Queen's University, the effect of proton irradiation at MeV-range energies on live cells has been investigated at dose rates exceeding 109 Gy/s as a single exposure. A clonogenic assay showed consistent lethal effects on V-79 live cells, which, even at these dose rates, appear to be in line with previously published results employing conventional sources. A Relative Biological Effectiveness (RBE) of 1.4±0.2 at 10% survival is estimated from a comparison with a 225 kVp X-ray source.

  18. Biological effectiveness on live cells of laser driven protons at dose rates exceeding 10{sup 9} Gy/s

    Energy Technology Data Exchange (ETDEWEB)

    Doria, D.; Kakolee, K. F.; Kar, S.; Litt, S. K.; Ahmed, H.; Lewis, C. L.; Nersisyan, G.; Prasad, R.; Zepf, M.; Borghesi, M. [Centre for Plasma Physics, Queen' s University Belfast, BT7 1NN (United Kingdom); Fiorini, F.; Kirby, D. [School of Physics and Astronomy, University of Birmingham, B15 2TT (United Kingdom); Green, S. [Hall Edwards Radiotherapy Research Group, Dept. of Medical Physics, University Hospital Birmingham, B15 2TH (United Kingdom); Jeynes, J. C. G.; Kirkby, K. J.; Merchant, M. J. [Ion Beam Centre, Advanced Technology Institute, University of Surrey, Guildford GU2 7XH (United Kingdom); Kavanagh, J.; Prise, K. M.; Schettino, G. [Centre for Cancer Research and Cell Biology, Queen' s University Belfast, BT9 7BL (United Kingdom)

    2012-03-15

    The ultrashort duration of laser-driven multi-MeV ion bursts offers the possibility of radiobiological studies at extremely high dose rates. Employing the TARANIS Terawatt laser at Queen's University, the effect of proton irradiation at MeV-range energies on live cells has been investigated at dose rates exceeding 10{sup 9} Gy/s as a single exposure. A clonogenic assay showed consistent lethal effects on V-79 live cells, which, even at these dose rates, appear to be in line with previously published results employing conventional sources. A Relative Biological Effectiveness (RBE) of 1.4{+-}0.2 at 10% survival is estimated from a comparison with a 225 kVp X-ray source.

  19. Method on Process Driven Software Development Based on BPM%基于BPM的流程驱动型软件开发方法设计

    Institute of Scientific and Technical Information of China (English)

    王涛; 邵国强; 蔡朝晖

    2015-01-01

    BPM has the merits of improving the efficiency of organization's business operations, linking different departments, and integrating existing software systems, which helps to better manage the processes and it resources. There are some shortcomings when developing the process driven software using the classical methods. A new method model named PDSD has been proposed to provide some references. This model focuses on the perspective of it implementation, and it divides the development process into four phases, which are immersed experiencing, hierarchical process modeling, publicizing service interface of existing system and component-based software implementation. A demo about the development of graduation project support system is provided to ex-emplify the usage of PDSD model.%BPM思想有助于组织机构提升业务运营效率,打通部门隔离及集成既有业务系统,支撑组织机构更好地管理业务流程和IT技术资源,从而在竞争中取得优势.在开发流程驱动型软件时,现有的软件开发方法存在些许不足,该文提出了一种新的基于BPM的PDSD开发方法模型,以期为此类软件的开发提供借鉴和参考.模型主要从IT实现的角度切入,将主要开发过程划分为四个阶段,分别是:代入式流程实践、层次性流程建模、服务化既有系统和组件化软件实现,并通过高校毕设支持系统的开发实现做了示例性说明.

  20. Biologically inspired molecular machines driven by light. Optimal control of a unidirectional rotor

    International Nuclear Information System (INIS)

    We investigate the extent to which unidirectional intramolecular torsional motion can be created in an oriented bicyclic model system driven solely by laser light. We apply the machinery of quantum control via specifically tailored laser pulses to induce such motion, eliminating the need for the thermally constrained steps conventionally used in molecular motor systems. Our approach does not rely on specific details of the potential surfaces to create a preferred direction. Rather, we use matter-field interaction and the tools of coherent optimal control to create a wave packet with nonzero angular momentum among unbound torsional states on an excited electronic surface. Analysis of the results of the control algorithm provides general insight into when and how optimal control theory can find solutions that could not be generated through simple intuitive schemes. We find that, under constrained polarization, the control algorithm reduces to a simple intuitive coherent control strategy wherein a first IR pulse creates a non-stationary wave packet on the ground surface and a subsequent UV pulse transfers it to the excited state. Allowing for polarization shaping, however, we find new control routes that go beyond the intuitive scheme.

  1. Decomposing the effects of ocean warming on chlorophyll a concentrations into physically and biologically driven contributions

    International Nuclear Information System (INIS)

    Recently compiled observational data suggest a substantial decline in the global median chlorophyll a concentration over the 20th century, a trend that appears to be linked to ocean warming. Several modelling studies have considered changes in the ocean’s physical structure as a possible cause, while experimental work supports a biological mechanism, namely an observed increase in zooplankton grazing rate that outpaces phytoplankton production at higher temperatures. Here, we present transient simulations derived from a coupled ocean general circulation and carbon cycle model forced by atmospheric fields under unabated anthropogenic global warming (IPCC SRES A1FI scenario). The simulations account for both physical and biological mechanisms, and can reproduce about one quarter of the observed chlorophyll a decline during the 20th century, when using realistically parameterized temperature sensitivity of zooplankton metabolism (Q10 between 2 and 4) and phytoplankton growth (Q10 ∼ 1.9). Therefore, we have employed and re-calibrated the standard ecosystem model which assumes a lower temperature sensitivity of zooplankton grazing (Q10 = 1.1049) by re-scaling phytoplankton growth rates and zooplankton grazing rates. Our model projects a global chlorophyll a decline of >50% by the end of the 21st century. While phytoplankton abundance and chlorophyll a experience pronounced negative effects, primary production and zooplankton concentrations are less sensitive to ocean warming. Although changes in physical structure play an important role, much of the simulated change in chlorophyll a and productivity is related to the uneven temperature sensitivity of the marine ecosystem. (letter)

  2. Laser-assisted skin closure at 1.32 microns: the use of a software-driven medical laser system

    Science.gov (United States)

    Dew, Douglas K.; Hsu, Tung M.; Hsu, Long S.; Halpern, Steven J.; Michaels, Charles E.

    1991-06-01

    This study investigated the use of a computerized 1 .3 micron Nd:YAG laser to seal approximated wound edges in pig skin. The medical laser system used was the DLS Type 1 , 1 .32 micron Nd:YAG laser (Laser Surgery Software, Inc.). The purpose of this study was to evaluate the effectiveness of laser assisted skin closure using the DLS YAG laser in a large animal model. Effectiveness was judged on the basis of wound dehiscence, infection, unusual healing result and consistency of results. Comparative cosmetic result was also evaluated. In this study, the DLS YAG laser was used to close scalpel-induced, full-thickness wounds. The pig model was chosen for its many integumentary similarities to man. Controls included scalpel-induced wounds closed using suture, staple and some with norepair. After adequate anesthesia was achieved, the dorsum of Yucutan pigs (approximately 75- 100 pounds) each was clipped with animal hair clippers from the shoulder area to the hind legs. The area was then shaved with a razor blade, avoiding any inadvertent cuts or abrasions of the skin. The dorsum was divided into four rows of four parallel incisions made by a #15 scalpel blade. Full-thickness incisions, 9 cm long, were placed over the dorsum of the pigs and then closed either with one loosely approximating Prolene" suture (the "no repair' group), multiple interrupted 6-0 nylon sutures, staples or laser. The experimental tissue sealing group consisted of 1 69 laser assisted closures on 1 3 pigs. Sutured control wounds were closed with 6-0 nylon, full thickness, simple, interrupted sutures. Eight sutures were placed 1 cm apart along the 9 cm incision. Stapled control wounds were approximated using two evenly spaced 3-0 VicryP' sub-dermal sutures and the dermis closed using Proximate' skin staples. Eight staples were placed 1 cm apart along the 9 cm incision. The no-repair incisions were grossly approximated using a single 2-0 Prolene full thickness, simple, interrupted suture located at the

  3. Modelling of a biologically inspired robotic fish driven by compliant parts.

    Science.gov (United States)

    El Daou, Hadi; Salumäe, Taavi; Chambers, Lily D; Megill, William M; Kruusmaa, Maarja

    2014-03-01

    Inspired by biological swimmers such as fish, a robot composed of a rigid head, a compliant body and a rigid caudal fin was built. It has the geometrical properties of a subcarangiform swimmer of the same size. The head houses a servo-motor which actuates the compliant body and the caudal fin. It achieves this by applying a concentrated moment on a point near the compliant body base. In this paper, the dynamics of the compliant body driving the robotic fish is modelled and experimentally validated. Lighthill's elongated body theory is used to define the hydrodynamic forces on the compliant part and Rayleigh proportional damping is used to model damping. Based on the assumed modes method, an energetic approach is used to write the equations of motion of the compliant body and to compute the relationship between the applied moment and the resulting lateral deflections. Experiments on the compliant body were carried out to validate the model predictions. The results showed that a good match was achieved between the measured and predicted deformations. A discussion of the swimming motions between the real fish and the robot is presented. PMID:24451164

  4. A new model for biological effects of radiation and the driven force of molecular evolution

    Science.gov (United States)

    Wada, Takahiro; Manabe, Yuichiro; Nakajima, Hiroo; Tsunoyama, Yuichi; Bando, Masako

    We proposed a new mathematical model to estimate biological effects of radiation, which we call Whack-A-Mole (WAM) model. A special feature of WAM model is that it involves the dose rate of radiation as a key ingredient. We succeeded to reproduce the experimental data of various species concerning the radiation induced mutation frequencies. From the analysis of the mega-mouse experiments, we obtained the mutation rate per base-pair per year for mice which is consistent with the so-called molecular clock in evolution genetics, 10-9 mutation/base-pair/year. Another important quantity is the equivalent dose rate for the whole spontaneous mutation, deff. The value of deff for mice is 1.1*10-3 Gy/hour which is much larger than the dose rate of natural radiation (10- (6 - 7) Gy/hour) by several orders of magnitude. We also analyzed Drosophila data and obtained essentially the same numbers. This clearly indicates that the natural radiation is not the dominant driving force of the molecular evolution, but we should look for other factors, such as miscopy of DNA in duplication process. We believe this is the first quantitative proof of the small contribution of the natural radiation in the molecular evolution.

  5. Modelling of a biologically inspired robotic fish driven by compliant parts

    International Nuclear Information System (INIS)

    Inspired by biological swimmers such as fish, a robot composed of a rigid head, a compliant body and a rigid caudal fin was built. It has the geometrical properties of a subcarangiform swimmer of the same size. The head houses a servo-motor which actuates the compliant body and the caudal fin. It achieves this by applying a concentrated moment on a point near the compliant body base. In this paper, the dynamics of the compliant body driving the robotic fish is modelled and experimentally validated. Lighthill’s elongated body theory is used to define the hydrodynamic forces on the compliant part and Rayleigh proportional damping is used to model damping. Based on the assumed modes method, an energetic approach is used to write the equations of motion of the compliant body and to compute the relationship between the applied moment and the resulting lateral deflections. Experiments on the compliant body were carried out to validate the model predictions. The results showed that a good match was achieved between the measured and predicted deformations. A discussion of the swimming motions between the real fish and the robot is presented. (paper)

  6. The community-driven BiG CZ software system for integration and analysis of bio- and geoscience data in the critical zone

    Science.gov (United States)

    Aufdenkampe, A. K.; Mayorga, E.; Horsburgh, J. S.; Lehnert, K. A.; Zaslavsky, I.; Valentine, D. W., Jr.; Richard, S. M.; Cheetham, R.; Meyer, F.; Henry, C.; Berg-Cross, G.; Packman, A. I.; Aronson, E. L.

    2014-12-01

    Here we present the prototypes of a new scientific software system designed around the new Observations Data Model version 2.0 (ODM2, https://github.com/UCHIC/ODM2) to substantially enhance integration of biological and Geological (BiG) data for Critical Zone (CZ) science. The CZ science community takes as its charge the effort to integrate theory, models and data from the multitude of disciplines collectively studying processes on the Earth's surface. The central scientific challenge of the CZ science community is to develop a "grand unifying theory" of the critical zone through a theory-model-data fusion approach, for which the key missing need is a cyberinfrastructure for seamless 4D visual exploration of the integrated knowledge (data, model outputs and interpolations) from all the bio and geoscience disciplines relevant to critical zone structure and function, similar to today's ability to easily explore historical satellite imagery and photographs of the earth's surface using Google Earth. This project takes the first "BiG" steps toward answering that need. The overall goal of this project is to co-develop with the CZ science and broader community, including natural resource managers and stakeholders, a web-based integration and visualization environment for joint analysis of cross-scale bio and geoscience processes in the critical zone (BiG CZ), spanning experimental and observational designs. We will: (1) Engage the CZ and broader community to co-develop and deploy the BiG CZ software stack; (2) Develop the BiG CZ Portal web application for intuitive, high-performance map-based discovery, visualization, access and publication of data by scientists, resource managers, educators and the general public; (3) Develop the BiG CZ Toolbox to enable cyber-savvy CZ scientists to access BiG CZ Application Programming Interfaces (APIs); and (4) Develop the BiG CZ Central software stack to bridge data systems developed for multiple critical zone domains into a single

  7. Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes

    Directory of Open Access Journals (Sweden)

    de Hoon Michiel JL

    2007-02-01

    Full Text Available Abstract Background Computational prediction methods are currently used to identify genes in prokaryote genomes. However, identification of the correct translation initiation sites remains a difficult task. Accurate translation initiation sites (TISs are important not only for the annotation of unknown proteins but also for the prediction of operons, promoters, and small non-coding RNA genes, as this typically makes use of the intergenic distance. A further problem is that most existing methods are optimized for Escherichia coli data sets; applying these methods to newly sequenced bacterial genomes may not result in an equivalent level of accuracy. Results Based on a biological representation of the translation process, we applied Bayesian statistics to create a score function for predicting translation initiation sites. In contrast to existing programs, our combination of methods uses supervised learning to optimally use the set of known translation initiation sites. We combined the Ribosome Binding Site (RBS sequence, the distance between the translation initiation site and the RBS sequence, the base composition of the start codon, the nucleotide composition (A-rich sequences following start codons, and the expected distribution of the protein length in a Bayesian scoring function. To further increase the prediction accuracy, we also took into account the operon orientation. The outcome of the procedure achieved a prediction accuracy of 93.2% in 858 E. coli genes from the EcoGene data set and 92.7% accuracy in a data set of 1243 Bacillus subtilis 'non-y' genes. We confirmed the performance in the GC-rich Gamma-Proteobacteria Herminiimonas arsenicoxydans, Pseudomonas aeruginosa, and Burkholderia pseudomallei K96243. Conclusion Hon-yaku, being based on a careful choice of elements important in translation, improved the prediction accuracy in B. subtilis data sets and other bacteria except for E. coli. We believe that most remaining

  8. Implementation of mechanism of action biology-driven early drug development for children with cancer.

    Science.gov (United States)

    Pearson, Andrew D J; Herold, Ralf; Rousseau, Raphaël; Copland, Chris; Bradley-Garelik, Brigid; Binner, Debbie; Capdeville, Renaud; Caron, Hubert; Carleer, Jacqueline; Chesler, Louis; Geoerger, Birgit; Kearns, Pamela; Marshall, Lynley V; Pfister, Stefan M; Schleiermacher, Gudrun; Skolnik, Jeffrey; Spadoni, Cesare; Sterba, Jaroslav; van den Berg, Hendrick; Uttenreuther-Fischer, Martina; Witt, Olaf; Norga, Koen; Vassal, Gilles

    2016-07-01

    An urgent need remains for new paediatric oncology drugs to cure children who die from cancer and to reduce drug-related sequelae in survivors. In 2007, the European Paediatric Regulation came into law requiring industry to create paediatric drug (all types of medicinal products) development programmes alongside those for adults. Unfortunately, paediatric drug development is still largely centred on adult conditions and not a mechanism of action (MoA)-based model, even though this would be more logical for childhood tumours as these have much fewer non-synonymous coding mutations than adult malignancies. Recent large-scale sequencing by International Genome Consortium and Paediatric Cancer Genome Project has further shown that the genetic and epigenetic repertoire of driver mutations in specific childhood malignancies differs from more common adult-type malignancies. To bring about much needed change, a Paediatric Platform, ACCELERATE, was proposed in 2013 by the Cancer Drug Development Forum, Innovative Therapies for Children with Cancer, the European Network for Cancer Research in Children and Adolescents and the European Society for Paediatric Oncology. The Platform, comprising multiple stakeholders in paediatric oncology, has three working groups, one with responsibility for promoting and developing high-quality MoA-informed paediatric drug development programmes, including specific measures for adolescents. Key is the establishment of a freely accessible aggregated database of paediatric biological tumour drug targets to be aligned with an aggregated pipeline of drugs. This will enable prioritisation and conduct of early phase clinical paediatric trials to evaluate these drugs against promising therapeutic targets and to generate clinical paediatric efficacy and safety data in an accelerated time frame. Through this work, the Platform seeks to ensure that potentially effective drugs, where the MoA is known and thought to be relevant to paediatric

  9. Development of software for management of radioactive waste in biological research and clinical assistance; Desenvolvimento do software para gerenciamento de rejeitos radioativos em pesquisa biologica e assistencia clinica

    Energy Technology Data Exchange (ETDEWEB)

    Maciel, Bianca; Mattos, Maria Fernanda S.S.; Medeiros, Regina B. [Universidade Federal de Sao Paulo (UNIFESP/EPM), Sao Paulo, SP (Brazil). Dept. de Diagnostico por Imagem. Nucleo de Protecao Radiologica; Franca Junior, Jose Antonio de, E-mail: fernanda@cfhr.epm.b, E-mail: rbitelli@cfhr.epm.b, E-mail: jafjunior@unifesp.b [Universidade Federal de Sao Paulo (UNIFESP/EPM), Sao Paulo, SP (Brazil). Dept. de Tecnologia da Informacao. Div. de Sistema de Informacao

    2011-10-26

    This paper describes the development of software which facilitates the automation of this process by mean of the Safety Analysis Report generating a data base allowing the statistic analysis and elaboration of radioactive wastes inventory. The software was developed in PHP language and the information is stored in a data base generated in Oracle and organized in different tables which allows to calculate the storage time of waste and to register the specificities of radioisotopes, cadastral data of the professionals which handle that radioisotope and also the characteristics of handling laboratories. That tool collaborates for a effective control on the use of radioisotopes in research laboratories and assistance areas as well

  10. Biologically and mechanically driven design of an RGD-mimetic macroporous foam for adipose tissue engineering applications.

    Science.gov (United States)

    Rossi, Eleonora; Gerges, Irini; Tocchio, Alessandro; Tamplenizza, Margherita; Aprile, Paola; Recordati, Camilla; Martello, Federico; Martin, Ivan; Milani, Paolo; Lenardi, Cristina

    2016-10-01

    Despite clinical treatments for adipose tissue defects, in particular breast tissue reconstruction, have certain grades of efficacy, many drawbacks are still affecting the long-term survival of new formed fat tissue. To overcome this problem, in the last decades, several scaffolding materials have been investigated in the field of adipose tissue engineering. However, a strategy able to recapitulate a suitable environment for adipose tissue reconstruction and maintenance is still missing. To address this need, we adopted a biologically and mechanically driven design to fabricate an RGD-mimetic poly(amidoamine) oligomer macroporous foam (OPAAF) for adipose tissue reconstruction. The scaffold was designed to fulfil three fundamental criteria: capability to induce cell adhesion and proliferation, support of in vivo vascularization and match of native tissue mechanical properties. Poly(amidoamine) oligomers were formed into soft scaffolds with hierarchical porosity through a combined free radical polymerization and foaming reaction. OPAAF is characterized by a high water uptake capacity, progressive degradation kinetics and ideal mechanical properties for adipose tissue reconstruction. OPAAF's ability to support cell adhesion, proliferation and adipogenesis was assessed in vitro using epithelial, fibroblast and endothelial cells (MDCK, 3T3L1 and HUVEC respectively). In addition, in vivo subcutaneous implantation in murine model highlighted OPAAF potential to support both adipogenesis and vessels infiltration. Overall, the reported results support the use of OPAAF as a scaffold for engineered adipose tissue construct. PMID:27428768

  11. Innovation and Practices of Software Document Composition Course for Case Driven%面向案例驱动的《软件文档写作》课程改革与实践

    Institute of Scientific and Technical Information of China (English)

    施庆平

    2013-01-01

    软件文档是整个软件开发工作的基础,现代工程化的软件开发离不开软件文档。在《软件文档写作》课程中,软件文档的内容和格式被强调得较多,而对学生编写文档的实践能力训练不够。针对这种情况,提出面向案例驱动的软件文档写作课程的教学方法,其目的是让学生结合实际项目的开发完整地理解和把握软件文档写作的方法和技能。%Software documentation is the basis of the entire software development work, modern engineer-ing, software development can not be separated from the software documentation. Software Doc-ument Composition course, the content and format of the software documentation to be empha-sized more, and the practical ability of students to write documentation is not enough training. Proposes project case driven Software Document Composition course, teaching methods, and its purpose is to allow students to complete understanding and grasp of writing software documen-tation and skills combined with the development of the actual project and scope.

  12. Model Driven Engineering

    Science.gov (United States)

    Gaševic, Dragan; Djuric, Dragan; Devedžic, Vladan

    A relevant initiative from the software engineering community called Model Driven Engineering (MDE) is being developed in parallel with the Semantic Web (Mellor et al. 2003a). The MDE approach to software development suggests that one should first develop a model of the system under study, which is then transformed into the real thing (i.e., an executable software entity). The most important research initiative in this area is the Model Driven Architecture (MDA), which is Model Driven Architecture being developed under the umbrella of the Object Management Group (OMG). This chapter describes the basic concepts of this software engineering effort.

  13. Using XMind Software to Draw Senior High School Biol-ogy Mind Maps%利用XMind软件绘制高中生物思维导图

    Institute of Scientific and Technical Information of China (English)

    祁永青

    2014-01-01

    本文利用XMind软件简要绘制了光合作用一节的思维导图,以此说明高中生物思维导图的绘制方法。%This article uses XMind software to draw a mind map for the section of photosynthesis, aiming to introduce the method of drawing senior high school biology mind maps.

  14. OCT-based three-dimensional, three vector component imaging of cilia-driven fluid flow for developmental biology (Conference Presentation)

    Science.gov (United States)

    Huang, Brendan K.; Zhou, Kevin C.; Gamm, Ute A.; Bhandari, Vineet; Khokha, Mustafa K.; Choma, Michael A.

    2016-03-01

    One critical barrier to the robust study of cilia-driven fluid flow in developmental biology is a lack of methods for acquiring three-dimensional (3D) images of three vector component (3C) measurements of flow velocities. A 3D3C map of cilia-driven fluid flow quantifies the flow speed along three axes (e.g. three Cartesian vector components v_x, v_y, v_z) at each point in 3D space. 3D3C quantification is important because cilia-driven fluid flow is not amenable to simplifying assumptions (e.g. parabolic flow profile. Such quantification may enable systematically detailed characterization of performance using shear force and power dissipation metrics derived from 3D3C flow velocity fields. We report our OCT-based results in developing methods for the 3D3C quantification of cilia-driven flow fields. First, we used custom scan protocols and reconstruction algorithms to synthesize 3D3C flow velocity fields from 2D2C fields generated using correlation-based methods (directional dynamic light scattering and digital particle image velocimetry). Xenopus results include flow driven by ciliated embryo skin and flow driven by ciliated ependymal cells in developing brain ventricles. Second, we developed a new approach to particle tracking velocimetry that generates 2D2.5C (2.5C: v_x,|v_y|,v_z) velocity fields from single-plane 2D image acquisitions. We demonstrated this particle streak velocimetry method in calibrated flow phantoms and in flow driven by ciliated Xenopus embryo skin. Additionally, we have preliminary results extending particle streak velocimetry to 3D3C in calibrated flow phantoms with ongoing work in Xenopus embryos.

  15. Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs

    Directory of Open Access Journals (Sweden)

    Khan Suleiman A

    2012-05-01

    Full Text Available Abstract Background Detailed and systematic understanding of the biological effects of millions of available compounds on living cells is a significant challenge. As most compounds impact multiple targets and pathways, traditional methods for analyzing structure-function relationships are not comprehensive enough. Therefore more advanced integrative models are needed for predicting biological effects elicited by specific chemical features. As a step towards creating such computational links we developed a data-driven chemical systems biology approach to comprehensively study the relationship of 76 structural 3D-descriptors (VolSurf, chemical space of 1159 drugs with the microarray gene expression responses (biological space they elicited in three cancer cell lines. The analysis covering 11350 genes was based on data from the Connectivity Map. We decomposed the biological response profiles into components, each linked to a characteristic chemical descriptor profile. Results Integrated analysis of both the chemical and biological space was more informative than either dataset alone in predicting drug similarity as measured by shared protein targets. We identified ten major components that link distinct VolSurf chemical features across multiple compounds to specific cellular responses. For example, component 2 (hydrophobic properties strongly linked to DNA damage response, while component 3 (hydrogen bonding was associated with metabolic stress. Individual structural and biological features were often linked to one cell line only, such as leukemia cells (HL-60 specifically responding to cardiac glycosides. Conclusions In summary, our approach identified several novel links between specific chemical structure properties and distinct biological responses in cells incubated with these drugs. Importantly, the analysis focused on chemical-biological properties that emerge across multiple drugs. The decoding of such systematic relationships is necessary

  16. Bridging the Gap Between Software Process and Software Development

    OpenAIRE

    Rouillé, Emmanuelle; Combemale, Benoit; Barais, Olivier; David, Touzet; Jézéquel, Jean-Marc

    2011-01-01

    National audience Model Driven Engineering (MDE) benefits software development (a.k.a. Model Driven Software Development) as well as software processes (a.k.a. Software Process Modeling). Nevertheless, the gap between processes and development is still too great. Indeed, information from processes is not always used to improve development and vice versa. For instance, it is possible to define the development tools used in a process description without linking them to the real tools. This p...

  17. A New Methodology for User-Driven Domain-Specific Application Software Development%一种用户主导的面向领域应用软件开发新方法

    Institute of Scientific and Technical Information of China (English)

    李明树

    2000-01-01

    This paper presents a new methodology for application software development, named as "user engineering". It is a user-driven domain-specific application software development methodology based on component-based software architecture, strengthening driving effect of users to make software development as a detailed definition process rather than a coding process only. It indicates an effective way to meet increasing application software requirements.%提出一种应用软件开发的新方法,称为"用户工程".这是一种基于构件化软件系统结构的用户主导的面向领域的应用软件开发方法,强调用户在应用软件开发中的主导作用,试图将应用软件的开发过程变成用户详细定义过程,而不仅仅是传统的编程过程.它为越来越多的应用软件开发需求提供了可能有效的一个途径.

  18. 计划驱动下敏捷开发过程的软件质量管理%Software Quality Management of Agile Development Process Based on Plan-Driven Development

    Institute of Scientific and Technical Information of China (English)

    商惠华

    2011-01-01

    对计划驱动开发和敏捷软件开发作了简要分析.结合两者的优点建立了基于计划驱动的敏捷软件开发的流程模型.该模型分为三大阶段来实现对软件开发过程和质量的管理.并给出每个阶段不同的管理方法,最后用一个非典型的实例来验证该模型的可行性.%In this paper, the plan-driven development and agile software development are analyzed briefly. Combining the advantages of these two kinds of methods, an agile software development process based on plan-driven model is established. The model is divided into three stages to realize the management of software development process and quality. A different management method was given in the every stage. Finally, the feasibility of the model is illustrated by an atypical example.

  19. Software architecture

    CERN Document Server

    Vogel, Oliver; Chughtai, Arif

    2011-01-01

    As a software architect you work in a wide-ranging and dynamic environment. You have to understand the needs of your customer, design architectures that satisfy both functional and non-functional requirements, and lead development teams in implementing the architecture. And it is an environment that is constantly changing: trends such as cloud computing, service orientation, and model-driven procedures open up new architectural possibilities. This book will help you to develop a holistic architectural awareness and knowledge base that extends beyond concrete methods, techniques, and technologi

  20. ATLAS software packaging

    CERN Document Server

    Rybkin, G

    2012-01-01

    Software packaging is indispensable part of build and prerequisite for deployment processes. Full ATLAS software stack consists of TDAQ, HLT, and Offline software. These software groups depend on some 80 external software packages. We present tools, package PackDist, developed and used to package all this software except for TDAQ project. PackDist is based on and driven by CMT, ATLAS software configuration and build tool, and consists of shell and Python scripts. The packaging unit used is CMT project. Each CMT project is packaged as several packages - platform dependent (one per platform available), source code excluding header files, other platform independent files, documentation, and debug information packages (the last two being built optionally). Packaging can be done recursively to package all the dependencies. The whole set of packages for one software release, distribution kit, also includes configuration packages and contains some 120 packages for one platform. Also packaged are physics analysis pro...

  1. Increasing URM Undergraduate Student Success through Assessment-Driven Interventions: A Multiyear Study Using Freshman-Level General Biology as a Model System

    Science.gov (United States)

    Carmichael, Mary C.; St. Clair, Candace; Edwards, Andrea M.; Barrett, Peter; McFerrin, Harris; Davenport, Ian; Awad, Mohamed; Kundu, Anup; Ireland, Shubha Kale

    2016-01-01

    Xavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students. In this multiyear study with ∼5500 participants, data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course. The three hour-long exams were common and administered concurrently to all students. New exam questions were developed using Bloom’s taxonomy, and exam results were analyzed statistically with validated assessment tools. All but the comprehensive final exam were returned to students for self-evaluation and remediation. Among other approaches, course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters. Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 72.9% (2010) to 83.5% (2015). Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions. Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20% increase in the course pass rates over time, also for the high-risk population. These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention, particularly for our academically at-risk students. PMID:27543637

  2. MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics

    OpenAIRE

    Egea, Jose A; Henriques, David; Cokelaer, Thomas; Villaverde, Alejandro F; Banga, Julio R.; Saez-Rodriguez, Julio

    2013-01-01

    Optimization is key to solve many problems in computational biology. Global optimization methods provide a robust methodology, and metaheuristics in particular have proven to be the most efficient methods for many applications. Despite their utility, there is limited availability of metaheuristic tools. We present MEIGO, an R and Matlab optimization toolbox (also available in Python via a wrapper of the R version), that implements metaheuristics capable of solving diverse problems arising in ...

  3. Biologic

    CERN Document Server

    Kauffman, L H

    2002-01-01

    In this paper we explore the boundary between biology and the study of formal systems (logic). In the end, we arrive at a summary formalism, a chapter in "boundary mathematics" where there are not only containers but also extainers ><, entities open to interaction and distinguishing the space that they are not. The boundary algebra of containers and extainers is to biologic what boolean algebra is to classical logic. We show how this formalism encompasses significant parts of the logic of DNA replication, the Dirac formalism for quantum mechanics, formalisms for protein folding and the basic structure of the Temperley Lieb algebra at the foundations of topological invariants of knots and links.

  4. Systems biology of cancer: entropy, disorder, and selection-driven evolution to independence, invasion and "swarm intelligence".

    Science.gov (United States)

    Tarabichi, M; Antoniou, A; Saiselet, M; Pita, J M; Andry, G; Dumont, J E; Detours, V; Maenhaut, C

    2013-12-01

    Our knowledge of the biology of solid cancer has greatly progressed during the last few years, and many excellent reviews dealing with the various aspects of this biology have appeared. In the present review, we attempt to bring together these subjects in a general systems biology narrative. It starts from the roles of what we term entropy of signaling and noise in the initial oncogenic events, to the first major transition of tumorigenesis: the independence of the tumor cell and the switch in its physiology, i.e., from subservience to the organism to its own independent Darwinian evolution. The development after independence involves a constant dynamic reprogramming of the cells and the emergence of a sort of collective intelligence leading to invasion and metastasis and seldom to the ultimate acquisition of immortality through inter-individual infection. At each step, the probability of success is minimal to infinitesimal, but the number of cells possibly involved and the time scale account for the relatively high occurrence of tumorigenesis and metastasis in multicellular organisms.

  5. Computer Software.

    Science.gov (United States)

    Kay, Alan

    1984-01-01

    Discusses the nature and development of computer software. Programing, programing languages, types of software (including dynamic spreadsheets), and software of the future are among the topics considered. (JN)

  6. MODIS vegetation products as proxies of photosynthetic potential: a look across meteorological and biologic driven ecosystem productivity

    Science.gov (United States)

    Restrepo-Coupe, N.; Huete, A.; Davies, K.; Cleverly, J.; Beringer, J.; Eamus, D.; van Gorsel, E.; Hutley, L. B.; Meyer, W. S.

    2015-12-01

    A direct relationship between gross ecosystem productivity (GEP) measured by the eddy covariance (EC) method and Moderate Resolution Imaging Spectroradiometer (MODIS) vegetation indices (VIs) has been observed in many temperate and tropical ecosystems. However, in Australian evergreen forests, and particularly sclerophyll woodlands, MODIS VIs do not capture seasonality of GEP. In this study, we re-evaluate the connection between satellite and flux tower data at four contrasting Australian ecosystems, through comparisons of ecosystem photosynthetic activity (GEP) and potential (e.g. ecosystem light use efficiency and quantum yield) with MODIS vegetation satellite products, including VIs, gross primary productivity (GPPMOD), leaf area index (LAIMOD), and fraction of photosynthetic active radiation (fPARMOD). We found that satellite derived greenness products constitute a measurement of ecosystem structure (e.g. leaf area index - quantity of leaves) and function (e.g. leaf level photosynthetic assimilation capacity - quality of leaves), rather than productivity. Our results show that in primarily meteorological-driven (e.g. photosynthetic active radiation, air temperature and/or precipitation) and relatively aseasonal vegetation photosynthetic potential ecosystems (e.g. evergreen wet sclerophyll forests), there were no statistically significant relationships between GEP and satellite derived measures of greenness. In contrast, for phenology-driven ecosystems (e.g. tropical savannas), changes in the vegetation status drove GEP, and tower-based measurements of photosynthetic activity were best represented by VIs. We observed the highest correlations between MODIS products and GEP in locations where key meteorological variables and vegetation phenology were synchronous (e.g. semi-arid Acacia woodlands) and low correlation at locations where they were asynchronous (e.g. Mediterranean ecosystems). Eddy covariance data offer much more than validation and/or calibration of

  7. SU-E-T-253: Open-Source Automatic Software for Quantifying Biological Assays of Radiation Effects

    Energy Technology Data Exchange (ETDEWEB)

    Detappe, A [University of Lyon (France); Dana-Farber Cancer Institute, Boston, MA (United States); Korideck, H [Dana-Farber Cancer Institute, Boston, MA (United States); Makrigiorgos, G; Berbeco, R [Dana-Farber Cancer Institute, Boston, MA (United States); Brigham and Women' s Hospital, Boston, MA (United States)

    2014-06-01

    Purpose: Clonogenic cell survival is a common assay for quantifying the effect of drugs and radiation. Manual counting of surviving colonies can take 30–90seconds per plate, a major limitation for large studies. Currently available automatic counting tools are not easily modified for radiation oncology research. Our goal is to provide an open-source toolkit for precise, accurate and fast analysis of biological assays in radiation oncology. Methods: As an example analysis, we used HeLa cells incubated with gadolinium nanoparticles prior to irradiation. After treatment, the cells are grown for 14days to allow for colony formation. To analyze the colony growth, we capture images of each dish for archiving and automatic computer-based analysis. A FujifilmX20 camera is placed at the top of a box setup, 20cm above the sample, which is backlit by a LED lamp placed at the bottom of the box. We use a Gaussian filter (width=1.3mm) and color threshold (19–255). The minimum size for a colony to be counted is 1mm. For this example, 20 dishes with a large range of colonies were analyzed. Each dish was counted 3 times manually by 3 different users and then compared to our counter. Results: Automatic counting of cell colonies takes an average of 7seconds, enabling the analysis process to be accelerated 4–12 times. The average precision of the automatic counter was 1.7%. The Student t-test demonstrated the non-significant differences between the two counting methods (p=0.64). The ICC demonstrated the reliability of each method with ICC>0.999 (automatic) and ICC=0.95 (manual). Conclusion: We developed an open-source automatic toolkit for the analysis of biological assays in radiation oncology and demonstrated the accuracy, precision and effort savings for clonogenic cell survival quantification. This toolkit is currently being used in two laboratories for routine experimental analysis and will be made freely available on our departmental website.

  8. Biological Visualization, Imaging and Simulation(Bio-VIS) at NASA Ames Research Center: Developing New Software and Technology for Astronaut Training and Biology Research in Space

    Science.gov (United States)

    Smith, Jeffrey

    2003-01-01

    The Bio- Visualization, Imaging and Simulation (BioVIS) Technology Center at NASA's Ames Research Center is dedicated to developing and applying advanced visualization, computation and simulation technologies to support NASA Space Life Sciences research and the objectives of the Fundamental Biology Program. Research ranges from high resolution 3D cell imaging and structure analysis, virtual environment simulation of fine sensory-motor tasks, computational neuroscience and biophysics to biomedical/clinical applications. Computer simulation research focuses on the development of advanced computational tools for astronaut training and education. Virtual Reality (VR) and Virtual Environment (VE) simulation systems have become important training tools in many fields from flight simulation to, more recently, surgical simulation. The type and quality of training provided by these computer-based tools ranges widely, but the value of real-time VE computer simulation as a method of preparing individuals for real-world tasks is well established. Astronauts routinely use VE systems for various training tasks, including Space Shuttle landings, robot arm manipulations and extravehicular activities (space walks). Currently, there are no VE systems to train astronauts for basic and applied research experiments which are an important part of many missions. The Virtual Glovebox (VGX) is a prototype VE system for real-time physically-based simulation of the Life Sciences Glovebox where astronauts will perform many complex tasks supporting research experiments aboard the International Space Station. The VGX consists of a physical display system utilizing duel LCD projectors and circular polarization to produce a desktop-sized 3D virtual workspace. Physically-based modeling tools (Arachi Inc.) provide real-time collision detection, rigid body dynamics, physical properties and force-based controls for objects. The human-computer interface consists of two magnetic tracking devices

  9. How can software SMEs become medical device software SMEs

    OpenAIRE

    Mc Caffery, Fergal; Casey, Valentine; Mc Hugh, Martin

    2011-01-01

    peer-reviewed Today the amount of software content within medical devices has grown considerably and will continue to do so as the level of complexity of medical devices continues to increase. This is driven by the fact that software is introduced to produce sophisticated medical devices that would not be possible using only hardware. This therefore presents opportunities for software development SMEs to become medical device software development organisations. However, some obstacles need...

  10. Open source software for electric field Monte Carlo simulation of coherent backscattering in biological media containing birefringence.

    Science.gov (United States)

    Radosevich, Andrew J; Rogers, Jeremy D; Capoğlu, Ilker R; Mutyal, Nikhil N; Pradhan, Prabhakar; Backman, Vadim

    2012-11-01

    ABSTRACT. We present an open source electric field tracking Monte Carlo program to model backscattering in biological media containing birefringence, with computation of the coherent backscattering phenomenon as an example. These simulations enable the modeling of tissue scattering as a statistically homogeneous continuous random media under the Whittle-Matérn model, which includes the Henyey-Greenstein phase function as a special case, or as a composition of discrete spherical scatterers under Mie theory. The calculation of the amplitude scattering matrix for the above two cases as well as the implementation of birefringence using the Jones N-matrix formalism is presented. For ease of operator use and data processing, our simulation incorporates a graphical user interface written in MATLAB to interact with the underlying C code. Additionally, an increase in computational speed is achieved through implementation of message passing interface and the semi-analytical approach. Finally, we provide demonstrations of the results of our simulation for purely scattering media and scattering media containing linear birefringence.

  11. Biodegradability enhancement of a leachate after biological lagooning using a solar driven photo-Fenton reaction, and further combination with an activated sludge biological process, at pre-industrial scale.

    Science.gov (United States)

    Silva, Tânia F C V; Fonseca, Amélia; Saraiva, Isabel; Vilar, Vítor J P; Boaventura, Rui A R

    2013-06-15

    This work proposes an integrated leachate treatment strategy, combining a solar photo-Fenton reaction, to enhance the biodegradability of the leachate from an aerated lagoon, with an activated sludge process, under aerobic and anoxic conditions, to achieve COD target values and nitrogen content according to the legislation. The efficiency and performance of the photo-Fenton reaction, concerning a sludge removal step after acidification, defining the optimum phototreatment time to reach a biodegradable wastewater that can be further oxidized in a biological reactor and, activation sludge biological process, defining the nitrification and denitrification reaction rates, alkalinity balance and methanol dose necessary as external carbon source, was evaluated in the integrated system at a scale close to industrial. The pre-industrial plant presents a photocatalytic system with 39.52 m(2) of compound parabolic collectors (CPCs) and 2 m(3) recirculation tank and, an activated sludge biological reactor with 3 m(3) capacity. Leachate biodegradability enhancement by means of a solar driven photo-Fenton process was evaluated using direct biodegradability tests, as Zahn-Wellens method, and indirect measure according to average oxidation state (AOS), low molecular carboxylic acids content (fast biodegradable character) and humic substances (recalcitrant character) concentration. Due to high variability of leachate composition, UV absorbance on-line measurement was established as a useful parameter for photo-Fenton reaction control.

  12. Biodegradability enhancement of a leachate after biological lagooning using a solar driven photo-Fenton reaction, and further combination with an activated sludge biological process, at pre-industrial scale.

    Science.gov (United States)

    Silva, Tânia F C V; Fonseca, Amélia; Saraiva, Isabel; Vilar, Vítor J P; Boaventura, Rui A R

    2013-06-15

    This work proposes an integrated leachate treatment strategy, combining a solar photo-Fenton reaction, to enhance the biodegradability of the leachate from an aerated lagoon, with an activated sludge process, under aerobic and anoxic conditions, to achieve COD target values and nitrogen content according to the legislation. The efficiency and performance of the photo-Fenton reaction, concerning a sludge removal step after acidification, defining the optimum phototreatment time to reach a biodegradable wastewater that can be further oxidized in a biological reactor and, activation sludge biological process, defining the nitrification and denitrification reaction rates, alkalinity balance and methanol dose necessary as external carbon source, was evaluated in the integrated system at a scale close to industrial. The pre-industrial plant presents a photocatalytic system with 39.52 m(2) of compound parabolic collectors (CPCs) and 2 m(3) recirculation tank and, an activated sludge biological reactor with 3 m(3) capacity. Leachate biodegradability enhancement by means of a solar driven photo-Fenton process was evaluated using direct biodegradability tests, as Zahn-Wellens method, and indirect measure according to average oxidation state (AOS), low molecular carboxylic acids content (fast biodegradable character) and humic substances (recalcitrant character) concentration. Due to high variability of leachate composition, UV absorbance on-line measurement was established as a useful parameter for photo-Fenton reaction control. PMID:23642652

  13. Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools

    Directory of Open Access Journals (Sweden)

    Tilton Susan C

    2012-11-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are noncoding RNAs that direct post-transcriptional regulation of protein coding genes. Recent studies have shown miRNAs are important for controlling many biological processes, including nervous system development, and are highly conserved across species. Given their importance, computational tools are necessary for analysis, interpretation and integration of high-throughput (HTP miRNA data in an increasing number of model species. The Bioinformatics Resource Manager (BRM v2.3 is a software environment for data management, mining, integration and functional annotation of HTP biological data. In this study, we report recent updates to BRM for miRNA data analysis and cross-species comparisons across datasets. Results BRM v2.3 has the capability to query predicted miRNA targets from multiple databases, retrieve potential regulatory miRNAs for known genes, integrate experimentally derived miRNA and mRNA datasets, perform ortholog mapping across species, and retrieve annotation and cross-reference identifiers for an expanded number of species. Here we use BRM to show that developmental exposure of zebrafish to 30 uM nicotine from 6–48 hours post fertilization (hpf results in behavioral hyperactivity in larval zebrafish and alteration of putative miRNA gene targets in whole embryos at developmental stages that encompass early neurogenesis. We show typical workflows for using BRM to integrate experimental zebrafish miRNA and mRNA microarray datasets with example retrievals for zebrafish, including pathway annotation and mapping to human ortholog. Functional analysis of differentially regulated (p Conclusions BRM provides the ability to mine complex data for identification of candidate miRNAs or pathways that drive phenotypic outcome and, therefore, is a useful hypothesis generation tool for systems biology. The miRNA workflow in BRM allows for efficient processing of multiple miRNA and mRNA datasets in a single

  14. 分子生物学图像分析系统软件设计%The Software Design for the Molecular Biological Image Processing System

    Institute of Scientific and Technical Information of China (English)

    徐秀林; 朱乃硕; 果忠祥

    2001-01-01

    With the use of Visual Basic 6.0 language and molecularbiological technology, we have developed a new molecular biological information processing system to detect the characteristic parameter of molecular biological electrophoresis image. The software can determine the molecular weight of the restriction endonuclease hydrolytic DNA fragment and protein or other macromolecules. The application indicates that the system with its accuracy reliability high officiency and a large capacity of data to be stored,It is very useful to gene diagnosis and molecular biological researches.%利用VisualBasic6.0(简称VB6)编程技术和分子生物学实验技术,研制开发一套用于测定DNA基因扩增片段或限制性内切酶水解后形成的不同大小片段的特征参数的分子生物学图像分析软件,该软件能对不同DNA分子、蛋白质分子和其它生物大分子的电泳图像进行定量分析。应用表明,该软件系统准确可靠,速度快,能储存大量信息,便于检索和信息处理,对分子生物学及基因工程基础研究和临床基因诊断都具有重要的应用价值。

  15. TF-finder: A software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base

    Directory of Open Access Journals (Sweden)

    Cui Xiaoqi

    2010-08-01

    Full Text Available Abstract Background Identification of transcription factors (TFs involved in a biological process is the first step towards a better understanding of the underlying regulatory mechanisms. However, due to the involvement of a large number of genes and complicated interactions in a gene regulatory network (GRN, identification of the TFs involved in a biology process remains to be very challenging. In reality, the recognition of TFs for a given a biological process can be further complicated by the fact that most eukaryotic genomes encode thousands of TFs, which are organized in gene families of various sizes and in many cases with poor sequence conservation except for small conserved domains. This poses a significant challenge for identification of the exact TFs involved or ranking the importance of a set of TFs to a process of interest. Therefore, new methods for recognizing novel TFs are desperately needed. Although a plethora of methods have been developed to infer regulatory genes using microarray data, it is still rare to find the methods that use existing knowledge base in particular the validated genes known to be involved in a process to bait/guide discovery of novel TFs. Such methods can replace the sometimes-arbitrary process of selection of candidate genes for experimental validation and significantly advance our knowledge and understanding of the regulation of a process. Results We developed an automated software package called TF-finder for recognizing TFs involved in a biological process using microarray data and existing knowledge base. TF-finder contains two components, adaptive sparse canonical correlation analysis (ASCCA and enrichment test, for TF recognition. ASCCA uses positive target genes to bait TFS from gene expression data while enrichment test examines the presence of positive TFs in the outcomes from ASCCA. Using microarray data from salt and water stress experiments, we showed TF-finder is very efficient in recognizing

  16. LESM: a laser-driven sub-MeV electron source delivering ultra-high dose rate on thin biological samples

    Science.gov (United States)

    Labate, L.; Andreassi, M. G.; Baffigi, F.; Bizzarri, R.; Borghini, A.; Bussolino, G. C.; Fulgentini, L.; Ghetti, F.; Giulietti, A.; Köster, P.; Lamia, D.; Levato, T.; Oishi, Y.; Pulignani, S.; Russo, G.; Sgarbossa, A.; Gizzi, L. A.

    2016-07-01

    We present a laser-driven source of electron bunches with average energy 260~\\text{keV} and picosecond duration, which has been setup for radiobiological tests covering the previously untested sub-MeV energy range. Each bunch combines high charge with short duration and sub-millimeter range into a record instantaneous dose rate, as high as {{10}9}~\\text{Gy}~{{\\text{s}}-1} . The source can be operated at 10~\\text{Hz} and its average dose rate is 35~\\text{mGy}~{{\\text{s}}-1} . Both the high instantaneous dose rate and high level of relative biological effectiveness, attached to sub-MeV electrons, make this source very attractive for studies of ultrafast radiobiology on thin cell samples. The source reliability, in terms of shot-to-shot stability of features such as mean energy, bunch charge and transverse beam profile, is discussed, along with a dosimetric characterization. Finally, a few preliminary biological tests performed with this source are presented.

  17. Computer Center: Software Review.

    Science.gov (United States)

    Duhrkopf, Richard, Ed.; Belshe, John F., Ed.

    1988-01-01

    Reviews a software package, "Mitosis-Meiosis," available for Apple II or IBM computers with colorgraphics capabilities. Describes the documentation, presentation and flexibility of the program. Rates the program based on graphics and usability in a biology classroom. (CW)

  18. Unit testing, model validation, and biological simulation.

    Science.gov (United States)

    Sarma, Gopal P; Jacobs, Travis W; Watts, Mark D; Ghayoomie, S Vahid; Larson, Stephen D; Gerkin, Richard C

    2016-01-01

    The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in the biological sciences, it is important to examine how these practices can accelerate biological software development and improve research quality. In this article, we give a focused case study of our experience with the practices of unit testing and test-driven development in OpenWorm, an open-science project aimed at modeling Caenorhabditis elegans. We identify and discuss the challenges of incorporating test-driven development into a heterogeneous, data-driven project, as well as the role of model validation tests, a category of tests unique to software which expresses scientific models. PMID:27635225

  19. Unit testing, model validation, and biological simulation

    Science.gov (United States)

    Watts, Mark D.; Ghayoomie, S. Vahid; Larson, Stephen D.; Gerkin, Richard C.

    2016-01-01

    The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in the biological sciences, it is important to examine how these practices can accelerate biological software development and improve research quality. In this article, we give a focused case study of our experience with the practices of unit testing and test-driven development in OpenWorm, an open-science project aimed at modeling Caenorhabditis elegans. We identify and discuss the challenges of incorporating test-driven development into a heterogeneous, data-driven project, as well as the role of model validation tests, a category of tests unique to software which expresses scientific models.

  20. Unit testing, model validation, and biological simulation

    Science.gov (United States)

    Watts, Mark D.; Ghayoomie, S. Vahid; Larson, Stephen D.; Gerkin, Richard C.

    2016-01-01

    The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in the biological sciences, it is important to examine how these practices can accelerate biological software development and improve research quality. In this article, we give a focused case study of our experience with the practices of unit testing and test-driven development in OpenWorm, an open-science project aimed at modeling Caenorhabditis elegans. We identify and discuss the challenges of incorporating test-driven development into a heterogeneous, data-driven project, as well as the role of model validation tests, a category of tests unique to software which expresses scientific models. PMID:27635225

  1. 极限编程和项目驱动相结合的软件工程教学方法探究%Research of extreme programming and project - driven teaching mode for software engineering

    Institute of Scientific and Technical Information of China (English)

    殷海明; 魏远旺

    2012-01-01

    In this paper, we propose an extreme programming and project - driven teaching model for software engineering. First we compare the project - driven teaching model with the traditional methods and address the advantages of the former, and list the standards for choosing the projects. The internal reason why extreme programming is suitable for students'practice in the course softer engineering is analyzed, and a scientific evaluation mechanism for this original teaching model is proposed, which is proved to be efficient.%论述了项目驱动教学方法相比于传统教学方法的优点,给出了适用于软件工程教学的项目选择标准,由此提出了一种将极限编程和项目驱动相结合的软件工程教学方法,并制定了适用于该教学方法的课程考核体系。

  2. 基于正反向工程的模型驱动的软件开发过程分析%Research on software development process driven model based on Reverse Engineering

    Institute of Scientific and Technical Information of China (English)

    周艳萍

    2013-01-01

    模型驱动就是将数据与处理分别实现,将数据独立的封装起来,再将处理形成一个独立的类别。当前被广泛使用的建模工具有RationaRose和PowerDesigner两种,本文对这两种常用工具都进行了简要的介绍,并对其实现建模的途径进行了分析,以PowerDesigner进行了正反向工程模型驱动进行软件开发的过程。%Model driven is the data and processing are realized, the data independent of the package,and then form a separate category.Modeling tool is currently widely used are RationaRose and PowerDesigner two, this paper introduces two kinds of commonly used tools,and the realization of modeling the way to carry on the analysis,the PowerDesigner for the process of reverse engineering model driven software development.

  3. Effect of elevated CO2 and temperature on abiotic and biologically-driven basalt weathering and C sequestration

    Science.gov (United States)

    Juarez, Sabrina; Dontsova, Katerina; Le Galliard, Jean-François; Chollet, Simon; Llavata, Mathieu; Massol, Florent; Cros, Alexis; Barré, Pierre; Gelabert, Alexandre; Daval, Damien; Corvisier, Jérôme; Troch, Peter; Barron-Gafford, Greg; Van Haren, Joost; Ferrière, Régis

    2016-04-01

    Weathering of primary silicates is one of the mechanisms involved in carbon removal from the atmosphere, affecting the carbon cycle at geologic timescales with basalt significantly contributing to the global weathering CO2 flux. Mineral weathering can be enhanced by microbiota and plants. Increase in both temperature and amount of CO2 in the atmosphere can directly increase weathering and can also affect weathering through impact on biological systems. This would result in possible negative feedback on climate change. The goal of this research was to quantify direct and indirect effects of temperature and elevated CO2 on basalt weathering and carbon sequestration. In order to achieve this goal we performed controlled-environment mesocosm experiments at Ecotron Ile-de-France (France). Granular basalt collected in Flagstaff (AZ, USA) was exposed to rainfall at equilibrium with two different CO2 concentrations in the air, ambient (400 ppm) and elevated (800 ppm); and kept at two climate regimes, with ambient and elevated (+ 4° C) temperature. Four biological treatments were superimposed on this design: a plant-free control; N-fixing grass (Alfalfa, Medicago sativa), N-fixing tree (Velvet mesquite, Prosopis velutina); and grass that does not form symbiotic relationships with N fixers (Green Sprangletop, Leptochloa dubia). All used basalt had native microbial community. Mesocosms were equipped with solution and gas samplers. To monitor biogenic and lithogenic weathering product concentrations, soil solution samples were collected under vacuum after each rainfall event and analyzed to determine pH, electrical conductivity, major and trace elements concentrations, anions concentrations, and aqueous phase organic matter chemistry. Soil gases were monitored for CO2 using porous Teflon gas samplers connected to the Vaisala probes. Plant biomass was collected at the end of the experiment to determine dry weight, as well as removal of N and lithogenic elements by the plants

  4. A biology-driven receptor model for daily pollen allergy risk in Korea based on Weibull probability density function

    Science.gov (United States)

    Kim, Kyu Rang; Kim, Mijin; Choe, Ho-Seong; Han, Mae Ja; Lee, Hye-Rim; Oh, Jae-Won; Kim, Baek-Jo

    2016-07-01

    Pollen is an important cause of respiratory allergic reactions. As individual sanitation has improved, allergy risk has increased, and this trend is expected to continue due to climate change. Atmospheric pollen concentration is highly influenced by weather conditions. Regression analysis and modeling of the relationships between airborne pollen concentrations and weather conditions were performed to analyze and forecast pollen conditions. Traditionally, daily pollen concentration has been estimated using regression models that describe the relationships between observed pollen concentrations and weather conditions. These models were able to forecast daily concentrations at the sites of observation, but lacked broader spatial applicability beyond those sites. To overcome this limitation, an integrated modeling scheme was developed that is designed to represent the underlying processes of pollen production and distribution. A maximum potential for airborne pollen is first determined using the Weibull probability density function. Then, daily pollen concentration is estimated using multiple regression models. Daily risk grade levels are determined based on the risk criteria used in Korea. The mean percentages of agreement between the observed and estimated levels were 81.4-88.2 % and 92.5-98.5 % for oak and Japanese hop pollens, respectively. The new models estimated daily pollen risk more accurately than the original statistical models because of the newly integrated biological response curves. Although they overestimated seasonal mean concentration, they did not simulate all of the peak concentrations. This issue would be resolved by adding more variables that affect the prevalence and internal maturity of pollens.

  5. Ten recommendations for software engineering in research

    OpenAIRE

    Hastings, Janna; Haug, Kenneth; Steinbeck, Christoph

    2014-01-01

    Research in the context of data-driven science requires a backbone of well-written software, but scientific researchers are typically not trained at length in software engineering, the principles for creating better software products. To address this gap, in particular for young researchers new to programming, we give ten recommendations to ensure the usability, sustainability and practicality of research software.

  6. Ten recommendations for software engineering in research.

    Science.gov (United States)

    Hastings, Janna; Haug, Kenneth; Steinbeck, Christoph

    2014-01-01

    Research in the context of data-driven science requires a backbone of well-written software, but scientific researchers are typically not trained at length in software engineering, the principles for creating better software products. To address this gap, in particular for young researchers new to programming, we give ten recommendations to ensure the usability, sustainability and practicality of research software.

  7. Test-driven programming

    Science.gov (United States)

    Georgiev, Bozhidar; Georgieva, Adriana

    2013-12-01

    In this paper, are presented some possibilities concerning the implementation of a test-driven development as a programming method. Here is offered a different point of view for creation of advanced programming techniques (build tests before programming source with all necessary software tools and modules respectively). Therefore, this nontraditional approach for easier programmer's work through building tests at first is preferable way of software development. This approach allows comparatively simple programming (applied with different object-oriented programming languages as for example JAVA, XML, PYTHON etc.). It is predictable way to develop software tools and to provide help about creating better software that is also easier to maintain. Test-driven programming is able to replace more complicated casual paradigms, used by many programmers.

  8. Architecture design in global and model-centric software development

    NARCIS (Netherlands)

    Heijstek, Werner

    2012-01-01

    This doctoral dissertation describes a series of empirical investigations into representation, dissemination and coordination of software architecture design in the context of global software development. A particular focus is placed on model-centric and model-driven software development.

  9. 一种“用例+控例”驱动的软件分析与设计方法%"Use Case+Control Case" Driven Approach for Software Analysis and Design

    Institute of Scientific and Technical Information of China (English)

    刘春; 张伟; 赵海燕; 金芝

    2013-01-01

    As software systems and their operational environments become more and more complex,the topic of software dependability has attracted more and more attention.The software analysis and design are both required to focus on the functionality and the dependability.However,there still lacks an effective approach to consider the functionality and the dependability simultaneously during software analysis and design.Based on cybernetics,this paper proposes a "use case+control case" driven approach for software analysis and design,which aims to address the software functionality and dependability under a unified framework.During requirements analysis,the "use case+control case" model supports the co-modeling of the functional requirements and the dependability requirements.During system design,the design techniques proposed by ICONIX approach are extended to identify the functionality objects that realize the use cases,and the dependability objects that realize the control cases.A case is also used to illustrate the feasibility of the proposed approach.%随着软件本身及其运行环境的日益复杂,软件可信性引起人们越来越多的关注.软件的分析与设计也越来越需要综合考虑软件的功能性和可信性.然而,如何在软件的分析与设计过程中综合考虑软件的功能性和可信性,目前仍然缺乏系统而有效的方法.基于控制论,提出了一种基于“用例+控例”的方法,以在软件的分析与设计过程中综合考虑软件的功能性和可信性.在需求分析阶段,“用例+控例”模型支持需求工程师在同一个模型中自然地表达软件系统的功能性需求和可信性需求.在系统设计阶段,扩展了ICONIX开发方法的用例驱动的系统设计技术,用以分别识别实现用例的功能对象和实现控例的可信保障对象,以最终构建出既满足功能性需求又满足可信性需求的对象模型.应用一个实例来说明所提出方法的可行性.

  10. ATLAS software packaging

    Science.gov (United States)

    Rybkin, Grigory

    2012-12-01

    Software packaging is indispensable part of build and prerequisite for deployment processes. Full ATLAS software stack consists of TDAQ, HLT, and Offline software. These software groups depend on some 80 external software packages. We present tools, package PackDist, developed and used to package all this software except for TDAQ project. PackDist is based on and driven by CMT, ATLAS software configuration and build tool, and consists of shell and Python scripts. The packaging unit used is CMT project. Each CMT project is packaged as several packages—platform dependent (one per platform available), source code excluding header files, other platform independent files, documentation, and debug information packages (the last two being built optionally). Packaging can be done recursively to package all the dependencies. The whole set of packages for one software release, distribution kit, also includes configuration packages and contains some 120 packages for one platform. Also packaged are physics analysis projects (currently 6) used by particular physics groups on top of the full release. The tools provide an installation test for the full distribution kit. Packaging is done in two formats for use with the Pacman and RPM package managers. The tools are functional on the platforms supported by ATLAS—GNU/Linux and Mac OS X. The packaged software is used for software deployment on all ATLAS computing resources from the detector and trigger computing farms, collaboration laboratories computing centres, grid sites, to physicist laptops, and CERN VMFS and covers the use cases of running all applications as well as of software development.

  11. Software Reviews.

    Science.gov (United States)

    Smith, Richard L., Ed.

    1985-01-01

    Reviews software packages by providing extensive descriptions and discussions of their strengths and weaknesses. Software reviewed include (1) "VISIFROG: Vertebrate Anatomy" (grade seven-adult); (2) "Fraction Bars Computer Program" (grades three to six) and (3) four telecommunications utilities. (JN)

  12. Software reliability

    CERN Document Server

    Bendell, A

    1986-01-01

    Software Reliability reviews some fundamental issues of software reliability as well as the techniques, models, and metrics used to predict the reliability of software. Topics covered include fault avoidance, fault removal, and fault tolerance, along with statistical methods for the objective assessment of predictive accuracy. Development cost models and life-cycle cost models are also discussed. This book is divided into eight sections and begins with a chapter on adaptive modeling used to predict software reliability, followed by a discussion on failure rate in software reliability growth mo

  13. Bioboxes: standardised containers for interchangeable bioinformatics software.

    Science.gov (United States)

    Belmann, Peter; Dröge, Johannes; Bremges, Andreas; McHardy, Alice C; Sczyrba, Alexander; Barton, Michael D

    2015-01-01

    Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplified by the Docker platform, has the potential to solve the problems associated with sharing software. We propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable. PMID:26473029

  14. Applied software risk management a guide for software project managers

    CERN Document Server

    Pandian, C Ravindranath

    2006-01-01

    Few software projects are completed on time, on budget, and to their original specifications. Focusing on what practitioners need to know about risk in the pursuit of delivering software projects, Applied Software Risk Management: A Guide for Software Project Managers covers key components of the risk management process and the software development process, as well as best practices for software risk identification, risk planning, and risk analysis. Written in a clear and concise manner, this resource presents concepts and practical insight into managing risk. It first covers risk-driven project management, risk management processes, risk attributes, risk identification, and risk analysis. The book continues by examining responses to risk, the tracking and modeling of risks, intelligence gathering, and integrated risk management. It concludes with details on drafting and implementing procedures. A diary of a risk manager provides insight in implementing risk management processes.Bringing together concepts ...

  15. Programming language abstractions for extensible software components

    OpenAIRE

    Zenger, Matthias; Odersky, Martin

    2005-01-01

    With the growing demand for software systems that can cope with an increasing range of information processing tasks, the reuse of code from existing systems is essential to reduce the production costs of systems as well as the time to manufacture new software applications. For this reason, component-based software development techniques gain increasing attention in industry and research. Component technology is driven by the promise of building software by composing off-the-shelf components p...

  16. Programming language abstractions for extensible software components

    OpenAIRE

    Zenger, Matthias

    2004-01-01

    With the growing demand for software systems that can cope with an increasing range of information processing tasks, the reuse of code from existing systems is essential to reduce the production costs of systems as well as the time to manufacture new software applications. For this reason, component-based software development techniques gain increasing attention in industry and research. Component technology is driven by the promise of building software by composing off-the-shelf components p...

  17. From Agile Software Development to Mercury Business

    OpenAIRE

    Järvinen, Janne; Huomo, Tua; Mikkonen, Tommi; Tyrväinen, Pasi

    2014-01-01

    The rapid downfall of the Nokia software ecosystem has radically altered the landscape of software industry in Finland in recent years. There has been a shift from largely corporate driven way of working, which is often dominant in large companies, to more agile practices, and in general software organizations are seeking new, leaner ways of composing, delivering, and using software also inside already established companies. To accelerate this transformation in large scale, a collaborative re...

  18. Software engineering

    CERN Document Server

    Sommerville, Ian

    2016-01-01

    For courses in computer science and software engineering The Fundamental Practice of Software Engineering Software Engineering introduces readers to the overwhelmingly important subject of software programming and development. In the past few years, computer systems have come to dominate not just our technological growth, but the foundations of our world's major industries. This text seeks to lay out the fundamental concepts of this huge and continually growing subject area in a clear and comprehensive manner. The Tenth Edition contains new information that highlights various technological updates of recent years, providing readers with highly relevant and current information. Sommerville's experience in system dependability and systems engineering guides the text through a traditional plan-based approach that incorporates some novel agile methods. The text strives to teach the innovators of tomorrow how to create software that will make our world a better, safer, and more advanced place to live.

  19. Software process improvement in the NASA software engineering laboratory

    Science.gov (United States)

    Mcgarry, Frank; Pajerski, Rose; Page, Gerald; Waligora, Sharon; Basili, Victor; Zelkowitz, Marvin

    1994-01-01

    The Software Engineering Laboratory (SEL) was established in 1976 for the purpose of studying and measuring software processes with the intent of identifying improvements that could be applied to the production of ground support software within the Flight Dynamics Division (FDD) at the National Aeronautics and Space Administration (NASA)/Goddard Space Flight Center (GSFC). The SEL has three member organizations: NASA/GSFC, the University of Maryland, and Computer Sciences Corporation (CSC). The concept of process improvement within the SEL focuses on the continual understanding of both process and product as well as goal-driven experimentation and analysis of process change within a production environment.

  20. Model-integrating software components engineering flexible software systems

    CERN Document Server

    Derakhshanmanesh, Mahdi

    2015-01-01

    In his study, Mahdi Derakhshanmanesh builds on the state of the art in modeling by proposing to integrate models into running software on the component-level without translating them to code. Such so-called model-integrating software exploits all advantages of models: models implicitly support a good separation of concerns, they are self-documenting and thus improve understandability and maintainability and in contrast to model-driven approaches there is no synchronization problem anymore between the models and the code generated from them. Using model-integrating components, software will be

  1. A coordination model for global software development teams

    OpenAIRE

    Deshpande, Sadhana

    2012-01-01

    peer-reviewed Over the last two decades of globalisation, the software industry has witnessed the emergence of Global Software Development (GSD). Various business motives have driven software companies to outsource software development projects to software companies based in low cost economies. Given the highly competitive environment in which software companies operate, the client and the vendor have to equip themselves to operate successfully across national and interna...

  2. A Visual Basic simulation software tool for performance analysis of a membrane-based advanced water treatment plant.

    Science.gov (United States)

    Pal, P; Kumar, R; Srivastava, N; Chowdhury, J

    2014-02-01

    A Visual Basic simulation software (WATTPPA) has been developed to analyse the performance of an advanced wastewater treatment plant. This user-friendly and menu-driven software is based on the dynamic mathematical model for an industrial wastewater treatment scheme that integrates chemical, biological and membrane-based unit operations. The software-predicted results corroborate very well with the experimental findings as indicated in the overall correlation coefficient of the order of 0.99. The software permits pre-analysis and manipulation of input data, helps in optimization and exhibits performance of an integrated plant visually on a graphical platform. It allows quick performance analysis of the whole system as well as the individual units. The software first of its kind in its domain and in the well-known Microsoft Excel environment is likely to be very useful in successful design, optimization and operation of an advanced hybrid treatment plant for hazardous wastewater.

  3. Software requirements

    CERN Document Server

    Wiegers, Karl E

    2003-01-01

    Without formal, verifiable software requirements-and an effective system for managing them-the programs that developers think they've agreed to build often will not be the same products their customers are expecting. In SOFTWARE REQUIREMENTS, Second Edition, requirements engineering authority Karl Wiegers amplifies the best practices presented in his original award-winning text?now a mainstay for anyone participating in the software development process. In this book, you'll discover effective techniques for managing the requirements engineering process all the way through the development cy

  4. Software testing

    Science.gov (United States)

    Price-Whelan, Adrian M.

    2016-01-01

    Now more than ever, scientific results are dependent on sophisticated software and analysis. Why should we trust code written by others? How do you ensure your own code produces sensible results? How do you make sure it continues to do so as you update, modify, and add functionality? Software testing is an integral part of code validation and writing tests should be a requirement for any software project. I will talk about Python-based tools that make managing and running tests much easier and explore some statistics for projects hosted on GitHub that contain tests.

  5. Software Reviews.

    Science.gov (United States)

    Dwyer, Donna; And Others

    1989-01-01

    Reviewed are seven software packages for Apple and IBM computers. Included are: "Toxicology"; "Science Corner: Space Probe"; "Alcohol and Pregnancy"; "Science Tool Kit Plus"; Computer Investigations: Plant Growth"; "Climatrolls"; and "Animal Watch: Whales." (CW)

  6. Software Reviews.

    Science.gov (United States)

    Davis, Shelly J., Ed.; Knaupp, Jon, Ed.

    1984-01-01

    Reviewed is computer software on: (1) classification of living things, a tutorial program for grades 5-10; and (2) polynomial practice using tiles, a drill-and-practice program for algebra students. (MNS)

  7. Software Reviews.

    Science.gov (United States)

    Wulfson, Stephen, Ed.

    1987-01-01

    Reviews seven computer software programs that can be used in science education programs. Describes courseware which deals with muscles and bones, terminology, classifying animals without backbones, molecular structures, drugs, genetics, and shaping the earth's surface. (TW)

  8. Software Innovation

    DEFF Research Database (Denmark)

    Rose, Jeremy

      Innovation is the forgotten key to modern systems development - the element that defines the enterprising engineer, the thriving software firm and the cutting edge software application.  Traditional forms of technical education pay little attention to creativity - often encouraging overly...... rationalistic ways of thinking which stifle the ability to innovate. Professional software developers are often drowned in commercial drudgery and overwhelmed by work pressure and deadlines. The topic that will both ensure success in the market and revitalize their work lives is never addressed. This book sets...... out the new field of software innovation. It organizes the existing scientific research into eight simple heuristics - guiding principles for organizing a system developer's work-life so that it focuses on innovation....

  9. Model driven product line engineering : core asset and process implications

    OpenAIRE

    Azanza Sesé, Maider

    2012-01-01

    Reuse is at the heart of major improvements in productivity and quality in Software Engineering. Both Model Driven Engineering (MDE) and Software Product Line Engineering (SPLE) are software development paradigms that promote reuse. Specifically, they promote systematic reuse and a departure from craftsmanship towards an industrialization of the software development process. MDE and SPLE have established their benefits separately. Their combination, here called Model Driven Product Line Engin...

  10. Distributed simulation a model driven engineering approach

    CERN Document Server

    Topçu, Okan; Oğuztüzün, Halit; Yilmaz, Levent

    2016-01-01

    Backed by substantive case studies, the novel approach to software engineering for distributed simulation outlined in this text demonstrates the potent synergies between model-driven techniques, simulation, intelligent agents, and computer systems development.

  11. 涉众驱动的服务软件系统需求语义协作式获取方法%Stakeholders-driven Requirements Semantics Acquisition for Networked Software

    Institute of Scientific and Technical Information of China (English)

    文斌; 何克清; 梁鹏; 曹步清

    2012-01-01

    基于需求语义的服务工程旨在将无序需求变为有序规约,并最终关联到服务生产,以期提供按需服务能力,本文关注面向服务的软件需求语义的分布式协作获取方法的研究,针对基于服务资源聚合而成的网络化软件使用涉众的全球广域分布的特征,以面向服务软件的需求语义模型为核心,采用语义WIKIS引擎为协作平台基础,充分发挥涉众群体智能参与实例化需求要素标注,同时提供需求验证和推理功能以及与连接开放数据的映射关系,可即时生成阶段性需求语义制品.需求语义由网上涉众分布式协作获取,即用户需求(知识)表示,一致的、大众认可的需求语义为后续按需服务聚合与资源定制提供了自动化按需服务能力.理论与实证研究也证明了所提方法的有效性和可操作性,完成与现有的以需求主导、面向领域的应用系统的全面整合,支持实现需求语义为核心的按需服务工程应用.%Semantics-enabled requirements engineering for services aims to transfer the un-ordered needs into the ordered specification including requirements-semantics eliciting, requirements semantics-driven services aggregation and services customization in order to supply on-demand capability. The paper mainly focuses on distributing collarative acquisition of requirements semantics for services. Faced to the feature that stakeholds are worldwide distribution, innovative mechanism for requirements acquisition is put forward. Requirements-semantics model for service-oriented software is the core of the method which it adopts the semantic wikis engine as the base and fully applys group intelligence marked contribution and requirements verification, reasoning functions to generate gradual semantics artifact. Theoretical and empirical studying has proven the validity of the proposed method and practicability for on-demand services engineering.

  12. Software reengineering

    Science.gov (United States)

    Fridge, Ernest M., III

    1991-01-01

    Today's software systems generally use obsolete technology, are not integrated properly with other software systems, and are difficult and costly to maintain. The discipline of reverse engineering is becoming prominent as organizations try to move their systems up to more modern and maintainable technology in a cost effective manner. JSC created a significant set of tools to develop and maintain FORTRAN and C code during development of the Space Shuttle. This tool set forms the basis for an integrated environment to re-engineer existing code into modern software engineering structures which are then easier and less costly to maintain and which allow a fairly straightforward translation into other target languages. The environment will support these structures and practices even in areas where the language definition and compilers do not enforce good software engineering. The knowledge and data captured using the reverse engineering tools is passed to standard forward engineering tools to redesign or perform major upgrades to software systems in a much more cost effective manner than using older technologies. A beta vision of the environment was released in Mar. 1991. The commercial potential for such re-engineering tools is very great. CASE TRENDS magazine reported it to be the primary concern of over four hundred of the top MIS executives.

  13. MIAWARE Software

    DEFF Research Database (Denmark)

    Wilkowski, Bartlomiej; Pereira, Oscar N. M.; Dias, Paulo;

    2008-01-01

    pathologies on images and report their characteristics. The reporting process is normalized - radiologists cannot describe pathological changes with their own words, but can only use some terms from a specific vocabulary set provided by the software. Consequently, a normalized radiological report......This article presents MIAWARE, a software for Medical Image Analysis With Automated Reporting Engine, which was designed and developed for doctor/radiologist assistance. It allows to analyze an image stack from computed axial tomography scan of lungs (thorax) and, at the same time, to mark all......, a deductive report search was obtained, which may be helpful for doctors while diagnosing patients’ cases. Finally, the MIAWARE software can be considered also as a teaching tool for future radiologists and physicians....

  14. Software engineering

    CERN Document Server

    Thorin, Marc

    1985-01-01

    Software Engineering describes the conceptual bases as well as the main methods and rules on computer programming. This book presents software engineering as a coherent and logically built synthesis and makes it possible to properly carry out an application of small or medium difficulty that can later be developed and adapted to more complex cases. This text is comprised of six chapters and begins by introducing the reader to the fundamental notions of entities, actions, and programming. The next two chapters elaborate on the concepts of information and consistency domains and show that a proc

  15. A Multi-mission Event-Driven Component-Based System for Support of Flight Software Development, ATLO, and Operations first used by the Mars Science Laboratory (MSL) Project

    Science.gov (United States)

    Dehghani, Navid; Tankenson, Michael

    2006-01-01

    This paper details an architectural description of the Mission Data Processing and Control System (MPCS), an event-driven, multi-mission ground data processing components providing uplink, downlink, and data management capabilities which will support the Mars Science Laboratory (MSL) project as its first target mission. MPCS is developed based on a set of small reusable components, implemented in Java, each designed with a specific function and well-defined interfaces. An industry standard messaging bus is used to transfer information among system components. Components generate standard messages which are used to capture system information, as well as triggers to support the event-driven architecture of the system. Event-driven systems are highly desirable for processing high-rate telemetry (science and engineering) data, and for supporting automation for many mission operations processes.

  16. Software Systems

    Institute of Scientific and Technical Information of China (English)

    崔涛; 周淼

    1996-01-01

    The information used with computers is known as software and includesprograms and data. Programs are sets of instructions telling the computerwhat operations have to be carried out and in what order they should be done. Specialised programs which enable the computer to be used for particularpurposes are called applications programs. A collection of these programs kept

  17. Software Reviews.

    Science.gov (United States)

    Science and Children, 1990

    1990-01-01

    Reviewed are seven computer software packages for IBM and/or Apple Computers. Included are "Windows on Science: Volume 1--Physical Science"; "Science Probe--Physical Science"; "Wildlife Adventures--Grizzly Bears"; "Science Skills--Development Programs"; "The Clean Machine"; "Rock Doctor"; and "Geology Search." Cost, quality, hardware, and…

  18. Software Review.

    Science.gov (United States)

    McGrath, Diane, Ed.

    1989-01-01

    Reviewed is a computer software package entitled "Audubon Wildlife Adventures: Grizzly Bears" for Apple II and IBM microcomputers. Included are availability, hardware requirements, cost, and a description of the program. The murder-mystery flavor of the program is stressed in this program that focuses on illegal hunting and game management. (CW)

  19. Software Reviews.

    Science.gov (United States)

    Mathematics and Computer Education, 1987

    1987-01-01

    Presented are reviews of several microcomputer software programs. Included are reviews of: (1) Microstat (Zenith); (2) MathCAD (MathSoft); (3) Discrete Mathematics (True Basic); (4) CALCULUS (True Basic); (5) Linear-Kit (John Wiley); and (6) Geometry Sensei (Broderbund). (RH)

  20. Method for critical software event execution reliability in high integrity software

    Energy Technology Data Exchange (ETDEWEB)

    Kidd, M.E. [Sandia National Labs., Albuquerque, NM (United States)

    1997-11-01

    This report contains viewgraphs on a method called SEER, which provides a high level of confidence that critical software driven event execution sequences faithfully exceute in the face of transient computer architecture failures in both normal and abnormal operating environments.

  1. Consistent model driven architecture

    Science.gov (United States)

    Niepostyn, Stanisław J.

    2015-09-01

    The goal of the MDA is to produce software systems from abstract models in a way where human interaction is restricted to a minimum. These abstract models are based on the UML language. However, the semantics of UML models is defined in a natural language. Subsequently the verification of consistency of these diagrams is needed in order to identify errors in requirements at the early stage of the development process. The verification of consistency is difficult due to a semi-formal nature of UML diagrams. We propose automatic verification of consistency of the series of UML diagrams originating from abstract models implemented with our consistency rules. This Consistent Model Driven Architecture approach enables us to generate automatically complete workflow applications from consistent and complete models developed from abstract models (e.g. Business Context Diagram). Therefore, our method can be used to check practicability (feasibility) of software architecture models.

  2. Unit testing, model validation, and biological simulation [version 1; referees: 2 approved, 1 approved with reservations

    Directory of Open Access Journals (Sweden)

    Gopal P. Sarma

    2016-08-01

    Full Text Available The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in the biological sciences, it is important to examine how these practices can accelerate biological software development and improve research quality. In this article, we give a focused case study of our experience with the practices of unit testing and test-driven development in OpenWorm, an open-science project aimed at modeling Caenorhabditis elegans. We identify and discuss the challenges of incorporating test-driven development into a heterogeneous, data-driven project, as well as the role of model validation tests, a category of tests unique to software which expresses scientific models.

  3. Process-driven architecture: design techniques and methods

    NARCIS (Netherlands)

    Jaskiewicz, T.

    2007-01-01

    This paper explores the notion of process-driven architecture and, as a consequence, application of complex systems in the newly defined area of digital process-driven architectural design in order to formulate a suitable design method. Protospace software environment and SwarmCAD software applicati

  4. Software preservation

    Directory of Open Access Journals (Sweden)

    Tadej Vodopivec

    2011-01-01

    Full Text Available Comtrade Ltd. covers a wide range of activities related to information and communication technologies; its deliverables include web applications, locally installed programs,system software, drivers, embedded software (used e.g. in medical devices, auto parts,communication switchboards. Also the extensive knowledge and practical experience about digital long-term preservation technologies have been acquired. This wide spectrum of activities puts us in the position to discuss the often overlooked aspect of the digital preservation - preservation of software programs. There are many resources dedicated to digital preservation of digital data, documents and multimedia records,but not so many about how to preserve the functionalities and features of computer programs. Exactly these functionalities - dynamic response to inputs - render the computer programs rich compared to documents or linear multimedia. The article opens the questions on the beginning of the way to the permanent digital preservation. The purpose is to find a way in the right direction, where all relevant aspects will be covered in proper balance. The following questions are asked: why at all to preserve computer programs permanently, who should do this and for whom, when we should think about permanent program preservation, what should be persevered (such as source code, screenshots, documentation, and social context of the program - e.g. media response to it ..., where and how? To illustrate the theoretic concepts given the idea of virtual national museum of electronic banking is also presented.

  5. Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems.

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    2016-01-01

    Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment, and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1) enumeration of the repertoire of model phenotypes, (2) prediction of values for the parameters for any model phenotype, and (3) analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3, and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between three stable states by transient stimulation through one of two input channels: a positive channel that increases the count

  6. Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems

    Science.gov (United States)

    Lomnitz, Jason G.; Savageau, Michael A.

    2016-01-01

    Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment, and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1) enumeration of the repertoire of model phenotypes, (2) prediction of values for the parameters for any model phenotype, and (3) analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3, and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between three stable states by transient stimulation through one of two input channels: a positive channel that increases the count

  7. Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems.

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    2016-01-01

    Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment, and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1) enumeration of the repertoire of model phenotypes, (2) prediction of values for the parameters for any model phenotype, and (3) analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3, and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between three stable states by transient stimulation through one of two input channels: a positive channel that increases the count

  8. Software Engineering to Professionalize Software Development

    Directory of Open Access Journals (Sweden)

    Juan Miguel Alonso

    2011-12-01

    Full Text Available The role, increasingly important, that plays the software in the systems with widespread effects presents new challenges for the formation of Software Engineers. Not only because social dependence software is increasing, but also because the character of software development is also changing and with it the demands for software developers certified. In this paper are propose some challenges and aspirations that guide the learning processes Software Engineering and help to identify the need to train professionals in software development.

  9. EDS operator and control software

    International Nuclear Information System (INIS)

    The Enrichment Diagnostic System (EDS) was developed at Lawrence Livermore National Laboratory (LLNL) to acquire, display and analyze large quantities of transient data for a real-time Advanced Vapor Laser Isotope Separation (AVLIS) experiment. Major topics discussed in this paper are the EDS operator interface (SHELL) program, the data acquisition and analysis scheduling software, and the graphics software. The workstation concept used in EDS, the software used to configure a user's workstation, and the ownership and management of a diagnostic are described. An EDS diagnostic is a combination of hardware and software designed to study specific aspects of the process. Overall system performance is discussed from the standpoint of scheduling techniques, evaluation tools, optimization techniques, and program-to-program communication methods. EDS is based on a data driven design which keeps the need to modify software to a minimum. This design requires a fast and reliable data base management system. A third party data base management product, Berkeley Software System Database, written explicitly for HP1000's, is used for all EDS data bases. All graphics is done with an in-house graphics product, Device Independent Graphics Library (DIGLIB). Examples of devices supported by DIGLIB are: Versatec printer/plotters, Raster Technologies Graphic Display Controllers, and HP terminals (HP264x and HP262x). The benefits derived by using HP hardware and software as well as obstacles imposed by the HP environment are presented in relation to EDS development and implementation

  10. Controlling software acquisition: is supplier's software process capability determination enough?

    OpenAIRE

    Fabbrini, Fabrizio; Fusani, Mario; Lami, Giuseppe

    2008-01-01

    Innovation in automotive is principally due to the market-driven demand of electronic devices on the vehicles. Car manufacturers usually acquire software-intensive components from different suppliers, and they need to carefully manage such acquisitions to avoid losses in terms of time and quality of the final product. In the last decade, in Europe, many car manufacturers adopted Automotive SPICE-based mechanisms to face such a situation. In this paper we discuss the results achieved by adopti...

  11. Space Software

    Science.gov (United States)

    1990-01-01

    Xontech, Inc.'s software package, XonVu, simulates the missions of Voyager 1 at Jupiter and Saturn, Voyager 2 at Jupiter, Saturn, Uranus and Neptune, and Giotto in close encounter with Comet Halley. With the program, the user can generate scenes of the planets, moons, stars or Halley's nucleus and tail as seen by Giotto, all graphically reproduced with high accuracy in wireframe representation. Program can be used on a wide range of computers, including PCs. User friendly and interactive, with many options, XonVu can be used by a space novice or a professional astronomer. With a companion user's manual, it sells for $79.

  12. Design Driven Testing Test Smarter, Not Harder

    CERN Document Server

    Stephens, M

    2010-01-01

    The groundbreaking book Design Driven Testing brings sanity back to the software development process by flipping around the concept of Test Driven Development (TDD) - restoring the concept of using testing to verify a design instead of pretending that unit tests are a replacement for design. Anyone who feels that TDD is "Too Damn Difficult" will appreciate this book. Design Driven Testing shows that, by combining a forward-thinking development process with cutting-edge automation, testing can be a finely targeted, business-driven, rewarding effort. In other words, you'll learn how to test

  13. Global Software Engineering: A Software Process Approach

    Science.gov (United States)

    Richardson, Ita; Casey, Valentine; Burton, John; McCaffery, Fergal

    Our research has shown that many companies are struggling with the successful implementation of global software engineering, due to temporal, cultural and geographical distance, which causes a range of factors to come into play. For example, cultural, project managementproject management and communication difficulties continually cause problems for software engineers and project managers. While the implementation of efficient software processes can be used to improve the quality of the software product, published software process models do not cater explicitly for the recent growth in global software engineering. Our thesis is that global software engineering factors should be included in software process models to ensure their continued usefulness in global organisations. Based on extensive global software engineering research, we have developed a software process, Global Teaming, which includes specific practices and sub-practices. The purpose is to ensure that requirements for successful global software engineering are stipulated so that organisations can ensure successful implementation of global software engineering.

  14. Building Test Cases through Model Driven Engineering

    Science.gov (United States)

    Sousa, Helaine; Lopes, Denivaldo; Abdelouahab, Zair; Hammoudi, Slimane; Claro, Daniela Barreiro

    Recently, Model Driven Engineering (MDE) has been proposed to face the complexity in the development, maintenance and evolution of large and distributed software systems. Model Driven Architecture (MDA) is an example of MDE. In this context, model transformations enable a large reuse of software systems through the transformation of a Platform Independent Model into a Platform Specific Model. Although source code can be generated from models, defects can be injected during the modeling or transformation process. In order to delivery software systems without defects that cause errors and fails, the source code must be submitted to test. In this paper, we present an approach that takes care of test in the whole software life cycle, i.e. it starts in the modeling level and finishes in the test of source code of software systems. We provide an example to illustrate our approach.

  15. Software Engineering to Professionalize Software Development

    OpenAIRE

    Juan Miguel Alonso; Fernando García

    2011-01-01

    The role, increasingly important, that plays the software in the systems with widespread effects presents new challenges for the formation of Software Engineers. Not only because social dependence software is increasing, but also because the character of software development is also changing and with it the demands for software developers certified. In this paper are propose some challenges and aspirations that guide the learning processes Software Engineering and help to identify the need to...

  16. Improving Agile Software Practice

    DEFF Research Database (Denmark)

    Tjørnehøj, Gitte

    2006-01-01

    Software process improvement in small and agile organizations is often problematic, but achieving good SPI-assessments can still be necessary to stay in the marked or to meet demands of multinational owners. The traditional norm driven, centralized and control centered improvement approaches has...... agile and innovative, while striving for certification according to traditional rational SPI norms? This paper reports from a action research project in a small agile Danish firm (Techsoft) conducting a improvement initiative. The firm had just been met by the demand for a CMMI level-3 certification...... from their new multinational owners. In the project we experimented to reach a less centralized and control centered SPI approach trying to meet the agile culture of the firm both within diagnosing, improvement planning, process design and evaluation eventhough the goal was applying to the norm. After...

  17. 面向适航认证的模型驱动机载软件构件的安全性验证%Model-driven Safety Dependence Verification for Component-based Airborne Software Supporting Airworthiness Certification

    Institute of Scientific and Technical Information of China (English)

    徐丙凤; 黄志球; 胡军; 于笑丰

    2012-01-01

    Current research of airborne software focuses on providing airworthiness certification evidence in software development process. As modern complex airborne software architecture is component-based and distributed, this paper considers the issue of checking the safety dependence relationship of software components against objectives that the airworthiness certification standard stipulates, which is one of the key problems of airborne software development in the design phase. Firstly, the static structure of a system is specified by a systems modeling language (SysML) block definition diagram with the description of safety properties. Secondly, the SysML block definition diagram is transformed to a block dependence graph for precise formal description. Thirdly, a method for checking the consistency between the safety dependence relationship in the static system structure and objectives of the airworthiness certification standard is proposed. Finally, an example of an aircraft navigation system is provided to illustrate how to use the method in the airborne software development process. The integrated safety level of a system is promoted by applying this method, and it can be used to provide airworthiness certification evidence.%在软件开发的过程中为适航认证提供证据,已成为机载软件开发的研究热点.现代复杂机载软件多为构件化分布式架构,如何有效验证构件之间安全性依赖关系与适航认证标准当中规定目标的一致性,是机载软件设计阶段的一个重要问题.首先,使用系统建模语言(SysML)块图建立带有安全性特征的系统静态结构模型,将其转换为块依赖图以便进行精确的形式化描述.在此基础上给出形式验证方法,检验系统静态结构模型中的安全性依赖关系与适航认证标准中所规定目标之间是否一致.最后,通过一个飞机导航系统的例子说明如何将该方法应用于机载软件开发的过

  18. Biological programming

    OpenAIRE

    Ramsden, Jeremy J.; Bándi, Gergely

    2010-01-01

    Biology offers a tremendous set of concepts that are potentially very powerfully usable for the software engineer, but they have been barely exploited hitherto. In this position paper we propose a fresh attempt to create the building blocks of a programming technology that could be as successful as life. A key guiding principle is to develop and make use of unambiguous definitions of the essential features of life.

  19. Pivotal Role of Computers and Software in Mass Spectrometry - SEQUEST and 20 Years of Tandem MS Database Searching

    Science.gov (United States)

    Yates, John R.

    2015-11-01

    Advances in computer technology and software have driven developments in mass spectrometry over the last 50 years. Computers and software have been impactful in three areas: the automation of difficult calculations to aid interpretation, the collection of data and control of instruments, and data interpretation. As the power of computers has grown, so too has the utility and impact on mass spectrometers and their capabilities. This has been particularly evident in the use of tandem mass spectrometry data to search protein and nucleotide sequence databases to identify peptide and protein sequences. This capability has driven the development of many new approaches to study biological systems, including the use of "bottom-up shotgun proteomics" to directly analyze protein mixtures.

  20. 基于数据驱动的装备嵌入式软件自动化测试的研究与应用%Research and Application of Automatic Test Based on Data-Driven Method for Equipment Software

    Institute of Scientific and Technical Information of China (English)

    张玉晓; 孙伟; 张军

    2015-01-01

    随着新装备软件的发展,软件测试需要多轮迭代,带来测试工作量巨大、周期变长、费用超支和软件延迟交付等一系列问题;而人工测试受时间、费用等条件的限制,特别是受到软件频繁升级的影响,需要不断进行回归测试,效率很低。本文给出了一种基于数据驱动的装备软件自动化测试的解决方案,通过开发自动测试环境和测试脚本,自动进行激励获取、激励输入、测试结果获取判定和数据记录,后续回归测试仅需要修改少量测试脚本,能快速进行回归测试,大大减少测试工作量,是针对软件频繁升级的有效解决途径。将该自动化测试方法应用于具体的项目实践中,取得了很好的效果。%With the development of equipment software,software testing need multiple iterations.It results in a series of problems,such as huge testing workload,cycle longer,cost overruns,late delivery of software,etc.Manual test has lower efficiency due to the restrictions of test time and cost.Especially due to the impact of frequent software upgrading,it requires multiple cycles of regression test with low efficiency.This article provides one automatic test solution based on data-driven method for equipment software.By developing automatic test environment and test scripts,subsequent regression testing only need to modify a few test scripts to quickly regression testing,greatly reducing the testing effort.It is an effective way to solve frequent software upgrading.The automatic test method is a good way to apply specific programs.

  1. Software quality assurance and software safety in the Biomed Control System

    International Nuclear Information System (INIS)

    The Biomed Control System is a hardware/software system used for the delivery, measurement and monitoring of heavy-ion beams in the patient treatment and biology experiment rooms in the Bevalac at the Lawrence Berkeley Laboratory (LBL). This paper describes some aspects of this system including historical background philosophy, configuration management, hardware features that facilitate software testing, software testing procedures, the release of new software quality assurance, safety and operator monitoring. 3 refs

  2. SOFTWARE METRICS VALIDATION METHODOLOGIES IN SOFTWARE ENGINEERING

    Directory of Open Access Journals (Sweden)

    K.P. Srinivasan

    2014-12-01

    Full Text Available In the software measurement validations, assessing the validation of software metrics in software engineering is a very difficult task due to lack of theoretical methodology and empirical methodology [41, 44, 45]. During recent years, there have been a number of researchers addressing the issue of validating software metrics. At present, software metrics are validated theoretically using properties of measures. Further, software measurement plays an important role in understanding and controlling software development practices and products. The major requirement in software measurement is that the measures must represent accurately those attributes they purport to quantify and validation is critical to the success of software measurement. Normally, validation is a collection of analysis and testing activities across the full life cycle and complements the efforts of other quality engineering functions and validation is a critical task in any engineering project. Further, validation objective is to discover defects in a system and assess whether or not the system is useful and usable in operational situation. In the case of software engineering, validation is one of the software engineering disciplines that help build quality into software. The major objective of software validation process is to determine that the software performs its intended functions correctly and provides information about its quality and reliability. This paper discusses the validation methodology, techniques and different properties of measures that are used for software metrics validation. In most cases, theoretical and empirical validations are conducted for software metrics validations in software engineering [1-50].

  3. The role of software engineering in future automotive systems development

    OpenAIRE

    Clarke, Siobhán; Fitzgerald, Brian; Nixon, Paddy; Pohl, Klaus; Ryan, Kevin; Sinclair, David; Thiel, Steffen

    2008-01-01

    peer-reviewed The amount and complexity of software in automotive systems is constantly increasing. Today’s luxury cars include numerous electronic control units. A large part of the functionality of these units is driven by software. In the future even more software-intensive automotive systems are expected as automotive manufacturers and suppliers tend to integrate and combine applications on more powerful platforms. The increasing amount and complexity of software in these plat...

  4. Software for people fundamentals, trends and best practices

    CERN Document Server

    Maedche, Alexander; Neer, Ludwig

    2012-01-01

    The highly competitive and globalized software market is creating pressure on software companies. Given the current boundary conditions, it is critical to continuously increase time-to-market and reduce development costs. In parallel, driven by private life experiences with mobile computing devices, the World Wide Web and software-based services, people, general expectations with regards to software are growing. They expect software that is simple and joyful to use. In the light of the changes that have taken place in recent years, software companies need to fundamentally reconsider the way th

  5. Roundtable:Research Opportunities and Challenges for Emerging Software Systems

    Institute of Scientific and Technical Information of China (English)

    张翔宇; 张冬梅; Yves Le Traon; 王青; 张路

    2015-01-01

    For this special section on software systems, several research leaders in software systems, as guest editors for this special section, discuss important issues that will shape this field’s future directions. The essays included in this roundtable article cover research opportunities and challenges for emerging software systems such as data processing programs (Xiangyu Zhang) and online services (Dongmei Zhang), with new directions of technologies such as unifications in software testing (Yves Le Traon), data-driven and evidence-based software engineering (Qing Wang), and dynamic analysis of multiple traces (Lu Zhang). — Tao Xie, Leading Editor of Special Section on Software System.

  6. Educational Software Evaluation Form for Teachers

    Science.gov (United States)

    Kara, Yilmaz

    2007-01-01

    The purpose of the study was to develop an educational software evaluation form to provide an evaluation and selection instrument of educational software that met the requirements of some balance between mechanics, content and pedagogy that is user friendly. The subjects for the study comprised a group of 32 biology teachers working in secondary…

  7. The software life cycle

    CERN Document Server

    Ince, Darrel

    1990-01-01

    The Software Life Cycle deals with the software lifecycle, that is, what exactly happens when software is developed. Topics covered include aspects of software engineering, structured techniques of software development, and software project management. The use of mathematics to design and develop computer systems is also discussed. This book is comprised of 20 chapters divided into four sections and begins with an overview of software engineering and software development, paying particular attention to the birth of software engineering and the introduction of formal methods of software develop

  8. Evolvable Neural Software System

    Science.gov (United States)

    Curtis, Steven A.

    2009-01-01

    The Evolvable Neural Software System (ENSS) is composed of sets of Neural Basis Functions (NBFs), which can be totally autonomously created and removed according to the changing needs and requirements of the software system. The resulting structure is both hierarchical and self-similar in that a given set of NBFs may have a ruler NBF, which in turn communicates with other sets of NBFs. These sets of NBFs may function as nodes to a ruler node, which are also NBF constructs. In this manner, the synthetic neural system can exhibit the complexity, three-dimensional connectivity, and adaptability of biological neural systems. An added advantage of ENSS over a natural neural system is its ability to modify its core genetic code in response to environmental changes as reflected in needs and requirements. The neural system is fully adaptive and evolvable and is trainable before release. It continues to rewire itself while on the job. The NBF is a unique, bilevel intelligence neural system composed of a higher-level heuristic neural system (HNS) and a lower-level, autonomic neural system (ANS). Taken together, the HNS and the ANS give each NBF the complete capabilities of a biological neural system to match sensory inputs to actions. Another feature of the NBF is the Evolvable Neural Interface (ENI), which links the HNS and ANS. The ENI solves the interface problem between these two systems by actively adapting and evolving from a primitive initial state (a Neural Thread) to a complicated, operational ENI and successfully adapting to a training sequence of sensory input. This simulates the adaptation of a biological neural system in a developmental phase. Within the greater multi-NBF and multi-node ENSS, self-similar ENI s provide the basis for inter-NBF and inter-node connectivity.

  9. Software Model Of Software-Development Process

    Science.gov (United States)

    Lin, Chi Y.; Synott, Debra J.; Levary, Reuven R.

    1990-01-01

    Collection of computer programs constitutes software tool for simulation of medium- to large-scale software-development projects. Necessary to include easily identifiable and more-readily quantifiable characteristics like costs, times, and numbers of errors. Mathematical model incorporating these and other factors of dynamics of software-development process implemented in the Software Life Cycle Simulator (SLICS) computer program. Simulates dynamics of software-development process. In combination with input and output expert software systems and knowledge-based management software system, develops information for use in managing large software-development project. Intended to aid managers in planning, managing, and controlling software-development processes by reducing uncertainties in budgets, required personnel, and schedules.

  10. Semantic Web and Model-Driven Engineering

    CERN Document Server

    Parreiras, Fernando S

    2012-01-01

    The next enterprise computing era will rely on the synergy between both technologies: semantic web and model-driven software development (MDSD). The semantic web organizes system knowledge in conceptual domains according to its meaning. It addresses various enterprise computing needs by identifying, abstracting and rationalizing commonalities, and checking for inconsistencies across system specifications. On the other side, model-driven software development is closing the gap among business requirements, designs and executables by using domain-specific languages with custom-built syntax and se

  11. Evolvability of Software Systems

    OpenAIRE

    Nasir, Muhammad-Iftikhar; Iqbal, Rizwan

    2008-01-01

    Software evolvability, meeting the future requirements of the customer is one of the emerging challenges which software industry is facing nowadays. Software evolvability is the ability of software system to accommodate future requirements. Studies have shown that software evolvability has large economic benefits but at the same time it’s difficult to assess. Over the time many methods have been derived to assess the software evolvability. Software evolvability depends upon various characteri...

  12. Software fault tolerance

    OpenAIRE

    Kazinov, Tofik Hasanaga; Mostafa, Jalilian Shahrukh

    2009-01-01

    Because of our present inability to produce errorfree software, software fault tolerance is and will contiune to be an important consideration in software system. The root cause of software design errors in the complexity of the systems. This paper surveys various software fault tolerance techniquest and methodologies. They are two gpoups: Single version and Multi version software fault tolerance techniques. It is expected that software fault tolerance research will benefit from this research...

  13. Assessment and Comparison of Fuzzy Based Test Suite Prioritization Method for GUI Based Software

    OpenAIRE

    Neha Chaudhary; O.P. Sangwan

    2016-01-01

    The testing of event driven software has significant role to improve overall quality of software. Due to event driven nature of GUI based software many test cases are generated and it is difficult to identify test cases whose fault revealing capability is high. To identify those test cases test suite prioritization is done. Various test suite prioritization methods exists for GUI based software in literature. Prioritization methods improve the rate of fault detection. In our previous work we ...

  14. Economics of Software Engineering

    OpenAIRE

    Mohamed Mohamed Al Hady

    2007-01-01

    An article about the economic aspects of software engineering, it discusses many important issues in this field, like; knowledge economics, history of software engineering, prosperities of software industry, and economics of software, then it discusses the methods followed to improvement of software economics

  15. Software attribute visualization for high integrity software

    Energy Technology Data Exchange (ETDEWEB)

    Pollock, G.M.

    1998-03-01

    This report documents a prototype tool developed to investigate the use of visualization and virtual reality technologies for improving software surety confidence. The tool is utilized within the execution phase of the software life cycle. It provides a capability to monitor an executing program against prespecified requirements constraints provided in a program written in the requirements specification language SAGE. The resulting Software Attribute Visual Analysis Tool (SAVAnT) also provides a technique to assess the completeness of a software specification.

  16. Ontologies for software engineering and software technology

    CERN Document Server

    Calero, Coral; Piattini, Mario

    2006-01-01

    Covers two applications of ontologies in software engineering and software technology: sharing knowledge of the problem domain and using a common terminology among all stakeholders; and filtering the knowledge when defining models and metamodels. This book is of benefit to software engineering researchers in both academia and industry.

  17. An Integrating Approach for Developing Distributed Software Systems -Combining Formal Methods, Software Reuse, and the Experience Base-

    OpenAIRE

    Feldmann, Raimund L.; Geppert, Birgit; Rößler, Frank

    1999-01-01

    The development of complex software systems is driven by many diverse and sometimes contradictory requirements such as correctness and maintainability of resulting products, development costs, and time-to-market. To alleviate these difficulties, we propose a development method for distributed systems that integrates different basic approaches. First, it combines the use of the formal description technique SDL with software reuse concepts. This results in the definition of a use-case driven, i...

  18. The 7 Qualities of Highly Secure Software

    CERN Document Server

    Paul, Mano

    2012-01-01

    The 7 Qualities of Highly Secure Software provides a framework for designing, developing, and deploying hacker-resilient software. It uses engaging anecdotes and analogies-ranging from Aesop's fables, athletics, architecture, biology, nursery rhymes, and video games-to illustrate the qualities that are essential for the development of highly secure software. Each chapter details one of the seven qualities that can make your software highly secure and less susceptible to hacker threats. Leveraging real-world experiences and examples, the book: Explains complex security concepts in language that

  19. Space Flight Software Development Software for Intelligent System Health Management

    Science.gov (United States)

    Trevino, Luis C.; Crumbley, Tim

    2004-01-01

    The slide presentation examines the Marshall Space Flight Center Flight Software Branch, including software development projects, mission critical space flight software development, software technical insight, advanced software development technologies, and continuous improvement in the software development processes and methods.

  20. Software Development Practices in Global Software Work : Developing Quality Software

    OpenAIRE

    2005-01-01

    This thesis is about software development practices, including the project management aspects, in the context of global software outsourcing. It was focused on the issues of achieving quality product namely here: software. It is built on the premise that the global context, in which the stakeholders are geographically separated by national boundaries, poses unique and inherent challenges derived from separation of place, time and culture.

  1. Software Engineering Guidebook

    Science.gov (United States)

    Connell, John; Wenneson, Greg

    1993-01-01

    The Software Engineering Guidebook describes SEPG (Software Engineering Process Group) supported processes and techniques for engineering quality software in NASA environments. Three process models are supported: structured, object-oriented, and evolutionary rapid-prototyping. The guidebook covers software life-cycles, engineering, assurance, and configuration management. The guidebook is written for managers and engineers who manage, develop, enhance, and/or maintain software under the Computer Software Services Contract.

  2. Software and systems traceability

    CERN Document Server

    Cleland-Huang, Jane; Zisman, Andrea

    2012-01-01

    ""Software and Systems Traceability"" provides a comprehensive description of the practices and theories of software traceability across all phases of the software development lifecycle. The term software traceability is derived from the concept of requirements traceability. Requirements traceability is the ability to track a requirement all the way from its origins to the downstream work products that implement that requirement in a software system. Software traceability is defined as the ability to relate the various types of software artefacts created during the development of software syst

  3. Maximizing ROI on software development

    CERN Document Server

    Sikka, Vijay

    2004-01-01

    A brief review of software development history. Software complexity crisis. Software development ROI. The case for global software development and testing. Software quality and test ROI. How do you implement global software development and testing. Case studies.

  4. Muscle-driven nanogenerators

    Science.gov (United States)

    Wang, Zhong L.; Yang, Rusen

    2011-03-01

    In a method of generating electricity, a plurality of living cells are grown on an array of piezoelectric nanowires so that the cells engage the piezoelectric nanowires. Induced static potentials are extracted from at least one of the piezoelectric nanowires when at least one of the cells deforms the at least one of the piezoelectric nanowires. A cell-driven electrical generator that includes a substrate and a plurality of spaced-apart piezoelectric nanowires disposed on the substrate. A plurality of spaced-apart conductive electrodes interact with the plurality of piezoelectric nanowires. A biological buffer layer that is configured to promote growth of cells is disposed on the substrate so that cells placed on the substrate will grow and engage the piezoelectric nanowires.

  5. Software Testing Techniques and Strategies

    OpenAIRE

    Isha,; Sunita Sangwan

    2014-01-01

    Software testing provides a means to reduce errors, cut maintenance and overall software costs. Numerous software development and testing methodologies, tools, and techniques have emerged over the last few decades promising to enhance software quality. This paper describes Software testing, need for software testing, Software testing goals and principles. Further it describe about different Software testing techniques and different software testing strategies.

  6. Balancing Agility and Discipline in a Medical Device Software Organisation

    OpenAIRE

    Mc Hugh, Martin; McCaffery, Fergal; Fitzgerald, Brian; Stol, Klass-Jan; COADY, Garret; Casey, Valentine

    2013-01-01

    peer-reviewed Agile development techniques are becoming increasingly popular in the generic software development industry as they appear to offer solutions to the problems associated with following a plan-driven Software Development Life Cycle (SDLC). However, agile methods may not be suited to all industries or organisations. For agile methods to succeed, an organisation must be structured in a way to accommodate agile methods. Medical device software development organisations are bound b...

  7. Towards Value-Based requirements prioritization for software product management

    OpenAIRE

    Samer I. Mohamed; Islam A. M. ElMaddah; Ayman M. Wahba

    2008-01-01

    Meeting stakeholders' requirements and expectations becomes one of the critical aspects on which any software organization in market-driven environment focuses on, and pays a lot of effort and expenses to maximize the satisfaction of their stakeholders. Therefore identifying the software product release contents becomes one of the critical decisions for software product success. Requirements prioritization refers to that activity through which product releases contents that maximize stakehold...

  8. Software productivity improvement through software engineering technology

    Science.gov (United States)

    Mcgarry, F. E.

    1985-01-01

    It has been estimated that NASA expends anywhere from 6 to 10 percent of its annual budget on the acquisition, implementation and maintenance of computer software. Although researchers have produced numerous software engineering approaches over the past 5-10 years; each claiming to be more effective than the other, there is very limited quantitative information verifying the measurable impact htat any of these technologies may have in a production environment. At NASA/GSFC, an extended research effort aimed at identifying and measuring software techniques that favorably impact productivity of software development, has been active over the past 8 years. Specific, measurable, software development technologies have been applied and measured in a production environment. Resulting software development approaches have been shown to be effective in both improving quality as well as productivity in this one environment.

  9. Improving Software Developer's Competence

    DEFF Research Database (Denmark)

    Abrahamsson, Pekka; Kautz, Karlheinz; Sieppi, Heikki;

    2002-01-01

    Emerging agile software development methods are people oriented development approaches to be used by the software industry. The personal software process (PSP) is an accepted method for improving the capabilities of a single software engineer. Five original hypotheses regarding the impact of the ...

  10. Software distribution using xnetlib

    Energy Technology Data Exchange (ETDEWEB)

    Dongarra, J.J. [Univ. of Tennessee, Knoxville, TN (US). Dept. of Computer Science]|[Oak Ridge National Lab., TN (US); Rowan, T.H. [Oak Ridge National Lab., TN (US); Wade, R.C. [Univ. of Tennessee, Knoxville, TN (US). Dept. of Computer Science

    1993-06-01

    Xnetlib is a new tool for software distribution. Whereas its predecessor netlib uses e-mail as the user interface to its large collection of public-domain mathematical software, xnetlib uses an X Window interface and socket-based communication. Xnetlib makes it easy to search through a large distributed collection of software and to retrieve requested software in seconds.

  11. Ensuring Software IP Cleanliness

    Directory of Open Access Journals (Sweden)

    Mahshad Koohgoli

    2007-12-01

    Full Text Available At many points in the life of a software enterprise, determination of intellectual property (IP cleanliness becomes critical. The value of an enterprise that develops and sells software may depend on how clean the software is from the IP perspective. This article examines various methods of ensuring software IP cleanliness and discusses some of the benefits and shortcomings of current solutions.

  12. Agile Software Development

    Science.gov (United States)

    Biju, Soly Mathew

    2008-01-01

    Many software development firms are now adopting the agile software development method. This method involves the customer at every level of software development, thus reducing the impact of change in the requirement at a later stage. In this article, the principles of the agile method for software development are explored and there is a focus on…

  13. Just-in-time Database-Driven Web Applications

    OpenAIRE

    Ong, Kenneth R

    2003-01-01

    "Just-in-time" database-driven Web applications are inexpensive, quickly-developed software that can be put to many uses within a health care organization. Database-driven Web applications garnered 73873 hits on our system-wide intranet in 2002. They enabled collaboration and communication via user-friendly Web browser-based interfaces for both mission-critical and patient-care-critical functions. Nineteen database-driven Web applications were developed. The application categories that compri...

  14. Great software debates

    CERN Document Server

    Davis, A

    2004-01-01

    The industry’s most outspoken and insightful critic explains how the software industry REALLY works. In Great Software Debates, Al Davis, shares what he has learned about the difference between the theory and the realities of business and encourages you to question and think about software engineering in ways that will help you succeed where others fail. In short, provocative essays, Davis fearlessly reveals the truth about process improvement, productivity, software quality, metrics, agile development, requirements documentation, modeling, software marketing and sales, empiricism, start-up financing, software research, requirements triage, software estimation, and entrepreneurship.

  15. Ontology-Driven Information Integration

    Science.gov (United States)

    Tissot, Florence; Menzel, Chris

    2005-01-01

    Ontology-driven information integration (ODII) is a method of computerized, automated sharing of information among specialists who have expertise in different domains and who are members of subdivisions of a large, complex enterprise (e.g., an engineering project, a government agency, or a business). In ODII, one uses rigorous mathematical techniques to develop computational models of engineering and/or business information and processes. These models are then used to develop software tools that support the reliable processing and exchange of information among the subdivisions of this enterprise or between this enterprise and other enterprises.

  16. Software Engineering for Practiced Software Enhancement

    Directory of Open Access Journals (Sweden)

    Rashmi Yadav

    2011-03-01

    Full Text Available Software development scenario particularly in IT industries is very competitive and demands for development with minimum resources. Software development started and prevailed up to an extent in industry without the use of software engineering practices, which was perceived as an overhead. This approach causes over use of resources, such as money, man-hours, hardware components. This paper attempts to present the causes of inefficiencies in an almost exhaustive way. Further, an attempt has been made to elaborate the software engineering methods as remedies against the listed causes of inefficiencies of development.

  17. Software Cost Estimation Review

    OpenAIRE

    Ongere, Alphonce

    2013-01-01

    Software cost estimation is the process of predicting the effort, the time and the cost re-quired to complete software project successfully. It involves size measurement of the soft-ware project to be produced, estimating and allocating the effort, drawing the project schedules, and finally, estimating overall cost of the project. Accurate estimation of software project cost is an important factor for business and the welfare of software organization in general. If cost and effort estimat...

  18. Views on Software Testability

    OpenAIRE

    Shimeall, Timothy; Friedman, Michael; Chilenski, John; Voas, Jeffrey

    1994-01-01

    The field of testability is an active, well-established part of engineering of modern computer systems. However, only recently have technologies for software testability began to be developed. These technologies focus on accessing the aspects of software that improve or depreciate the ease of testing. As both the size of implemented software and the amount of effort required to test that software increase, so will the important of software testability technologies in influencing the softwa...

  19. Data-Driven Method for High Level Rendering Pipeline Construction

    OpenAIRE

    Krasnoproshin, V. V.; Mazouka, D.

    2014-01-01

    The paper describes a software methodology for the graphics pipeline extension. It is argued that common modern visualization techniques do not satisfy current visualization software development requirements adequately enough. The proposed approach is based on specialized formal language called visualization algebra. By invoking data-driven design principles inherited from the existing programmable pipeline technology, the technique has a potential to reduce visualization software development...

  20. Software Engineering Program: Software Process Improvement Guidebook

    Science.gov (United States)

    1996-01-01

    The purpose of this document is to provide experience-based guidance in implementing a software process improvement program in any NASA software development or maintenance community. This guidebook details how to define, operate, and implement a working software process improvement program. It describes the concept of the software process improvement program and its basic organizational components. It then describes the structure, organization, and operation of the software process improvement program, illustrating all these concepts with specific NASA examples. The information presented in the document is derived from the experiences of several NASA software organizations, including the SEL, the SEAL, and the SORCE. Their experiences reflect many of the elements of software process improvement within NASA. This guidebook presents lessons learned in a form usable by anyone considering establishing a software process improvement program within his or her own environment. This guidebook attempts to balance general and detailed information. It provides material general enough to be usable by NASA organizations whose characteristics do not directly match those of the sources of the information and models presented herein. It also keeps the ideas sufficiently close to the sources of the practical experiences that have generated the models and information.

  1. Software Defined Radio with Parallelized Software Architecture

    Science.gov (United States)

    Heckler, Greg

    2013-01-01

    This software implements software-defined radio procession over multicore, multi-CPU systems in a way that maximizes the use of CPU resources in the system. The software treats each processing step in either a communications or navigation modulator or demodulator system as an independent, threaded block. Each threaded block is defined with a programmable number of input or output buffers; these buffers are implemented using POSIX pipes. In addition, each threaded block is assigned a unique thread upon block installation. A modulator or demodulator system is built by assembly of the threaded blocks into a flow graph, which assembles the processing blocks to accomplish the desired signal processing. This software architecture allows the software to scale effortlessly between single CPU/single-core computers or multi-CPU/multi-core computers without recompilation. NASA spaceflight and ground communications systems currently rely exclusively on ASICs or FPGAs. This software allows low- and medium-bandwidth (100 bps to approx.50 Mbps) software defined radios to be designed and implemented solely in C/C++ software, while lowering development costs and facilitating reuse and extensibility.

  2. Generic Software Architecture for Launchers

    Science.gov (United States)

    Carre, Emilien; Gast, Philippe; Hiron, Emmanuel; Leblanc, Alain; Lesens, David; Mescam, Emmanuelle; Moro, Pierre

    2015-09-01

    The definition and reuse of generic software architecture for launchers is not so usual for several reasons: the number of European launcher families is very small (Ariane 5 and Vega for these last decades); the real time constraints (reactivity and determinism needs) are very hard; low levels of versatility are required (implying often an ad hoc development of the launcher mission). In comparison, satellites are often built on a generic platform made up of reusable hardware building blocks (processors, star-trackers, gyroscopes, etc.) and reusable software building blocks (middleware, TM/TC, On Board Control Procedure, etc.). If some of these reasons are still valid (e.g. the limited number of development), the increase of the available CPU power makes today an approach based on a generic time triggered middleware (ensuring the full determinism of the system) and a centralised mission and vehicle management (offering more flexibility in the design and facilitating the long term maintenance) achievable. This paper presents an example of generic software architecture which could be envisaged for future launchers, based on the previously described principles and supported by model driven engineering and automatic code generation.

  3. Table-driven software architecture for a stitching system

    Science.gov (United States)

    Thrash, Patrick J. (Inventor); Miller, Jeffrey L. (Inventor); Pallas, Ken (Inventor); Trank, Robert C. (Inventor); Fox, Rhoda (Inventor); Korte, Mike (Inventor); Codos, Richard (Inventor); Korolev, Alexandre (Inventor); Collan, William (Inventor)

    2001-01-01

    Native code for a CNC stitching machine is generated by generating a geometry model of a preform; generating tool paths from the geometry model, the tool paths including stitching instructions for making stitches; and generating additional instructions indicating thickness values. The thickness values are obtained from a lookup table. When the stitching machine runs the native code, it accesses a lookup table to determine a thread tension value corresponding to the thickness value. The stitching machine accesses another lookup table to determine a thread path geometry value corresponding to the thickness value.

  4. Development of software phantoms for software validation

    International Nuclear Information System (INIS)

    Nuclear medicine software is expected to meet certain criteria. The specifications are frequently not available to the user and, as a consequence, the performance of a particular software package may not meet the users' expectations. Under most circumstances this may be evident immediately, but frequently the user will assume certain specifications based upon the clinical procedure that is being performed, and assume that the software should function in a certain fashion to give the value of a desired parameter. To this end, it is useful to have a number of software phantoms which can act as standard data sets for validation of the software and ensure that the results obtained do meet expectations. A number of problems surround the development of a set of software phantoms that can be transported between different systems. One solution is the creation of mathematical phantoms, in which case algorithms or source code may be transportable. This paper describes four such mathematical phantoms that have been used to validate an ejection fraction and Fourier analysis package. This particular software package has been found lacking in several respects, none of which would have been evident from the documentation provided. (author). 12 refs, 4 figs

  5. Improving Software Reliability Forecasting

    NARCIS (Netherlands)

    Burtsy, Bernard; Albeanu, Grigore; Boros, Dragos N.; Popentiu, Florin; Nicola, Victor

    1997-01-01

    This work investigates some methods for software reliability forecasting. A supermodel is presented as a suited tool for prediction of reliability in software project development. Also, times series forecasting for cumulative interfailure time is proposed and illustrated.

  6. Pragmatic Software Innovation

    DEFF Research Database (Denmark)

    Aaen, Ivan; Jensen, Rikke Hagensby

    2014-01-01

    , for creating new markets, or for curbing rising public expenses, and software intensive systems are core elements in most such strategies. Software innovation therefore is vital for about every sector of the economy. Changes in software technologies over the last decades have opened up for experimentation......, learning, and flexibility in ongoing software projects, but how can this change be used to facilitate software innovation? How can a team systematically identify and pursue opportunities to create added value in ongoing projects? In this paper, we describe Deweyan pragmatism as the philosophical foundation......We understand software innovation as concerned with introducing innovation into the development of software intensive systems, i.e. systems in which software development and/or integration are dominant considerations. Innovation is key in almost any strategy for competitiveness in existing markets...

  7. Software Engineering Improvement Plan

    Science.gov (United States)

    2006-01-01

    In performance of this task order, bd Systems personnel provided support to the Flight Software Branch and the Software Working Group through multiple tasks related to software engineering improvement and to activities of the independent Technical Authority (iTA) Discipline Technical Warrant Holder (DTWH) for software engineering. To ensure that the products, comments, and recommendations complied with customer requirements and the statement of work, bd Systems personnel maintained close coordination with the customer. These personnel performed work in areas such as update of agency requirements and directives database, software effort estimation, software problem reports, a web-based process asset library, miscellaneous documentation review, software system requirements, issue tracking software survey, systems engineering NPR, and project-related reviews. This report contains a summary of the work performed and the accomplishments in each of these areas.

  8. Temporal Code-Driven Stimulation: Definition and Application to Electric Fish Signaling

    Science.gov (United States)

    Lareo, Angel; Forlim, Caroline G.; Pinto, Reynaldo D.; Varona, Pablo; Rodriguez, Francisco de Borja

    2016-01-01

    Closed-loop activity-dependent stimulation is a powerful methodology to assess information processing in biological systems. In this context, the development of novel protocols, their implementation in bioinformatics toolboxes and their application to different description levels open up a wide range of possibilities in the study of biological systems. We developed a methodology for studying biological signals representing them as temporal sequences of binary events. A specific sequence of these events (code) is chosen to deliver a predefined stimulation in a closed-loop manner. The response to this code-driven stimulation can be used to characterize the system. This methodology was implemented in a real time toolbox and tested in the context of electric fish signaling. We show that while there are codes that evoke a response that cannot be distinguished from a control recording without stimulation, other codes evoke a characteristic distinct response. We also compare the code-driven response to open-loop stimulation. The discussed experiments validate the proposed methodology and the software toolbox. PMID:27766078

  9. Developer Driven and User Driven Usability Evaluations

    OpenAIRE

    Bruun, Anders

    2013-01-01

    Usability evaluation provide software development teams with insights on the degree to which a software application enables a user to achieve his/her goals, how fast these goals can be achieved, how easy it is to learn and how satisfactory it is in use Although usability evaluations are crucial in the process of developing software systems with a high level of usability, its use is still limited in the context of small software development companies.Several approaches have been proposed to su...

  10. Software Testing Requires Variability

    DEFF Research Database (Denmark)

    Christensen, Henrik Bærbak

    2003-01-01

    Software variability is the ability of a software system or artefact to be changed, customized or configured for use in a particular context. Variability in software systems is important from a number of perspectives. Some perspectives rightly receive much attention due to their direct economic...... impact in software production. As is also apparent from the call for papers these perspectives focus on qualities such as reuse, adaptability, and maintainability....

  11. Healthcare Software Assurance

    OpenAIRE

    Cooper, Jason G.; Pauley, Keith A.

    2006-01-01

    Software assurance is a rigorous, lifecycle phase-independent set of activities which ensure completeness, safety, and reliability of software processes and products. This is accomplished by guaranteeing conformance to all requirements, standards, procedures, and regulations. These assurance processes are even more important when coupled with healthcare software systems, embedded software in medical instrumentation, and other healthcare-oriented life-critical systems. The current Food and Dru...

  12. SOFAS: Software Analysis Services

    OpenAIRE

    Ghezzi, G

    2010-01-01

    We propose a distributed and collaborative software analysis platform to enable seamless interoperability of software analysis tools across platform, geographical and organizational boundaries. In particular, we devise software analysis tools as services that can be accessed and composed over the Internet. These distributed services shall be widely accessible through a software analysis broker where organizations and research groups can register and share their tools. To enable (semi)-automat...

  13. Software engineering measurement

    CERN Document Server

    Munson, PhD, John C

    2003-01-01

    By demonstrating how to develop simple experiments for the empirical validation of theoretical research and showing how to convert measurement data into meaningful and valuable information, this text fosters more precise use of software measurement in the computer science and software engineering literature. Software Engineering Measurement shows you how to convert your measurement data to valuable information that can be used immediately for software process improvement.

  14. Software engineer's pocket book

    CERN Document Server

    Tooley, Michael

    2013-01-01

    Software Engineer's Pocket Book provides a concise discussion on various aspects of software engineering. The book is comprised of six chapters that tackle various areas of concerns in software engineering. Chapter 1 discusses software development, and Chapter 2 covers programming languages. Chapter 3 deals with operating systems. The book also tackles discrete mathematics and numerical computation. Data structures and algorithms are also explained. The text will be of great use to individuals involved in the specification, design, development, implementation, testing, maintenance, and qualit

  15. Software Language Evolution

    NARCIS (Netherlands)

    Vermolen, S.D.

    2012-01-01

    Software plays a critical role in our daily life. Vast amounts of money are spent on more and more complex systems. All software, regardless if it controls a plane or the game on your phone is never finished. Software changes when it contains bugs or when new functionality is added. This process of

  16. Software Architecture Evolution

    Science.gov (United States)

    Barnes, Jeffrey M.

    2013-01-01

    Many software systems eventually undergo changes to their basic architectural structure. Such changes may be prompted by new feature requests, new quality attribute requirements, changing technology, or other reasons. Whatever the causes, architecture evolution is commonplace in real-world software projects. Today's software architects, however,…

  17. Java for flight software

    Science.gov (United States)

    Benowitz, E.; Niessner, A.

    2003-01-01

    This work involves developing representative mission-critical spacecraft software using the Real-Time Specification for Java (RTSJ). This work currently leverages actual flight software used in the design of actual flight software in the NASA's Deep Space 1 (DSI), which flew in 1998.

  18. Software engineering: a roadmap

    OpenAIRE

    Finkelstein, A.; Kramer, J.

    2000-01-01

    This paper provides a roadmap for software engineering. It identifies the principal research challenges being faced by the discipline and brings together the threads derived from the key research specialisations within software engineering. The paper draws heavily on the roadmaps covering specific areas of software engineering research collected in this volume.

  19. Computer software quality assurance

    International Nuclear Information System (INIS)

    The author defines some criteria for the evaluation of software quality assurance elements for applicability to the regulation of the nuclear industry. The author then analyses a number of software quality assurance (SQA) standards. The major extracted SQA elements are then discussed, and finally specific software quality assurance recommendations are made for the nuclear industry

  20. Software test attacks to break mobile and embedded devices

    CERN Document Server

    Hagar, Jon Duncan

    2013-01-01

    Address Errors before Users Find Them Using a mix-and-match approach, Software Test Attacks to Break Mobile and Embedded Devices presents an attack basis for testing mobile and embedded systems. Designed for testers working in the ever-expanding world of ""smart"" devices driven by software, the book focuses on attack-based testing that can be used by individuals and teams. The numerous test attacks show you when a software product does not work (i.e., has bugs) and provide you with information about the software product under test. The book guides you step by step starting with the basics. It

  1. Software Development Of Sugar Cane Plantation And Harvesting Management

    International Nuclear Information System (INIS)

    This software is a management system based on database-driven computer software application. It is intended to improve the quality of sugar cane through increased efficiency in managing, harvesting and transporting of sugar cane, as part of a sugar factory operation. The software was developed using the Borland Delphi development platform, with database manipulation using Microsoft Access. The software is intended for Personal Computer with Windows 95 (or later) installed. The application has been tested with acceptable result and can be used in Sragi Sugar Factory's related activities; namely sugar cane plantation management, harvesting and transporting of sugar cane, payment process and other related administrative processes

  2. Biological aerosol background characterization

    Science.gov (United States)

    Blatny, Janet; Fountain, Augustus W., III

    2011-05-01

    To provide useful information during military operations, or as part of other security situations, a biological aerosol detector has to respond within seconds or minutes to an attack by virulent biological agents, and with low false alarms. Within this time frame, measuring virulence of a known microorganism is extremely difficult, especially if the microorganism is of unknown antigenic or nucleic acid properties. Measuring "live" characteristics of an organism directly is not generally an option, yet only viable organisms are potentially infectious. Fluorescence based instruments have been designed to optically determine if aerosol particles have viability characteristics. Still, such commercially available biological aerosol detection equipment needs to be improved for their use in military and civil applications. Air has an endogenous population of microorganisms that may interfere with alarm software technologies. To design robust algorithms, a comprehensive knowledge of the airborne biological background content is essential. For this reason, there is a need to study ambient live bacterial populations in as many locations as possible. Doing so will permit collection of data to define diverse biological characteristics that in turn can be used to fine tune alarm algorithms. To avoid false alarms, improving software technologies for biological detectors is a crucial feature requiring considerations of various parameters that can be applied to suppress alarm triggers. This NATO Task Group will aim for developing reference methods for monitoring biological aerosol characteristics to improve alarm algorithms for biological detection. Additionally, they will focus on developing reference standard methodology for monitoring biological aerosol characteristics to reduce false alarm rates.

  3. Test and Behaviour Driven Development with Python

    CERN Document Server

    CERN. Geneva

    2016-01-01

    Experience has taught us that bugs are impossible to avoid when programming. Specially on continuous delivery processes where there are new versions that refactor or incorporate new modules to the project. Although, there are different tools which help us to ensure code quality by enabling developers to catch bugs while still in the development stage. In this talk, I will talk about Test-driven development(TDD) and Behaviour-Driven development (BDD) methodologies focused on web development. Also, I will present an overview of unit testing tools as Selenium or Behave, which help us to produce working software, with fewer bugs, quickly and consistently.

  4. Test-driven development with Mockito

    CERN Document Server

    Acharya, Sujoy

    2013-01-01

    This book is a hands-on guide, full of practical examples to illustrate the concepts of Test Driven Development.If you are a developer who wants to develop software following Test Driven Development using Mockito and leveraging various Mockito features, this book is ideal for you. You don't need prior knowledge of TDD, Mockito, or JUnit.It is ideal for developers, who have some experience in Java application development as well as a basic knowledge of unit testing, but it covers the basic fundamentals of TDD and JUnit testing to get you acquainted with these concepts before delving into them.

  5. Software Metrics: Calculation and Optimization of Thresholds

    OpenAIRE

    Abhishek Kumar Maheswari

    2011-01-01

    In this article, we present a algorithmic method for the calculation of thresholds (the starting point for a new state) for a software metric set. To this aim, machine learning and data mining techniques are utilized. We define a data-driven methodology that can be used for efficiency optimization of existing metric sets, for the simplification of complex classification models, and for the calculation of thresholds for a metric set in an environment where no metric set yet exists. The methodo...

  6. Software Maintenance Success Recipes

    CERN Document Server

    Reifer, Donald J

    2011-01-01

    Dispelling much of the folklore surrounding software maintenance, Software Maintenance Success Recipes identifies actionable formulas for success based on in-depth analysis of more than 200 real-world maintenance projects. It details the set of factors that are usually present when effective software maintenance teams do their work and instructs on the methods required to achieve success. Donald J. Reifer--an award winner for his contributions to the field of software engineering and whose experience includes managing the DoD Software Initiatives Office--provides step-by-step guidance on how t

  7. Code Generator Composition for Model-Driven Engineering of Robotics Component & Connector Systems

    OpenAIRE

    Ringert, Jan Oliver; Roth, Alexander; Rumpe, Bernhard; Wortmann, Andreas

    2015-01-01

    Engineering software for robotics applications requires multidomain and application-specific solutions. Model-driven engineering and modeling language integration provide means for developing specialized, yet reusable models of robotics software architectures. Code generators transform these platform independent models into executable code specific to robotic platforms. Generative software engineering for multidomain applications requires not only the integration of modeling languages but als...

  8. GENII Version 2 Software Design Document

    Energy Technology Data Exchange (ETDEWEB)

    Napier, Bruce A.; Strenge, Dennis L.; Ramsdell, James V.; Eslinger, Paul W.; Fosmire, Christian J.

    2004-03-08

    This document describes the architectural design for the GENII-V2 software package. This document defines details of the overall structure of the software, the major software components, their data file interfaces, and specific mathematical models to be used. The design represents a translation of the requirements into a description of the software structure, software components, interfaces, and necessary data. The design focuses on the major components and data communication links that are key to the implementation of the software within the operating framework. The purpose of the GENII-V2 software package is to provide the capability to perform dose and risk assessments of environmental releases of radionuclides. The software also has the capability of calculating environmental accumulation and radiation doses from surface water, groundwater, and soil (buried waste) media when an input concentration of radionuclide in these media is provided. This report represents a detailed description of the capabilities of the software product with exact specifications of mathematical models that form the basis for the software implementation and testing efforts. This report also presents a detailed description of the overall structure of the software package, details of main components (implemented in the current phase of work), details of data communication files, and content of basic output reports. The GENII system includes the capabilities for calculating radiation doses following chronic and acute releases. Radionuclide transport via air, water, or biological activity may be considered. Air transport options include both puff and plume models, each allow use of an effective stack height or calculation of plume rise from buoyant or momentum effects (or both). Building wake effects can be included in acute atmospheric release scenarios. The code provides risk estimates for health effects to individuals or populations; these can be obtained using the code by applying

  9. User driven innovation in mobile technologies?

    DEFF Research Database (Denmark)

    Larsen, Casper Schultz; Koch, Christian

    2007-01-01

    Developing dedicated mobile technology systems for AEC demands the introduction of user driven innovation. A Danish research project collected international examples and user-experiences of mobile and handheld ICT in the building industry i.a. by reading off the functionality of the mobile...... technology systems relying on the concept of affordance. This paper examines how innovation processes mediate between user orientations and technology offers. There is a great potential for mobile handheld ICT-systems to support numerous work processes in the AEC-industry and this can be substantiated...... by systems already in function. Stories of prior business successes can be an important tool to ensure further innovative investments since lack of enterprise strategies is often an obstacle for innovation, especially user driven. Both small and large software houses develops dedicated software for coupling...

  10. Mathematical software production

    Energy Technology Data Exchange (ETDEWEB)

    Cowell, W. R.; Fosdick, L. D.

    1977-01-01

    Locally constructed collections of mathematical routines are gradually being replaced by mathematical software that has been produced for broad dissemination and use. The process of producing such software begins with algorithmic analysis, and proceeds through software construction and documentation to extensive testing and, finally, to distribution and support of the software products. These are demanding and costly activities which require such a range of skills that they are carried out in collaborative projects. The costs and effort are justified by the utility of high-quality software, the efficiency of producing it for general distribution, and the benefits of providing a conduit from research to applications. This paper first reviews certain of the early developments in the field of mathematical software. Then it examines the technical problems that distinguish software production as an intellectual activity, problems whose descriptions also serve to characterize ideal mathematical software. Next, three mathematical software projects are sketched with attention to their emphasis, accomplishments, organization, and costs. Finally, comments are offered on possible future directions for mathematical software production, as extrapolations of the present involvement of universities, government laboratories, and private industry. 48 references.

  11. The ATLAS Data Management Software Engineering Process

    CERN Document Server

    Lassnig, M; The ATLAS collaboration; Stewart, G A; Barisits, M; Beermann, T; Vigne, R; Serfon, C; Goossens, L; Nairz, A

    2013-01-01

    Rucio is the next-generation data management system of the ATLAS experiment. The software engineering process to develop Rucio is fundamentally different to existing software development approaches in the ATLAS distributed computing community. Based on a conceptual design document, development takes place using peer-reviewed code in a test-driven environment. The main objectives are to ensure that every engineer understands the details of the full project, even components usually not touched by them, that the design and architecture are coherent, that temporary contributors can be productive without delay, that programming mistakes are prevented before being committed to the source code, and that the source is always in a fully functioning state. This contribution will illustrate the workflows and products used, and demonstrate the typical development cycle of a component from inception to deployment within this software engineering process. Next to the technological advantages, this contribution will also hi...

  12. The ATLAS Data Management Software Engineering Process

    CERN Document Server

    Lassnig, M; The ATLAS collaboration; Stewart, G A; Barisits, M; Beermann, T; Vigne, R; Serfon, C; Goossens, L; Nairz, A; Molfetas, A

    2014-01-01

    Rucio is the next-generation data management system of the ATLAS experiment. The software engineering process to develop Rucio is fundamentally different to existing software development approaches in the ATLAS distributed computing community. Based on a conceptual design document, development takes place using peer-reviewed code in a test-driven environment. The main objectives are to ensure that every engineer understands the details of the full project, even components usually not touched by them, that the design and architecture are coherent, that temporary contributors can be productive without delay, that programming mistakes are prevented before being committed to the source code, and that the source is always in a fully functioning state. This contribution will illustrate the workflows and products used, and demonstrate the typical development cycle of a component from inception to deployment within this software engineering process. Next to the technological advantages, this contribution will also hi...

  13. Light-driven robotics for nanoscopy

    DEFF Research Database (Denmark)

    Glückstad, Jesper; Palima, Darwin

    2013-01-01

    The science fiction inspired shrinking of macro-scale robotic manipulation and handling down to the micro- and nanoscale regime opens new doors for exploiting the forces and torques of light for micro- and nanoscopic probing, actuation and control. Advancing light-driven micro-robotics requires...... and matter for robotically probing at the smallest biological length scales....

  14. Developer Driven and User Driven Usability Evaluations

    DEFF Research Database (Denmark)

    Bruun, Anders

    2013-01-01

    in the process of developing software systems with a high level of usability, its use is still limited in the context of small software development companies. Several approaches have been proposed to support software development practitioners (SWPs) in conducting usability evaluations, and my thesis explores two...... of these: 1) The first approach is to support SWPs by training them to drive usability evaluations. 2) The second approach to support SWPs involves minimalist training of end users to drive usability evaluations. In related work, a set of five quality criteria for usability evaluations is applied...

  15. Software Defined Networking Demands on Software Technologies

    DEFF Research Database (Denmark)

    Galinac Grbac, T.; Caba, Cosmin Marius; Soler, José

    2015-01-01

    Software Defined Networking (SDN) is a networking approach based on a centralized control plane architecture with standardised interfaces between control and data planes. SDN enables fast configuration and reconfiguration of the network to enhance resource utilization and service performances....... This new approach enables a more dynamic and flexible network, which may adapt to user needs and application requirements. To this end, systemized solutions must be implemented in network software, aiming to provide secure network services that meet the required service performance levels. In this paper......, we review this new approach to networking from an architectural point of view, and identify and discuss some critical quality issues that require new developments in software technologies. These issues we discuss along with use case scenarios. Here in this paper we aim to identify challenges...

  16. Trace Software Pipelining

    Institute of Scientific and Technical Information of China (English)

    王剑; AndreasKrall; 等

    1995-01-01

    Global software pipelining is a complex but efficient compilation technique to exploit instruction-level parallelism for loops with branches.This paper presents a novel global software pipelining technique,called Trace Software Pipelining,targeted to the instruction-level parallel processors such as Very Long Instruction Word (VLIW) and superscalar machines.Trace software pipelining applies a global code scheduling technique to compact the original loop body.The resulting loop is called a trace software pipelined (TSP) code.The trace softwrae pipelined code can be directly executed with special architectural support or can be transformed into a globally software pipelined loop for the current VLIW and superscalar processors.Thus,exploiting parallelism across all iterations of a loop can be completed through compacting the original loop body with any global code scheduling technique.This makes our new technique very promising in practical compilers.Finally,we also present the preliminary experimental results to support our new approach.

  17. Social software in global software development

    DEFF Research Database (Denmark)

    Giuffrida, Rosalba; Dittrich, Yvonne

    2010-01-01

    Social software (SoSo) is defined by Farkas as tools that (1) allow people to communicate, collaborate, and build community online (2) can be syndicated, shared, reused or remixed and (3) let people learn easily from and capitalize on the behavior and knowledge of others. [1]. SoSo include a wide...... variety of tools such as: instant messaging, internet forums, mailing lists, blogs, wikis, social network sites, social bookmarking, social libraries, virtual worlds. Though normally rather belonging to the private realm, the use of social software in corporate context has been reported, e.g. as a way...

  18. Software Quality Assurance in Software Projects: A Study of Pakistan

    Directory of Open Access Journals (Sweden)

    Faisal Shafique Butt

    2013-05-01

    Full Text Available Software quality is specific property which tells what kind of standard software should have. In a software project, quality is the key factor of success and decline of software related organization. Many researches have been done regarding software quality. Software related organization follows standards introduced by Capability Maturity Model Integration (CMMI to achieve good quality software. Quality is divided into three main layers which are Software Quality Assurance (SQA, Software Quality Plan (SQP and Software Quality Control (SQC. So In this study, we are discussing the quality standards and principles of software projects in Pakistan software Industry and how these implemented quality standards are measured and managed. In this study, we will see how many software firms are following the rules of CMMI to create software. How many are reaching international standards and how many firms are measuring the quality of their projects. The results show some of the companies are using software quality assurance techniques in Pakstan.

  19. Ontology Based Feature Driven Development Life Cycle

    Directory of Open Access Journals (Sweden)

    Farheen Siddiqui

    2012-01-01

    Full Text Available The upcoming technology support for semantic web promises fresh directions for Software Engineering community. Also semantic web has its roots in knowledge engineering that provoke software engineers to look for application of ontology applications throughout the Software Engineering lifecycle. The internal components of a semantic web are "light weight", and may be of less quality standards than the externally visible modules. In fact the internal components are generated from external (ontological component. That's the reason agile development approaches such as feature driven development are suitable for applications internal component development. As yet there is no particular procedure that describes the role of ontology in FDD processes. Therefore we propose an ontology based feature driven development for semantic web application that can be used form application model development to feature design and implementation. Features are precisely defined in the OWL-based domain model. Transition from OWL based domain model to feature list is directly defined in transformation rules. On the other hand the ontology based overall model can be easily validated through automated tools. Advantages of ontology-based feature Driven development are also discussed.

  20. Software engineering the current practice

    CERN Document Server

    Rajlich, Vaclav

    2011-01-01

    INTRODUCTION History of Software EngineeringSoftware PropertiesOrigins of SoftwareBirth of Software EngineeringThird Paradigm: Iterative ApproachSoftware Life Span ModelsStaged ModelVariants of Staged ModelSoftware Technologies Programming Languages and CompilersObject-Oriented TechnologyVersion Control SystemSoftware ModelsClass DiagramsUML Activity DiagramsClass Dependency Graphs and ContractsSOFTWARE CHANGEIntroduction to Software ChangeCharacteristics of Software ChangePhases of Software ChangeRequirements and Their ElicitationRequirements Analysis and Change InitiationConcepts and Concept

  1. A Developers Perspective: An Analysis of Processes Involved in Software Development of Health Care Industries

    OpenAIRE

    Prabu.M; Narasimhan.D; Michaelraj.T.F

    2015-01-01

    Software is now becoming the primary differentiator for medical devices manufacturer. Software development is driven by the risks, stringent quality requirements (such as safety, reliability), regulatory challenges, market pressures and significant complexity. To balance these, medical device industries need effective software development process to satisfy their client’s need. This paper identifies the actual barriers associated with software practices during development of medical softwa...

  2. Software Preservation Benefits Framework

    OpenAIRE

    Chue Hong, Neil; Crouch, Steve; Hettrick, Simon; Parkinson, Tim; Shreeve, Matt

    2010-01-01

    An investigation of software preservation has been carried out by Curtis+Cartwright Consulting Limited, in partnership with the Software Sustainability Institute (SSI), on behalf of the JISC. The aim of the study was to raise awareness and build capacity throughout the Further and Higher Education (FE/HE) sector to engage with preservation issues as part of the process of software development. Part of this involved examining the purpose and benefits of employing preservation measures in relat...

  3. Software Process Improvement Defined

    DEFF Research Database (Denmark)

    Aaen, Ivan

    2002-01-01

    This paper argues in favor of the development of explanatory theory on software process improvement. The last one or two decades commitment to prescriptive approaches in software process improvement theory may contribute to the emergence of a gulf dividing theorists and practitioners....... It is proposed that this divide be met by the development of theory evaluating prescriptive approaches and informing practice with a focus on the software process policymaking and process control aspects of improvement efforts...

  4. The Other Software

    OpenAIRE

    McWilliams, Chandler B.

    2009-01-01

    This paper considers the absence of the human actor, specifically the programmer, from Friedrich Kittler’s analysis of software in his essay There is no Software. By focusing too intently on the machine and its specific, material existence, Kittler removes the human user / operator / writer from his analysis of software. Thus, he has no choice but to interpret the layers of language, assembler, opcode and WordPerfect, DOS, BIOS—both chains ending in an essentializing reduction to voltages—as ...

  5. Software architecture evolution

    DEFF Research Database (Denmark)

    Barais, Olivier; Le Meur, Anne-Francoise; Duchien, Laurence;

    2008-01-01

    Software architectures must frequently evolve to cope with changing requirements, and this evolution often implies integrating new concerns. Unfortunately, when the new concerns are crosscutting, existing architecture description languages provide little or no support for this kind of evolution...... one particular framework named Tran SAT, which addresses the above problems of software architecture evolution. Tran SAT provides a new element in the software architecture descriptions language, called an architectural aspect, for describing new concerns and their integration into an existing...

  6. Software configuration management

    CERN Document Server

    Keyes, Jessica

    2004-01-01

    Software Configuration Management discusses the framework from a standards viewpoint, using the original DoD MIL-STD-973 and EIA-649 standards to describe the elements of configuration management within a software engineering perspective. Divided into two parts, the first section is composed of 14 chapters that explain every facet of configuration management related to software engineering. The second section consists of 25 appendices that contain many valuable real world CM templates.

  7. Essential software architecture

    CERN Document Server

    Gorton, Ian

    2011-01-01

    Job titles like ""Technical Architect"" and ""Chief Architect"" nowadays abound in software industry, yet many people suspect that ""architecture"" is one of the most overused and least understood terms in professional software development. Gorton's book tries to resolve this dilemma. It concisely describes the essential elements of knowledge and key skills required to be a software architect. The explanations encompass the essentials of architecture thinking, practices, and supporting technologies. They range from a general understanding of structure and quality attributes through technical i

  8. Software evolution and maintenance

    CERN Document Server

    Tripathy, Priyadarshi

    2014-01-01

    Software Evolution and Maintenance: A Practitioner's Approach is an accessible textbook for students and professionals, which collates the advances in software development and provides the most current models and techniques in maintenance.Explains two maintenance standards: IEEE/EIA 1219 and ISO/IEC14764Discusses several commercial reverse and domain engineering toolkitsSlides for instructors are available onlineInformation is based on the IEEE SWEBOK (Software Engineering Body of Knowledge)

  9. Software Requirements Management

    OpenAIRE

    Ali Altalbe

    2015-01-01

    Requirements are defined as the desired set of characteristics of a product or a service. In the world of software development, it is estimated that more than half of the failures are attributed towards poor requirements management. This means that although the software functions correctly, it is not what the client requested. Modern software requirements management methodologies are available to reduce the occur-rence of such incidents. This paper performs a review on the available literatur...

  10. Gammasphere software development

    Energy Technology Data Exchange (ETDEWEB)

    Piercey, R.B.

    1993-01-01

    Activities of the nuclear physics group are described. Progress was made in organizing the Gammasphere Software Working Group, establishing a nuclear computing facility, participating in software development at Lawrence Berkeley, developing a common data file format, and adapting the ORNL UPAK software to run at Gammasphere. A universal histogram object was developed that defines a file format and provides for an objective-oriented programming model. An automated liquid nitrogen fill system was developed for Gammasphere (110 Ge detectors comprise the sphere).

  11. SWEBOS – The Software Engineering Body of Skills

    Directory of Open Access Journals (Sweden)

    Yvonne Sedelmaier

    2015-02-01

    Full Text Available The development of complex software systems requires a mixture of various technical and non-technical competencies. While some guidelines exist which technical knowledge is required to make a good software engineer, there is a lack of insight as to which non-technical or soft skills are necessary to master complex software projects. This paper proposes a body of skills (SWEBOS for soft-ware engineering. The collection of necessary skills is developed on the basis of a clear, data-driven research design. The resulting required soft skills for software engineering are described precisely and semantically rich in a three-level structure. This approach guarantees that skills are not just characterized in a broad and general manner, but rather they are specifically adapted to the domain of software engineering.

  12. 软件体系结构描述研究与进展%Overview on Software Architecture Description

    Institute of Scientific and Technical Information of China (English)

    孙昌爱; 金茂忠

    2003-01-01

    Recently,Software Architecture has become one focus in software Engineering community,and a key issue to successful large-scale software development. Software Architecture Description forms the base for architectural construction, evolution, verification, analysis, maintenance and architecture-driven software development. The concept related with Software Architecture Description is introduced,and Architecture Description Language and Typical Architecture Description Method are discussed in the paper. At the same time ,the industrial standards for Software Architecture Description,such as IEEE P1471 and Rational RAS-ADS,is also introduced. Finally,the conclusion and envision for Software Architecture Description are present in the paper.

  13. Test-driven modeling of embedded systems

    DEFF Research Database (Denmark)

    Munck, Allan; Madsen, Jan

    2015-01-01

    To benefit maximally from model-based systems engineering (MBSE) trustworthy high quality models are required. From the software disciplines it is known that test-driven development (TDD) can significantly increase the quality of the products. Using a test-driven approach with MBSE may have...... a similar positive effect on the quality of the system models and the resulting products and may therefore be desirable. To define a test-driven model-based systems engineering (TD-MBSE) approach, we must define this approach for numerous sub disciplines such as modeling of requirements, use cases...... suggest that our method provides a sound foundation for rapid development of high quality system models....

  14. Metamodel-Driven Evolution with Grammar Inference

    Science.gov (United States)

    Bryant, Barrett R.; Liu, Qichao; Mernik, Marjan

    2010-10-01

    Domain-specific modeling (DSM) has become one of the most popular techniques for incorporating model-driven engineering (MDE) into software engineering. In DSM, domain experts define metamodels to describe the essential problems in a domain. A model conforms to a schema definition represented by a metamodel in a similar manner to a programming language conforms to a grammar. Metamodel-driven evolution is when a metamodel undergoes evolutions to incorporate new concerns in the domain. However, this results in losing the ability to use existing model instances. Grammar inference is the problem of inferring a grammar from sample strings which the grammar should generate. This paper describes our work in solving the problem of metamodel-driven evolution with grammar inference, by inferring the metamodel from model instances.

  15. Marketing Mix del Software.

    OpenAIRE

    Yudith del Carmen Rodríguez Pérez

    2006-01-01

    La ingeniería del software y los modelos de calidad del software han consolidado sus esfuerzos en el proceso de producción del mismo, sin embargo son pocos sus aportes en el proceso de comercialización. Es esencial en la ciencia de la computación desarrollar un modelo de comercialización para las organizaciones productoras de software con el fin de elevar la productividad de las mismas. Sin embargo, es preciso primero conocer las características del producto software que los diferencian de ot...

  16. Software architecture 2

    CERN Document Server

    Oussalah, Mourad Chabanne

    2014-01-01

    Over the past 20 years, software architectures have significantly contributed to the development of complex and distributed systems. Nowadays, it is recognized that one of the critical problems in the design and development of any complex software system is its architecture, i.e. the organization of its architectural elements. Software Architecture presents the software architecture paradigms based on objects, components, services and models, as well as the various architectural techniques and methods, the analysis of architectural qualities, models of representation of architectural templa

  17. MYOB software for dummies

    CERN Document Server

    Curtis, Veechi

    2012-01-01

    Your complete guide to MYOB® AccountRight softwareNow in its seventh edition, MYOB® Software For Dummies walks you through everything you need to know, from starting your MYOB® file from scratch and recording payments and receipts, to tracking profit and analysing sales. This new edition includes all the information you need on the new generation of MYOB® AccountRight software, including the new cloud computing features. Set up MYOB® software - understand how to make it work the first time Keep track of purchases and sales - monitor customer accounts and ensure you get pai

  18. Agile software development

    CERN Document Server

    Dingsoyr, Torgeir; Moe, Nils Brede

    2010-01-01

    Agile software development has become an umbrella term for a number of changes in how software developers plan and coordinate their work, how they communicate with customers and external stakeholders, and how software development is organized in small, medium, and large companies, from the telecom and healthcare sectors to games and interactive media. Still, after a decade of research, agile software development is the source of continued debate due to its multifaceted nature and insufficient synthesis of research results. Dingsoyr, Dyba, and Moe now present a comprehensive snapshot of the kno

  19. Software architecture 1

    CERN Document Server

    Oussalah , Mourad Chabane

    2014-01-01

    Over the past 20 years, software architectures have significantly contributed to the development of complex and distributed systems. Nowadays, it is recognized that one of the critical problems in the design and development of any complex software system is its architecture, i.e. the organization of its architectural elements. Software Architecture presents the software architecture paradigms based on objects, components, services and models, as well as the various architectural techniques and methods, the analysis of architectural qualities, models of representation of architectural template

  20. Essence: Facilitating Software Innovation

    DEFF Research Database (Denmark)

    Aaen, Ivan

    2008-01-01

      This paper suggests ways to facilitate creativity and innovation in software development. The paper applies four perspectives – Product, Project, Process, and People –to identify an outlook for software innovation. The paper then describes a new facility–Software Innovation Research Lab (SIRL......) – and a new method concept for software innovation – Essence – based on views, modes, and team roles. Finally, the paper reports from an early experiment using SIRL and Essence and identifies further research....

  1. Architecture for Verifiable Software

    Science.gov (United States)

    Reinholtz, William; Dvorak, Daniel

    2005-01-01

    Verifiable MDS Architecture (VMA) is a software architecture that facilitates the construction of highly verifiable flight software for NASA s Mission Data System (MDS), especially for smaller missions subject to cost constraints. More specifically, the purpose served by VMA is to facilitate aggressive verification and validation of flight software while imposing a minimum of constraints on overall functionality. VMA exploits the state-based architecture of the MDS and partitions verification issues into elements susceptible to independent verification and validation, in such a manner that scaling issues are minimized, so that relatively large software systems can be aggressively verified in a cost-effective manner.

  2. Software Engineering Environment for Component-based Design of Embedded Software

    DEFF Research Database (Denmark)

    Guo, Yu

    2010-01-01

    by integrated model-driven development frameworks such as the Eclipse Modelling Framework, Graphical Modelling Framework, etc. Based on theoretical investigations and hands-on experiences, this thesis focuses on the practical aspects of building the COMDES software engineering environment on the Eclipse...... software technology, which is largely based on informal design methods and manual coding techniques. That is why it is necessary to develop new design methods and tools that will eventually help improve existing practices. These considerations have motivated the development of the framework -- Component...

  3. Software interface and data acquisition package for the LakeShore cryogenics vibrating sample magnetometer

    Energy Technology Data Exchange (ETDEWEB)

    O`Dell, B.H.

    1995-11-01

    A software package was developed to replace the software provided by LakeShore for their model 7300 vibrating sample magnetometer (VSM). Several problems with the original software`s functionality caused this group to seek a new software package. The new software utilizes many features that were unsupported in the LakeShore software, including a more functional step mode, point averaging mode, vector moment measurements, and calibration for field offset. The developed software interfaces the VSM through a menu driven graphical user interface, and bypasses the VSM`s on board processor leaving control of the VSM up to the software. The source code for this software is readily available to any one. By having the source, the experimentalist has full control of data acquisition and can add routines specific to their experiment.

  4. SOFTWARE MEASUREMENTS AND METRICS: ROLE IN EFFECTIVE SOFTWARE TESTING

    OpenAIRE

    Sheikh Umar Farooq; S. M. K. Quadri,; Nesar Ahmad

    2011-01-01

    Measurement has always been fundamental to the progress to any engineering discipline and software testing is no exception. Software metrics have been used in making quantitative/qualitative decisions as well as in risk assessment and reduction in software projects. In this paper we discuss software measurement and metrics and their fundamental role in software development life cycle. This paper focusing on software test metrics discusses their key role in software testing process and also cl...

  5. Who Owns Computer Software?

    Science.gov (United States)

    Branscomb, Anne Wells

    1995-01-01

    Discusses the protection of intellectual property as it applies to computer software and its impact on private enterprise and the public good. Highlights include the role of patents, copyrights, and trade secrets; some court cases; and recommendations for alternatives to the existing legal framework for protecting computer software. (KRN)

  6. Software evolution with XVCL

    DEFF Research Database (Denmark)

    Zhang, Weishan; Jarzabek, Stan; Zhang, Hongyu;

    2004-01-01

    This chapter introduces software evolution with XVCL (XML-based Variant Configuration Language), which is an XML-based metaprogramming technique. As the software evolves, a large number of variants may arise, especially whtn such kinds of evolutions are related to multiple platforms as shown in o...

  7. Measuring software technology

    Science.gov (United States)

    Agresti, W. W.; Card, D. N.; Church, V. E.; Page, G.; Mcgarry, F. E.

    1983-01-01

    Results are reported from a series of investigations into the effectiveness of various methods and tools used in a software production environment. The basis for the analysis is a project data base, built through extensive data collection and process instrumentation. The project profiles become an organizational memory, serving as a reference point for an active program of measurement and experimentation on software technology.

  8. Fastbus software progress

    International Nuclear Information System (INIS)

    The current status of the Fastbus software development program of the Fastbus Software Working Group is reported, and future plans are discussed. A package of Fastbus interface subroutines has been prepared as a proposed standard, language support for diagnostics and bench testing has been developed, and new documentation to help users find these resources and use them effectively is being written

  9. Marketing Mix del Software.

    Directory of Open Access Journals (Sweden)

    Yudith del Carmen Rodríguez Pérez

    2006-03-01

    Por ello, en este trabajo se define el concepto de producto software, se caracteriza al mismo y se exponen sus atributos de calidad. Además, se aborda la mezcla de marketing del software necesaria y diferente a la de otros productos para que este triunfe en el mercado.

  10. Measuring software design

    Science.gov (United States)

    1986-01-01

    An extensive series of studies of software design measures conducted by the Software Engineering Laboratory is described. Included are the objectives and results of the studies, the method used to perform the studies, and the problems encountered. The document should be useful to researchers planning similar studies as well as to managers and designers concerned with applying quantitative design measures.

  11. Threats to Bitcoin Software

    OpenAIRE

    Kateraas, Christian H

    2014-01-01

    Collect and analyse threat models to the Bitcoin ecosystem and its software. The create misuse case, attack trees, and sequence diagrams of the threats. Create a malicious client from the gathered threat models. Once the development of the client is complete, test the client and evaluate its performance. From this, assess the security of the Bitcoin software.

  12. Software business models and contexts for software innovation: key areas software business research

    OpenAIRE

    Käkölä, Timo

    2003-01-01

    This paper examines business, design, and product development aspects of software business models. Contexts of small and large companies for creating software innovations are also analysed. Finally, software business research is called for and an agenda for software business research is presented to better understand the dynamics of the software industry and help create and manage successful software-intensive ventures.

  13. Software quality in 1997

    Energy Technology Data Exchange (ETDEWEB)

    Jones, C. [Software Productivity Research, Inc., Burlington, MA (United States)

    1997-11-01

    For many years, software quality assurance lagged behind hardware quality assurance in terms of methods, metrics, and successful results. New approaches such as Quality Function Deployment (QFD) the ISO 9000-9004 standards, the SEI maturity levels, and Total Quality Management (TQM) are starting to attract wide attention, and in some cases to bring software quality levels up to a parity with manufacturing quality levels. Since software is on the critical path for many engineered products, and for internal business systems as well, the new approaches are starting to affect global competition and attract widespread international interest. It can be hypothesized that success in mastering software quality will be a key strategy for dominating global software markets in the 21st century.

  14. Developing Software Simulations

    Directory of Open Access Journals (Sweden)

    Tom Hall

    2007-06-01

    Full Text Available Programs in education and business often require learners to develop and demonstrate competence in specified areas and then be able to effectively apply this knowledge. One method to aid in developing a skill set in these areas is through the use of software simulations. These simulations can be used for learner demonstrations of competencies in a specified course as well as a review of the basic skills at the beginning of subsequent courses. The first section of this paper discusses ToolBook, the software used to develop our software simulations. The second section discusses the process of developing software simulations. The third part discusses how we have used software simulations to assess student knowledge of research design by providing simulations that allow the student to practice using SPSS and Excel.

  15. Software Requirements Management

    Directory of Open Access Journals (Sweden)

    Ali Altalbe

    2015-04-01

    Full Text Available Requirements are defined as the desired set of characteristics of a product or a service. In the world of software development, it is estimated that more than half of the failures are attributed towards poor requirements management. This means that although the software functions correctly, it is not what the client requested. Modern software requirements management methodologies are available to reduce the occur-rence of such incidents. This paper performs a review on the available literature in the area while tabulating possible methods of managing requirements. It also highlights the benefits of following a proper guideline for the requirements management task. With the introduction of specific software tools for the requirements management task, better software products are now been developed with lesser resources.

  16. Revisiting software ecosystems research

    DEFF Research Database (Denmark)

    Manikas, Konstantinos

    2016-01-01

    from evolving. We propose means for future research and the community to address them. Finally, our analysis shapes the view of the field having evolved outside the existing definitions of software ecosystems and thus propose the update of the definition of software ecosystems.......‘Software ecosystems’ is argued to first appear as a concept more than 10 years ago and software ecosystem research started to take off in 2010. We conduct a systematic literature study, based on the most extensive literature review in the field up to date, with two primarily aims: (a) to provide...... an updated overview of the field and (b) to document evolution in the field. In total, we analyze 231 papers from 2007 until 2014 and provide an overview of the research in software ecosystems. Our analysis reveals a field that is rapidly growing both in volume and empirical focus while becoming more mature...

  17. DIVERSIFICATION IN SOFTWARE ENGINEERING

    Directory of Open Access Journals (Sweden)

    Er.Kirtesh Jailia,

    2010-06-01

    Full Text Available In this paper we examine the factors that have promoted the iversification of software process models. The intention is to understand more clearly the problem-solving process in software engineering & try to find out the efficient way to manage the risk. A review of software process modeling is given first, followed by a discussion of process evaluation techniques. A taxonomy for categorizing process models, based on establishing decision criteria,is identified that can guide selecting the appropriate model from a set of alternatives on the basis of model characteristics and software project needs. We are proposing a model in this paper, for dealing with the diversification in software engineering.

  18. Software licenses: Stay honest!

    CERN Multimedia

    Computer Security Team

    2012-01-01

    Do you recall our article about copyright violation in the last issue of the CERN Bulletin, “Music, videos and the risk for CERN”? Now let’s be more precise. “Violating copyright” not only means the illegal download of music and videos, it also applies to software packages and applications.   Users must respect proprietary rights in compliance with the CERN Computing Rules (OC5). Not having legitimately obtained a program or the required licenses to run that software is not a minor offense. It violates CERN rules and puts the Organization at risk! Vendors deserve credit and compensation. Therefore, make sure that you have the right to use their software. In other words, you have bought the software via legitimate channels and use a valid and honestly obtained license. This also applies to “Shareware” and software under open licenses, which might also come with a cost. Usually, only “Freeware” is complete...

  19. Software safety hazard analysis

    Energy Technology Data Exchange (ETDEWEB)

    Lawrence, J.D. [Lawrence Livermore National Lab., CA (United States)

    1996-02-01

    Techniques for analyzing the safety and reliability of analog-based electronic protection systems that serve to mitigate hazards in process control systems have been developed over many years, and are reasonably well understood. An example is the protection system in a nuclear power plant. The extension of these techniques to systems which include digital computers is not well developed, and there is little consensus among software engineering experts and safety experts on how to analyze such systems. One possible technique is to extend hazard analysis to include digital computer-based systems. Software is frequently overlooked during system hazard analyses, but this is unacceptable when the software is in control of a potentially hazardous operation. In such cases, hazard analysis should be extended to fully cover the software. A method for performing software hazard analysis is proposed in this paper.

  20. Piezoelectrically-driven Thermoacoustic Refrigerator

    Science.gov (United States)

    Chinn, Daniel George

    Thermoacoustic refrigeration is an emerging refrigeration technology which does not require any moving parts or harmful refrigerants in its operation. This technology uses acoustic waves to pump heat across a temperature gradient. The vast majority of thermoacoustic refrigerators to date have used electromagnetic loudspeakers to generate the acoustic input. In this thesis, the design, construction, operation, and modeling of a piezoelectrically-driven thermoacoustic refrigerator are detailed. This refrigerator demonstrates the effectiveness of piezoelectric actuation in moving 0.3 W of heat across an 18 degree C temperature difference with an input power of 7.6 W. The performance characteristics of this class of thermoacoustic-piezoelectric refrigerators are modeled by using DeltaEC software and the predictions are experimentally validated. The obtained results confirm the validity of the developed model. Furthermore, the potential of piezoelectric actuation as effective means for driving thermoacoustic refrigerators is demonstrated as compared to the conventional electromagnetic loudspeakers which are heavy and require high actuation energy. The developed theoretical and experimental tools can serve as invaluable means for the design and testing of other piezoelectrically-driven thermoacoustic refrigerator configurations.

  1. Biological Threats

    Science.gov (United States)

    ... Workplace Plans School Emergency Plans Main Content Biological Threats Biological agents are organisms or toxins that can ... for Disease Control and Prevention . Before a Biological Threat Unlike an explosion, a biological attack may or ...

  2. Features of free software packages in flow cytometry: a comparison between four non-commercial software sources.

    Science.gov (United States)

    Sahraneshin Samani, Fazel; Moore, Jodene K; Khosravani, Pardis; Ebrahimi, Marzieh

    2014-08-01

    Flow cytometers designed to analyze large particles are enabling new applications in biology. Data analysis is a critical component of the process FCM. In this article we compare features of four free software packages including WinMDI, Cyflogic, Flowing software, and Cytobank.

  3. Improving collaboration by standardization efforts in systems biology.

    Science.gov (United States)

    Dräger, Andreas; Palsson, Bernhard Ø

    2014-01-01

    Collaborative genome-scale reconstruction endeavors of metabolic networks would not be possible without a common, standardized formal representation of these systems. The ability to precisely define biological building blocks together with their dynamic behavior has even been considered a prerequisite for upcoming synthetic biology approaches. Driven by the requirements of such ambitious research goals, standardization itself has become an active field of research on nearly all levels of granularity in biology. In addition to the originally envisaged exchange of computational models and tool interoperability, new standards have been suggested for an unambiguous graphical display of biological phenomena, to annotate, archive, as well as to rank models, and to describe execution and the outcomes of simulation experiments. The spectrum now even covers the interaction of entire neurons in the brain, three-dimensional motions, and the description of pharmacometric studies. Thereby, the mathematical description of systems and approaches for their (repeated) simulation are clearly separated from each other and also from their graphical representation. Minimum information definitions constitute guidelines and common operation protocols in order to ensure reproducibility of findings and a unified knowledge representation. Central database infrastructures have been established that provide the scientific community with persistent links from model annotations to online resources. A rich variety of open-source software tools thrives for all data formats, often supporting a multitude of programing languages. Regular meetings and workshops of developers and users lead to continuous improvement and ongoing development of these standardization efforts. This article gives a brief overview about the current state of the growing number of operation protocols, mark-up languages, graphical descriptions, and fundamental software support with relevance to systems biology. PMID:25538939

  4. Improving collaboration by standardization efforts in systems biology

    Directory of Open Access Journals (Sweden)

    Andreas eDräger

    2014-12-01

    Full Text Available Collaborative genome-scale reconstruction endeavors of metabolic networks would not be possible without a common, standardized formal representation of these systems. The ability to precisely define biological building blocks together with their dynamic behavior has even been considered a prerequisite for upcoming synthetic biology approaches.Driven by the requirements of such ambitious research goals, standardization itself has become an active field of research on nearly all levels of granularity in biology.In addition to the originally envisaged exchange of computational models and tool interoperability, new standards have been suggested for an unambiguous graphical display of biological phenomena, to annotate, archive, as well as to rank models, and to describe execution and the outcomes of simulation experiments. The spectrum now even covers the interaction of entire neurons in the brain, three-dimensional motions, and the description of pharmacometric studies.Thereby, the mathematical description of systems and approaches for their (repeated simulation are clearly separated from each other and also from their graphical representation. Minimum information definitions constitute guidelines and common operation protocols in order to ensure reproducibility of findings and a unified knowledge representation.Central database infrastructures have been established that provide the scientific community with persistent links from model annotations to on-line resources. A rich variety of open-source software tools thrives for all data formats, often supporting a multitude of programming languages. Regular meetings and workshops of developers and users lead to continuous improvement and ongoing development of these standardization efforts.This article gives a brief overview about the current state of the growing number of operation protocols, markup languages, graphical descriptions, and fundamental software support with relevance to systems biology.

  5. Power laws in software systems

    OpenAIRE

    Tonelli, Roberto

    2012-01-01

    The main topic of my PhD has been the study of power laws in software systems within the perspective of describing software quality. My PhD research contributes to a recent stream of studies in software engineering, where the investigation of power laws in software systems has become widely popular in recent years, since they appear on an incredible variety of different software quantities and properties, like, for example, software metrics, software faults, refactoring, Java byte-code,...

  6. Software Developers’ Perceptions of Productivity

    OpenAIRE

    Meyer, André; Fritz, Thomas; Murphy, Gail C.; Zimmermann, Thomas

    2014-01-01

    The better the software development community becomes at creating software, the more software the world seems to demand. Although there is a large body of research about measuring and investigating productivity from an organizational point of view, there is a paucity of research about how software developers, those at the front-line of software construction, think about, assess and try to improve their productivity. To investigate software developers' perceptions of software development produ...

  7. Survey of Traceability Approaches in Model-Driven Engineering

    OpenAIRE

    Galvao Lourenco da Silva, I.; Göknil, A.

    2007-01-01

    Models have been used in various engineering fields to help managing complexity and represent information in different abstraction levels, according to specific notations and stakeholder's viewpoints. Model-Driven Engineering (MDE) gives the basic principles for the use of models as primary artefacts throughout the software development phases and presents characteristics that simplify the engineering of software in various domains, such as Enterprise Computing Systems. Hence, for its successf...

  8. Quality management using model-driven engineering: an overview

    OpenAIRE

    Ruiz-Rube, Iván; Escalona, María José

    2014-01-01

    Quality Management (QM) is one of the critical points of any software development process. In recent years, several proposals have emerged on this issue, mainly with regard to maturity models, quality standards and best practices collections. Besides, Model Driven Engineering (MDE) aims to build software systems through the construction and transformation of models. However, MDE might be used for other different tasks. In this poster, we summarize the main contributions abou...

  9. Model Driven Management of Complex Systems: Implementing the Macroscope's vision

    OpenAIRE

    Barbero, Mikael; Bézivin, Jean

    2008-01-01

    Several years ago, first generation model driven engineering (MDE) tools focused on generating code from high-level platform-independent abstract descriptions. Since then, the target scope of MDE has much broadened and now addresses for example testing, verification, measurement, tool interoperability, software evolution, and many more hard issues in software engineering. In this paper we study the applicability of MDE to another difficult problem: the management of complex systems. We show h...

  10. Robotically Driven Architectural Production

    OpenAIRE

    Bier, H.H.

    2014-01-01

    Robotically driven architectural production advances seamless, computer-numerically controlled (CNC) and robotically supported design to production and operation processes enabling im-plementation of robotically driven buildings from conceptualisation to use. It enables production of free-formed, heterogeneous, optimized structures in order to address specific requirements in terms of properties (density, consistency, rigidity, etc.) and behaviours (re-configurability, responsiveness, etc.) i...

  11. LDUA software custodian's notebook

    International Nuclear Information System (INIS)

    This plan describes the activities to be performed and controls to be applied to the process of specifying, obtaining, and qualifying the control and data acquisition software for the Light Duty Utility Arm (LDUA) System. It serves the purpose of a software quality assurance plan, a verification and validation plan, and a configuration management plan. This plan applies to all software that is an integral part of the LDUA control and data acquisition system, that is, software that is installed in the computers that are part of the LDUA system as it is deployed in the field. This plan applies to the entire development process, including: requirements; design; implementation; and operations and maintenance. This plan does not apply to any software that is not integral with the LDUA system. This plan has-been prepared in accordance with WHC-CM-6-1 Engineering Practices, EP-2.1; WHC-CM-3-10 Software Practices; and WHC-CM-4-2, QR 19.0, Software Quality Assurance Requirements

  12. Software configuration management plan for the Hanford site technical database

    Energy Technology Data Exchange (ETDEWEB)

    GRAVES, N.J.

    1999-05-10

    The Hanford Site Technical Database (HSTD) is used as the repository/source for the technical requirements baseline and programmatic data input via the Hanford Site and major Hanford Project Systems Engineering (SE) activities. The Hanford Site SE effort has created an integrated technical baseline for the Hanford Site that supports SE processes at the Site and project levels which is captured in the HSTD. The HSTD has been implemented in Ascent Logic Corporation (ALC) Commercial Off-The-Shelf (COTS) package referred to as the Requirements Driven Design (RDD) software. This Software Configuration Management Plan (SCMP) provides a process and means to control and manage software upgrades to the HSTD system.

  13. Hardware-Software Co-Simulation for SOC Functional Verification

    Institute of Scientific and Technical Information of China (English)

    YAN Ying-jian; LIU Ming-ye

    2005-01-01

    A hardware-software co-simulation method for system on chip (SOC) design is discussed. It is based on an instruction set simulator (ISS) and an event-driven hardware simulator, and a bus interface model that is described in C language provides the interface between the two. The bus interface model and the ISS are linked into a singleton program the software simulator, which communicate with the hardware simulator through Windows sockets. The implementation of the bus interface model and the synchronization between hardware and software simulator are discussed in detail. Co-simulation control of the hardware simulator is also discussed.

  14. Software quality assurance handbook

    Energy Technology Data Exchange (ETDEWEB)

    1990-09-01

    There are two important reasons for Software Quality Assurance (SQA) at Allied-Signal Inc., Kansas City Division (KCD): First, the benefits from SQA make good business sense. Second, the Department of Energy has requested SQA. This handbook is one of the first steps in a plant-wide implementation of Software Quality Assurance at KCD. The handbook has two main purposes. The first is to provide information that you will need to perform software quality assurance activities. The second is to provide a common thread to unify the approach to SQA at KCD. 2 figs.

  15. Advanced fingerprint verification software

    Science.gov (United States)

    Baradarani, A.; Taylor, J. R. B.; Severin, F.; Maev, R. Gr.

    2016-05-01

    We have developed a fingerprint software package that can be used in a wide range of applications from law enforcement to public and private security systems, and to personal devices such as laptops, vehicles, and door- locks. The software and processing units are a unique implementation of new and sophisticated algorithms that compete with the current best systems in the world. Development of the software package has been in line with the third generation of our ultrasonic fingerprinting machine1. Solid and robust performance is achieved in the presence of misplaced and low quality fingerprints.

  16. Guide to software export

    CERN Document Server

    Philips, Roger A

    2014-01-01

    An ideal reference source for CEOs, marketing and sales managers, sales consultants, and students of international marketing, Guide to Software Export provides a step-by-step approach to initiating or expanding international software sales. It teaches you how to examine critically your candidate product for exportability; how to find distributors, agents, and resellers abroad; how to identify the best distribution structure for export; and much, much more!Not content with providing just the guidelines for setting up, expanding, and managing your international sales channels, Guide to Software

  17. Global Software Engineering

    DEFF Research Database (Denmark)

    Ebert, Christof; Kuhrmann, Marco; Prikladnicki, Rafael

    2016-01-01

    SOFTWARE, LIKE ALL industry products, is the result of complex multinational supply chains with many partners from concept to development to production and maintenance. Global software engineering (GSE), IT outsourcing, and business process outsourcing during the past decade have showed growth...... rates of 10 to 20 percent per year. This instalment of Practitioner’s Digest summarizes experiences and guidance from industry to facilitate knowledge and technology transfer for GSE. It’s based on industry feedback from the annual IEEE International Conference on Global Software Engineering, which had...

  18. CNEOST Control Software System

    Science.gov (United States)

    Wang, Xin; Zhao, Hai-bin; Xia, Yan; Lu, Hao; Li, Bin

    2016-01-01

    In 2013, CNEOST (China Near Earth Object Survey Telescope) adapted its hardware system for the new CCD camera. Based on the new system architecture, the control software is re-designed and implemented. The software system adopts the messaging mechanism based on the WebSocket protocol, and possesses good flexibility and expansibility. The user interface based on the responsive web design has realized the remote observations under both desktop and mobile devices. The stable operation of the software system has greatly enhanced the operation efficiency while reducing the complexity, and has also made a successful attempt for the future system design of telescope and telescope cloud.

  19. Systematic Software Development

    DEFF Research Database (Denmark)

    Kuhrmann, Marco; Méndez Fernández, Daniel

    2015-01-01

    The speed of innovation and the global allocation of resources to accelerate development or to reduce cost put pressure on the software industry. In the global competition, especially so-called high-price countries have to present arguments why the higher development cost is justified and what...... project- and quality management and their implementation in practice. So far, our results suggest that the necessity for a systematic software development is well recognized, while software development still follows an ad-hoc rather than a systematized style. Our results provide initial findings, which we...

  20. Speakeasy software development

    Science.gov (United States)

    Baskinger, Patricia J.; Ozarow, Larry; Chruscicki, Mary C.

    1993-08-01

    The Speakeasy Software Development Project had three primary objectives. The first objective was to perform Independent Verification and Validation (IV & V) of the software and documentation associated with the signal processor being developed by Hazeltine and TRW under the Speakeasy program. The IV & V task also included an analysis and assessment of the ability of the signal processor software to provide LPI communications functions. The second objective was to assist in the enhancement and modification of an existing Rome Lab signal processor workstation. Finally, TASC developed project management support tools and provided program management support to the Speakeasy Program Office.

  1. Orbit Software Suite

    Science.gov (United States)

    Osgood, Cathy; Williams, Kevin; Gentry, Philip; Brownfield, Dana; Hallstrom, John; Stuit, Tim

    2012-01-01

    Orbit Software Suite is used to support a variety of NASA/DM (Dependable Multiprocessor) mission planning and analysis activities on the IPS (Intrusion Prevention System) platform. The suite of Orbit software tools (Orbit Design and Orbit Dynamics) resides on IPS/Linux workstations, and is used to perform mission design and analysis tasks corresponding to trajectory/ launch window, rendezvous, and proximity operations flight segments. A list of tools in Orbit Software Suite represents tool versions established during/after the Equipment Rehost-3 Project.

  2. Biochemical software: Carbohydrates on Laboratory

    Directory of Open Access Journals (Sweden)

    D.N. Heidrich

    2005-07-01

    Full Text Available Educators around  the  world  are  being  challenged  to  develop  and  design  better and  more  effective strategies for student learning  using a variety  of modern  resources.  In this  present  work, an educa- tional  hypermedia  software  was constructed as a support tool to biochemistry teaching.  Occurrence, structure, main  characteristics and  biological  function  of the  biomolecule  Carbohydrates were pre- sented  through  modules.  The  software was developed  using concept  maps,  ISIS-Draw,  and  FLASH- MX animation program.  The chapter  Carbohydrates on Laboratory illustrates experimental methods of carbohydrates characterization, through  animation of a laboratory scenery.   The  subject was de- veloped showing reactions  as Bial, Benedict, Selliwanoff, Barfoed, Phenol  Sulphuric,  and Iodines, and also enzymatic  reactions  as glucose oxidase and amylase.  There are also links with short texts  in order to help the understanding of the contents  and principles of laboratory practice  as well as background reactions. Application of the software to undergraduate students and high school teachers  showed an excellent  acceptance.   All of them  considered  the  software  a very good learning  tool.  Both  teachers and students welcomed this program  as it is more flexible, and allows the learning in a more individual rhythm. In addition, application of the software would be suitable  to a more effective learning  and it is less expensive than conventional experimental teaching.

  3. Software Quality Attribute Analysis by Architecture Reconstruction (SQUA3RE)

    NARCIS (Netherlands)

    Stormer, C.

    2007-01-01

    Software Quality Attribute Analysis by Architecture Reconstruction (SQUA3RE) is a method that fosters a goal-driven process to evaluate the impact of what-if scenarios on existing systems. The method is partitioned into SQA2 and ARE. The SQA2 part provides the analysis models that can be used for q

  4. Improving Reuse in Software Development for the Life Sciences

    Science.gov (United States)

    Iannotti, Nicholas V.

    2013-01-01

    The last several years have seen unprecedented advancements in the application of technology to the life sciences, particularly in the area of data generation. Novel scientific insights are now often driven primarily by software development supporting new multidisciplinary and increasingly multifaceted data analysis. However, despite the…

  5. Hardware Ports - Getting Rid of Sandboxed Modelled Software

    NARCIS (Netherlands)

    Bezemer, Maarten M.; Broenink, Jan F.; Welch, P.H.; Barnes, F.R.M.; Broenink, J.F.; Chalmers, K.; Gibson-Robinson, T.; Ivimey-Cook, R.; McEwan, A.A.; Pedersen, J.B.; Sampson, A,; Smith, M.L.

    2014-01-01

    Software that is used to control machines and robots must be predictable and reliable. Model-Driven Design (MDD) techniques are used to comply with both the technical and business needs. This paper introduces a CSP meta-model that is suitable for these MDD techniques. The meta-model describes the st

  6. The Software Patent Debate

    OpenAIRE

    Guadamuz, Andres

    2006-01-01

    The paper discusses the proposed European Directive on the Patentability of Computer-Implemented Inventions and the subsequent debate that followed. Do software patents - as argued by policymakers' - result in increased innovation?

  7. Managing Software Process Evolution

    DEFF Research Database (Denmark)

    This book focuses on the design, development, management, governance and application of evolving software processes that are aligned with changing business objectives, such as expansion to new domains or shifting to global production. In the context of an evolving business world, it examines...... the complete software process lifecycle, from the initial definition of a product to its systematic improvement. In doing so, it addresses difficult problems, such as how to implement processes in highly regulated domains or where to find a suitable notation system for documenting processes, and provides...... essential insights and tips to help readers manage process evolutions. And last but not least, it provides a wealth of examples and cases on how to deal with software evolution in practice. Reflecting these topics, the book is divided into three parts. Part 1 focuses on software business transformation...

  8. eSoftwareList

    Data.gov (United States)

    US Agency for International Development — USAID Software Database reporting tool created in Oracle Application Express (APEX). This version provides read only access to a database view of the JIRA SAR...

  9. Project Portfolio Management Software

    OpenAIRE

    Paul POCATILU

    2006-01-01

    In order to design a methodology for the development of project portfolio management (PPM) applications, the existing applications have to be studied. This paper describes the main characteristics of the leading project portfolio management software applications.

  10. Software for nuclear spectrometry

    International Nuclear Information System (INIS)

    The Advisory Group Meeting (AGM) on Software for Nuclear Spectrometry was dedicated to review the present status of software for nuclear spectrometry and to advise on future activities in this field. Because similar AGM and consultant's meetings had been held in the past; together with an attempt to get more streamlined, this AGM was devoted to the specific field of software for gamma ray spectrometry. Nevertheless, many of the issues discussed and the recommendations made are of general concern for any software on nuclear spectrometry. The report is organized by sections. The 'Summary' gives conclusions and recommendations adopted at the AGM. These conclusions and recommendations resulted from the discussions held during and after presentations of the scientific and technical papers. These papers are reported here in their integral form in the following Sections

  11. Core Flight Software Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The mission of the CFS project is to provide reusable software in support of human space exploration programs.   The top-level technical approach to...

  12. Banking Software Applications Security

    Directory of Open Access Journals (Sweden)

    Ioan Alexandru Bubu

    2015-03-01

    Full Text Available Computer software products are among the most complex artifacts, if not the most complex artifacts mankind has created. Securing those artifacts against intelligent attackers who try to exploit flaws in software design and construct is a great challenge too.The purpose of this paper is to introduce a secure alternative to banking software applications that are currently in use. This new application aims to cover most of the well-known vulnerabilities that plague the majority of current software.First we will take a quick look at current security methods that are in use, and a few known vulnerabilities. After this, we will discuss the security measures implemented in my application, and finally, we will the results of implementing them.

  13. ACS: ALMA Common Software

    Science.gov (United States)

    Chiozzi, Gianluca; Šekoranja, Matej

    2013-02-01

    ALMA Common Software (ACS) provides a software infrastructure common to all ALMA partners and consists of a documented collection of common patterns and components which implement those patterns. The heart of ACS is based on a distributed Component-Container model, with ACS Components implemented as CORBA objects in any of the supported programming languages. ACS provides common CORBA-based services such as logging, error and alarm management, configuration database and lifecycle management. Although designed for ALMA, ACS can and is being used in other control systems and distributed software projects, since it implements proven design patterns using state of the art, reliable technology. It also allows, through the use of well-known standard constructs and components, that other team members whom are not authors of ACS easily understand the architecture of software modules, making maintenance affordable even on a very large project.

  14. Advanced Software Protection Now

    CERN Document Server

    Bendersky, Diego; Notarfrancesco, Luciano; Sarraute, Carlos; Waissbein, Ariel

    2010-01-01

    Software digital rights management is a pressing need for the software development industry which remains, as no practical solutions have been acclamaimed succesful by the industry. We introduce a novel software-protection method, fully implemented with today's technologies, that provides traitor tracing and license enforcement and requires no additional hardware nor inter-connectivity. Our work benefits from the use of secure triggers, a cryptographic primitive that is secure assuming the existence of an ind-cpa secure block cipher. Using our framework, developers may insert license checks and fingerprints, and obfuscate the code using secure triggers. As a result, this rises the cost that software analysis tools have detect and modify protection mechanisms. Thus rising the complexity of cracking this system.

  15. Spreadsheet Auditing Software

    CERN Document Server

    Nixon, David

    2010-01-01

    It is now widely accepted that errors in spreadsheets are both common and potentially dangerous. Further research has taken place to investigate how frequently these errors occur, what impact they have, how the risk of spreadsheet errors can be reduced by following spreadsheet design guidelines and methodologies, and how effective auditing of a spreadsheet is in the detection of these errors. However, little research exists to establish the usefulness of software tools in the auditing of spreadsheets. This paper documents and tests office software tools designed to assist in the audit of spreadsheets. The test was designed to identify the success of software tools in detecting different types of errors, to identify how the software tools assist the auditor and to determine the usefulness of the tools.

  16. Software Design Analyzer System

    Science.gov (United States)

    Tausworthe, R. C.

    1985-01-01

    CRISP80 software design analyzer system a set of programs that supports top-down, hierarchic, modular structured design, and programing methodologies. CRISP80 allows for expression of design as picture of program.

  17. Software Patent and its Impact on Software Innovation in Japan

    OpenAIRE

    Motohashi, Kazuyuki

    2009-01-01

    In Japan, the software patent system has been reformed and now software has become a patentable subject matter. In this paper, this pro-patent shift on software is surveyed and its impact on software innovation is analyzed. Before the 1990's, inventions related to software could not be patented by themselves, but they could be applied when combined with hardware related inventions. Therefore, integrated electronics firms used to be the major software patent applicants. However, during the per...

  18. NEW APPROACH FOR SOFTWARE PROCESSES REUSING BASED ON SOFTWARE ARCHITECTURES

    OpenAIRE

    Aoussat, Fadila; Ahmed-Nacer, Mohamed; Oussalah, Mourad Chabane

    2010-01-01

    International audience; This paper deals with reusing of software process models. Based on the insufficiencies of existing software process reusing approaches (limited reusability of the software process components), we propose a new approach that promotes a large reuse of existing proven software process models even not oriented components. Our approach is based on two steps: we use domain ontology to capitalize the software process knowledge and we handle the inferred knowledge as software ...

  19. Software Project Documentation - An Essence of Software Development

    OpenAIRE

    Vikas S. Chomal; Dr. Jatinderkumar R. Saini

    2015-01-01

    Software documentation is a critical attribute of both software projects and software engineering in general. Documentation is considered as a media of communication among the parties involved during software development as well the one who will be using the software. It consists of written particulars concerning software specifications as well as what it does, in which manner it accomplishes the specified details and even how to exercise it. In this paper, we tried to focus on the role of do...

  20. A Simple Complexity Measurement for Software Verification and Software Testing

    OpenAIRE

    Cheng, Zheng; Monahan, Rosemary; Power, James F.

    2012-01-01

    In this paper, we used a simple metric (i.e. Lines of Code) to measure the complexity involved in software verification and software testing. The goal is then, to argue for software verification over software testing, and motivate a discussion of how to reduce the complexity involved in software verification. We propose to reduce this complexity by translating the software to a simple intermediate representation which can be verified using an efficient verifier, such as Boog...

  1. Software Architecture: Architecture Constraints

    OpenAIRE

    Tibermacine, Chouki

    2014-01-01

    International audience In this chapter, we introduce an additional, yet essential, concept in describing software architectures : architecture constraints. We explain the precise role of these entities and their importance in object-oriented, component-based or service-oriented software engi-neering. We then describe the way in which they are specified and interpreted. An architect can define architecture constraints and then associate them to architectural descriptions to limit their stru...

  2. Occupational radiation protection software

    International Nuclear Information System (INIS)

    This paper presents a reflection on the basic essentials of a Radiation Work Permit (RWP). Based on the latest WANO Recommendations, this paper considers the RWP as a complete process rather than a simple administrative procedure. This process is implemented via software which is also presented in this paper. The software has been designed to achieve the following objectives: - To configure the radiological map of the plant. To plan radiological surveillance, to input data, to update radiological signposting and mandatory protective clothing in each area of the station. All this information can be checked from any personnel computer connected to a network. - To collect radiological data by means of a palmtop (PDA) and to upload it to a personnel computer, thereby speeding up the job and reducing human errors. - To implement the RWP by allowing on-line consultation of the permitted individual doses of the workers and the planned collective dose for each job. The software also supplies the radiological information to the workers. - To collect and arrange pictures, maps and sketches of equipment placed in rooms or in areas of the plant. - To allow the software to be used in real time from different workstations. - High reliability and speed of working. - Flexible data enquiry. The software provides a number of standard data enquiries such as numbers of workers on each job and their individual dose received...etc. It also allows data to be exported to other well-known software applications such as Excel and Access for further data analysis. The software has been designed by radiation protection professionals and developed by computer programmers who were integrated into the radiological work environment. The software would fulfill Occupational Radiation Protection Department requirements. (author)

  3. Deprogramming Large Software Systems

    OpenAIRE

    Coppel, Yohann; Candea, George

    2008-01-01

    Developers turn ideas, designs and patterns into source code, then compile the source code into executables. Decompiling turns executables back into source code, and deprogramming turns code back into designs and patterns. In this paper we introduce DeP, a tool for deprogramming software systems. DeP abstracts code into a dependency graph and mines this graph for patterns. It also gives programmers visual means for manipulating the program. We describe DeP's use in several software engineerin...

  4. SDN : Software defined networks

    OpenAIRE

    Wiklund, Petter

    2014-01-01

    This report is a specialization in Software defined networking. SDN really comes to revolutionize the industry and it’s under constant development. But is the technology ready to be launched into operation yet? The report would initially involve a number of problems that today's network technology is facing. It then follows a deeper description of what this software-based networking technology really is and how it works. Further, the technique is being tested in a lab assignment, using a prog...

  5. Personalised continuous software engineering

    OpenAIRE

    Papatheocharous, Efi; Belk, Marios; Nyfjord, Jaana; Germanakos, Panagiotis; Samaras, George

    2014-01-01

    This work describes how human factors can influence continuous software engineering. The reasoning begins from the Agile Manifesto promoting individuals and interactions over processes and tools. The organisational need to continuously develop, release and learn from software development in rapid cycles requires empowered and self-organised agile teams. However, these teams are formed without necessarily considering the members’ individual characteristics towards effective teamwork, from the ...

  6. Engineering and Software Engineering

    Science.gov (United States)

    Jackson, Michael

    The phrase ‘software engineering' has many meanings. One central meaning is the reliable development of dependable computer-based systems, especially those for critical applications. This is not a solved problem. Failures in software development have played a large part in many fatalities and in huge economic losses. While some of these failures may be attributable to programming errors in the narrowest sense—a program's failure to satisfy a given formal specification—there is good reason to think that most of them have other roots. These roots are located in the problem of software engineering rather than in the problem of program correctness. The famous 1968 conference was motivated by the belief that software development should be based on “the types of theoretical foundations and practical disciplines that are traditional in the established branches of engineering.” Yet after forty years of currency the phrase ‘software engineering' still denotes no more than a vague and largely unfulfilled aspiration. Two major causes of this disappointment are immediately clear. First, too many areas of software development are inadequately specialised, and consequently have not developed the repertoires of normal designs that are the indispensable basis of reliable engineering success. Second, the relationship between structural design and formal analytical techniques for software has rarely been one of fruitful synergy: too often it has defined a boundary between competing dogmas, at which mutual distrust and incomprehension deprive both sides of advantages that should be within their grasp. This paper discusses these causes and their effects. Whether the common practice of software development will eventually satisfy the broad aspiration of 1968 is hard to predict; but an understanding of past failure is surely a prerequisite of future success.

  7. Mining unstructured software data

    OpenAIRE

    Bacchelli, Alberto; Lanza, Michele

    2013-01-01

    Our thesis is that the analysis of unstructured data supports software understanding and evolution analysis, and complements the data mined from structured sources. To this aim, we implemented the necessary toolset and investigated methods for exploring, exposing, and exploiting unstructured data.To validate our thesis, we focused on development email data. We found two main challenges in using it to support program comprehension and software development: The disconnection between emai...

  8. Creative Software Engineering

    OpenAIRE

    Hooper, Clare J.; Millard, David E.

    2010-01-01

    Software engineering is traditionally seen as very structured and methodical. However, it often involves creative steps: consider requirements analysis, architecture engineering and GUI design. This poster describes three existing software engineering methods which include creative steps, alongside a method called 'experience deconstruction'. Deconstruction, which also includes a creative step, is used to help understand user experiences and re-provide these experiences in new contexts.

  9. Transformational Leadershipin Software Projects

    OpenAIRE

    MOUSAVIKHAH, MARYAM

    2013-01-01

    Lack of management in software projects is among the most important reasons for the failure of this kind of projects. Considering this fact, in addition to high rate of IS (Information System) projects’ failure, and the lack of leadership studies in IS field, it is necessary to pay more attention to the concept of leadership in software projects. Transformational leadership as one of the most popular leadership theories, although might bring specific advantages for this kind of projects, has ...

  10. Towards research on software cybernetics

    OpenAIRE

    Cai, KY; Chen, TY; Tse, TH

    2002-01-01

    Software cybernetics is a newly proposed area in software engineering. It makes better use of the interplay between control theory/engineering and software engineering. In this paper, we look into the research potentials of this emerging area.

  11. Intrinsic Motivation in Open Source Software Development

    DEFF Research Database (Denmark)

    Bitzer, J.; W., Schrettl,; Schröder, Philipp

    2004-01-01

    This papers sheds light on the puzzling evidence that even though open source software (OSS) is a public good, it is developed for free by highly qualified, young and motivated individuals, and evolves at a rapid pace. We show that once OSS development is understood as the private provision...... of a public good, these features emerge quite naturally. We adapt a dynamic private-provision-of-public-goods model to reflects key aspects of the OSS phenomenon. In particular, instead of relying on extrinsic motives for programmers (e.g. signaling) the present model is driven by intrinsic motives of OSS...

  12. Domain specific software architectures: Command and control

    Science.gov (United States)

    Braun, Christine; Hatch, William; Ruegsegger, Theodore; Balzer, Bob; Feather, Martin; Goldman, Neil; Wile, Dave

    1992-01-01

    GTE is the Command and Control contractor for the Domain Specific Software Architectures program. The objective of this program is to develop and demonstrate an architecture-driven, component-based capability for the automated generation of command and control (C2) applications. Such a capability will significantly reduce the cost of C2 applications development and will lead to improved system quality and reliability through the use of proven architectures and components. A major focus of GTE's approach is the automated generation of application components in particular subdomains. Our initial work in this area has concentrated in the message handling subdomain; we have defined and prototyped an approach that can automate one of the most software-intensive parts of C2 systems development. This paper provides an overview of the GTE team's DSSA approach and then presents our work on automated support for message processing.

  13. Professional Ethics of Software Engineers: An Ethical Framework.

    Science.gov (United States)

    Lurie, Yotam; Mark, Shlomo

    2016-04-01

    The purpose of this article is to propose an ethical framework for software engineers that connects software developers' ethical responsibilities directly to their professional standards. The implementation of such an ethical framework can overcome the traditional dichotomy between professional skills and ethical skills, which plagues the engineering professions, by proposing an approach to the fundamental tasks of the practitioner, i.e., software development, in which the professional standards are intrinsically connected to the ethical responsibilities. In so doing, the ethical framework improves the practitioner's professionalism and ethics. We call this approach Ethical-Driven Software Development (EDSD), as an approach to software development. EDSD manifests the advantages of an ethical framework as an alternative to the all too familiar approach in professional ethics that advocates "stand-alone codes of ethics". We believe that one outcome of this synergy between professional and ethical skills is simply better engineers. Moreover, since there are often different software solutions, which the engineer can provide to an issue at stake, the ethical framework provides a guiding principle, within the process of software development, that helps the engineer evaluate the advantages and disadvantages of different software solutions. It does not and cannot affect the end-product in and of-itself. However, it can and should, make the software engineer more conscious and aware of the ethical ramifications of certain engineering decisions within the process. PMID:26047575

  14. Professional Ethics of Software Engineers: An Ethical Framework.

    Science.gov (United States)

    Lurie, Yotam; Mark, Shlomo

    2016-04-01

    The purpose of this article is to propose an ethical framework for software engineers that connects software developers' ethical responsibilities directly to their professional standards. The implementation of such an ethical framework can overcome the traditional dichotomy between professional skills and ethical skills, which plagues the engineering professions, by proposing an approach to the fundamental tasks of the practitioner, i.e., software development, in which the professional standards are intrinsically connected to the ethical responsibilities. In so doing, the ethical framework improves the practitioner's professionalism and ethics. We call this approach Ethical-Driven Software Development (EDSD), as an approach to software development. EDSD manifests the advantages of an ethical framework as an alternative to the all too familiar approach in professional ethics that advocates "stand-alone codes of ethics". We believe that one outcome of this synergy between professional and ethical skills is simply better engineers. Moreover, since there are often different software solutions, which the engineer can provide to an issue at stake, the ethical framework provides a guiding principle, within the process of software development, that helps the engineer evaluate the advantages and disadvantages of different software solutions. It does not and cannot affect the end-product in and of-itself. However, it can and should, make the software engineer more conscious and aware of the ethical ramifications of certain engineering decisions within the process.

  15. Software bibliotecario abierto y gratuito

    OpenAIRE

    Lencinas, Verónica

    2001-01-01

    Free software, known also as Open Source software, has a number of advantages for implementation in libraries. It offers free and full source code of the software that can be used to correct errors, modify it and integrate with other programs. Because of these advantages, free software offers better opportunities for libraries as closed software. Library management systems will soon be available and can be a real alternative to commercial software. The methodology used to develop the open sof...

  16. Management aspects of software maintenance

    OpenAIRE

    Henderson, Brian J.; Sullivan, Brenda J.

    1984-01-01

    Approved for public release; distribution is unlimited The Federal government depends upon software systems to fulfill its missions. These software systems must be maintained and improved to continue to meet the growing demands placed on them. The process of software maintenance and improvement may be called "software evolution". The software manager must be educated in the complex nature cf soft- ware maintenance to be able to properly evaluate and manage the software maintenance effort. ...

  17. Software Engineering Reviews and Audits

    CERN Document Server

    Summers, Boyd L

    2011-01-01

    Accurate software engineering reviews and audits have become essential to the success of software companies and military and aerospace programs. These reviews and audits define the framework and specific requirements for verifying software development efforts. Authored by an industry professional with three decades of experience, Software Engineering Reviews and Audits offers authoritative guidance for conducting and performing software first article inspections, and functional and physical configuration software audits. It prepares readers to answer common questions for conducting and perform

  18. Computing and software

    Directory of Open Access Journals (Sweden)

    White, G. C.

    2004-06-01

    Full Text Available The reality is that the statistical methods used for analysis of data depend upon the availability of software. Analysis of marked animal data is no different than the rest of the statistical field. The methods used for analysis are those that are available in reliable software packages. Thus, the critical importance of having reliable, up–to–date software available to biologists is obvious. Statisticians have continued to develop more robust models, ever expanding the suite of potential analysis methods available. But without software to implement these newer methods, they will languish in the abstract, and not be applied to the problems deserving them. In the Computers and Software Session, two new software packages are described, a comparison of implementation of methods for the estimation of nest survival is provided, and a more speculative paper about how the next generation of software might be structured is presented. Rotella et al. (2004 compare nest survival estimation with different software packages: SAS logistic regression, SAS non–linear mixed models, and Program MARK. Nests are assumed to be visited at various, possibly infrequent, intervals. All of the approaches described compute nest survival with the same likelihood, and require that the age of the nest is known to account for nests that eventually hatch. However, each approach offers advantages and disadvantages, explored by Rotella et al. (2004. Efford et al. (2004 present a new software package called DENSITY. The package computes population abundance and density from trapping arrays and other detection methods with a new and unique approach. DENSITY represents the first major addition to the analysis of trapping arrays in 20 years. Barker & White (2004 discuss how existing software such as Program MARK require that each new model’s likelihood must be programmed specifically for that model. They wishfully think that future software might allow the user to combine

  19. Radiobiological modelling with MarCell software

    Energy Technology Data Exchange (ETDEWEB)

    Hasan, J.S.; Jones, T.D.

    1996-10-01

    Jones introduced a bone marrow radiation cell kinetics model with great potential for application in the fields of health physics, radiation research, and medicine. However, until recently, only the model developers have been able to apply it because of the complex array of biological and physical assignments needed for evaluation of a particular radiation exposure protocol. The purpose of this article is to illustrate the use of MarCell (MARrow CELL Kinetics) software for MS-DOS, a user-friendly computer implementation of that mathematical model that allows almost anyone with an elementary knowledge of radiation physics and/or medical procedures to apply the model. A hands-on demonstration of the software will be given by guiding the user through evaluation of a medical total body irradiation protocol and a nuclear fallout scenario. A brief overview of the software is given in the Appendix.

  20. SLIMarray: Lightweight software for microarray facility management

    Directory of Open Access Journals (Sweden)

    Marzolf Bruz

    2006-10-01

    Full Text Available Abstract Background Microarray core facilities are commonplace in biological research organizations, and need systems for accurately tracking various logistical aspects of their operation. Although these different needs could be handled separately, an integrated management system provides benefits in organization, automation and reduction in errors. Results We present SLIMarray (System for Lab Information Management of Microarrays, an open source, modular database web application capable of managing microarray inventories, sample processing and usage charges. The software allows modular configuration and is well suited for further development, providing users the flexibility to adapt it to their needs. SLIMarray Lite, a version of the software that is especially easy to install and run, is also available. Conclusion SLIMarray addresses the previously unmet need for free and open source software for managing the logistics of a microarray core facility.

  1. The NOvA software testing framework

    Science.gov (United States)

    Tamsett, M.; C Group

    2015-12-01

    The NOvA experiment at Fermilab is a long-baseline neutrino experiment designed to study vε appearance in a vμ beam. NOvA has already produced more than one million Monte Carlo and detector generated files amounting to more than 1 PB in size. This data is divided between a number of parallel streams such as far and near detector beam spills, cosmic ray backgrounds, a number of data-driven triggers and over 20 different Monte Carlo configurations. Each of these data streams must be processed through the appropriate steps of the rapidly evolving, multi-tiered, interdependent NOvA software framework. In total there are greater than 12 individual software tiers, each of which performs a different function and can be configured differently depending on the input stream. In order to regularly test and validate that all of these software stages are working correctly NOvA has designed a powerful, modular testing framework that enables detailed validation and benchmarking to be performed in a fast, efficient and accessible way with minimal expert knowledge. The core of this system is a novel series of python modules which wrap, monitor and handle the underlying C++ software framework and then report the results to a slick front-end web-based interface. This interface utilises modern, cross-platform, visualisation libraries to render the test results in a meaningful way. They are fast and flexible, allowing for the easy addition of new tests and datasets. In total upwards of 14 individual streams are regularly tested amounting to over 70 individual software processes, producing over 25 GB of output files. The rigour enforced through this flexible testing framework enables NOvA to rapidly verify configurations, results and software and thus ensure that data is available for physics analysis in a timely and robust manner.

  2. Discovery Driven Growth

    DEFF Research Database (Denmark)

    Bukh, Per Nikolaj

    2009-01-01

    Anmeldelse af Discovery Driven Growh : A breakthrough process to reduce risk and seize opportunity, af Rita G. McGrath & Ian C. MacMillan, Boston: Harvard Business Press. Udgivelsesdato: 14 august......Anmeldelse af Discovery Driven Growh : A breakthrough process to reduce risk and seize opportunity, af Rita G. McGrath & Ian C. MacMillan, Boston: Harvard Business Press. Udgivelsesdato: 14 august...

  3. On Rank Driven Dynamical Systems

    Science.gov (United States)

    Veerman, J. J. P.; Prieto, F. J.

    2014-08-01

    We investigate a class of models related to the Bak-Sneppen (BS) model, initially proposed to study evolution. The BS model is extremely simple and yet captures some forms of "complex behavior" such as self-organized criticality that is often observed in physical and biological systems. In this model, random fitnesses in are associated to agents located at the vertices of a graph . Their fitnesses are ranked from worst (0) to best (1). At every time-step the agent with the worst fitness and some others with a priori given rank probabilities are replaced by new agents with random fitnesses. We consider two cases: The exogenous case where the new fitnesses are taken from an a priori fixed distribution, and the endogenous case where the new fitnesses are taken from the current distribution as it evolves. We approximate the dynamics by making a simplifying independence assumption. We use Order Statistics and Dynamical Systems to define a rank-driven dynamical system that approximates the evolution of the distribution of the fitnesses in these rank-driven models, as well as in the BS model. For this simplified model we can find the limiting marginal distribution as a function of the initial conditions. Agreement with experimental results of the BS model is excellent.

  4. Evaluation of Test-Driven Development: An Industrial Case Study

    NARCIS (Netherlands)

    Wasmus, H.; Gross, H-G.

    2007-01-01

    Test-driven development is a novel software development practice and part of the Extreme Programming paradigm. It is based on the principle that tests should be designed and written for a module iteratively, while the code of the module is devised. This is the opposite of what is usual in current so

  5. Software Activation Using Multithreading

    Directory of Open Access Journals (Sweden)

    Jianrui Zhang

    2012-11-01

    Full Text Available Software activation is an anti-piracy technology designed to verify that software products have been legitimately licensed. Activation should be quick and simple while simultaneously being secure and protecting customer privacy. The most common form of software activation is for the user to enter a legitimate product serial number. However, software activation based on serial numbers appears to be weak, since cracks for many programs are readily available on the Internet. Users can employ such cracks to bypass software activation.Serial number verification logic usually executes sequentially in a single thread. Such an approach is relatively easy to break since attackers can trace the code to understand how the logic works. In this paper, we develop a practical multi-threaded verification design. Our results show that by proper use of multi-threading, the amount of traceable code in a debugger can be reduced to a low percentage of the total and the traceable code in each run can differ as well. This makes it significantly more difficult for an attacker to reverse engineer the code as a means of bypassing a security check. Finally, we attempt to quantify the increased effort needed to break our verification logic.

  6. Software reliability assessment

    International Nuclear Information System (INIS)

    The increased usage and sophistication of computers applied to real time safety-related systems in the United Kingdom has spurred on the desire to provide a standard framework within which to assess dependable computing systems. Recent accidents and ensuing legislation have acted as a catalyst in this area. One particular aspect of dependable computing systems is that of software, which is usually designed to reduce risk at the system level, but which can increase risk if it is unreliable. Various organizations have recognized the problem of assessing the risk imposed to the system by unreliable software, and have taken initial steps to develop and use such assessment frameworks. This paper relates the approach of Consultancy Services of AEA Technology in developing a framework to assess the risk imposed by unreliable software. In addition, the paper discusses the experiences gained by Consultancy Services in applying the assessment framework to commercial and research projects. The framework is applicable to software used in safety applications, including proprietary software. Although the paper is written with Nuclear Reactor Safety applications in mind, the principles discussed can be applied to safety applications in all industries

  7. Software Engineering Laboratory Series: Collected Software Engineering Papers. Volume 14

    Science.gov (United States)

    1996-01-01

    The Software Engineering Laboratory (SEL) is an organization sponsored by NASA/GSFC and created to investigate the effectiveness of software engineering technologies when applied to the development of application software. The activities, findings, and recommendations of the SEL are recorded in the Software Engineering Laboratory Series, a continuing series of reports that includes this document.

  8. Software Engineering Laboratory Series: Collected Software Engineering Papers. Volume 15

    Science.gov (United States)

    1997-01-01

    The Software Engineering Laboratory (SEL) is an organization sponsored by NASA/GSFC and created to investigate the effectiveness of software engineering technologies when applied to the development of application software. The activities, findings, and recommendations of the SEL are recorded in the Software Engineering Laboratory Series, a continuing series of reports that includes this document.

  9. Software Engineering Laboratory Series: Collected Software Engineering Papers. Volume 13

    Science.gov (United States)

    1995-01-01

    The Software Engineering Laboratory (SEL) is an organization sponsored by NASA/GSFC and created to investigate the effectiveness of software engineering technologies when applied to the development of application software. The activities, findings, and recommendations of the SEL are recorded in the Software Engineering Laboratory Series, a continuing series of reports that includes this document.

  10. Impact of Agile Software Development Model on Software Maintainability

    Science.gov (United States)

    Gawali, Ajay R.

    2012-01-01

    Software maintenance and support costs account for up to 60% of the overall software life cycle cost and often burdens tightly budgeted information technology (IT) organizations. Agile software development approach delivers business value early, but implications on software maintainability are still unknown. The purpose of this quantitative study…

  11. Fourth international workshop on model driven development of advanced user interfaces

    OpenAIRE

    Meixner, Gerrit; Gorlich, Daniel; Breiner, Karl; Hussmann, Heinrich; Pleuss, Andreas; Sauer, Stefan; VAN DEN BERGH, Jan

    2009-01-01

    Model Driven Development (MDD) is an important paradigm in Software Engineering. In MDD, applications are specified systematically using abstract, platform independent models. The models are then transformed into executable code for different platforms and target devices. Model-driven techniques become ever more prominent in any kind of application, such as multimedia and Web, ubiquitous and automotive applications.

  12. SOFTWARE MEASUREMENTS AND METRICS: ROLE IN EFFECTIVE SOFTWARE TESTING

    Directory of Open Access Journals (Sweden)

    Sheikh Umar Farooq

    2011-01-01

    Full Text Available Measurement has always been fundamental to the progress to any engineering discipline and software testing is no exception. Software metrics have been used in making quantitative/qualitative decisions as well as in risk assessment and reduction in software projects. In this paper we discuss software measurement and metrics and their fundamental role in software development life cycle. This paper focusing on software test metrics discusses their key role in software testing process and also classifies and systematically analyzes the various test metrics.

  13. Test af Software

    DEFF Research Database (Denmark)

    Dette dokument udgør slutrapporten for netværkssamarbejdet ”Testnet”, som er udført i perioden 1.4.2006 til 31.12.2008. Netværket beskæftiger sig navnlig med emner inden for test af indlejret og teknisk software, men et antal eksempler på problemstillinger og løsninger forbundet med test af...... administrativ software indgår også. Rapporten er opdelt i følgende 3 dele: Overblik. Her giver vi et resumé af netværkets formål, aktiviteter og resultater. State of the art af software test ridses op. Vi omtaler, at CISS og netværket tager nye tiltag. Netværket. Formål, deltagere og behandlede emner på ti...

  14. Astronomers as Software Developers

    Science.gov (United States)

    Pildis, Rachel A.

    2016-01-01

    Astronomers know that their research requires writing, adapting, and documenting computer software. Furthermore, they often have to learn new computer languages and figure out how existing programs work without much documentation or guidance and with extreme time pressure. These are all skills that can lead to a software development job, but recruiters and employers probably won't know that. I will discuss all the highly useful experience that astronomers may not know that they already have, and how to explain that knowledge to others when looking for non-academic software positions. I will also talk about some of the pitfalls I have run into while interviewing for jobs and working as a developer, and encourage you to embrace the curiosity employers might have about your non-standard background.

  15. The Ettention software package.

    Science.gov (United States)

    Dahmen, Tim; Marsalek, Lukas; Marniok, Nico; Turoňová, Beata; Bogachev, Sviatoslav; Trampert, Patrick; Nickels, Stefan; Slusallek, Philipp

    2016-02-01

    We present a novel software package for the problem "reconstruction from projections" in electron microscopy. The Ettention framework consists of a set of modular building-blocks for tomographic reconstruction algorithms. The well-known block iterative reconstruction method based on Kaczmarz algorithm is implemented using these building-blocks, including adaptations specific to electron tomography. Ettention simultaneously features (1) a modular, object-oriented software design, (2) optimized access to high-performance computing (HPC) platforms such as graphic processing units (GPU) or many-core architectures like Xeon Phi, and (3) accessibility to microscopy end-users via integration in the IMOD package and eTomo user interface. We also provide developers with a clean and well-structured application programming interface (API) that allows for extending the software easily and thus makes it an ideal platform for algorithmic research while hiding most of the technical details of high-performance computing. PMID:26686659

  16. Lecture 2: Software Security

    CERN Document Server

    CERN. Geneva

    2013-01-01

    Computer security has been an increasing concern for IT professionals for a number of years, yet despite all the efforts, computer systems and networks remain highly vulnerable to attacks of different kinds. Design flaws and security bugs in the underlying software are among the main reasons for this. This lecture addresses the following question: how to create secure software? The lecture starts with a definition of computer security and an explanation of why it is so difficult to achieve. It then introduces the main security principles (like least-privilege, or defense-in-depth) and discusses security in different phases of the software development cycle. The emphasis is put on the implementation part: most common pitfalls and security bugs are listed, followed by advice on best practice for security development, testing and deployment. Sebastian Lopienski is CERN’s deputy Computer Security Officer. He works on security strategy and policies; offers internal consultancy and audit services; develops and ...

  17. Secure software practices among Malaysian software practitioners: An exploratory study

    Science.gov (United States)

    Mohamed, Shafinah Farvin Packeer; Baharom, Fauziah; Deraman, Aziz; Yahya, Jamaiah; Mohd, Haslina

    2016-08-01

    Secure software practices is increasingly gaining much importance among software practitioners and researchers due to the rise of computer crimes in the software industry. It has become as one of the determinant factors for producing high quality software. Even though its importance has been revealed, its current practice in the software industry is still scarce, particularly in Malaysia. Thus, an exploratory study is conducted among software practitioners in Malaysia to study their experiences and practices in the real-world projects. This paper discusses the findings from the study, which involved 93 software practitioners. Structured questionnaire is utilized for data collection purpose whilst statistical methods such as frequency, mean, and cross tabulation are used for data analysis. Outcomes from this study reveal that software practitioners are becoming increasingly aware on the importance of secure software practices, however, they lack of appropriate implementation, which could affect the quality of produced software.

  18. A Software Reliability Estimation Method to Nuclear Safety Software

    Energy Technology Data Exchange (ETDEWEB)

    Park, Geeyong; Jang, Seung Cheol [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2014-02-15

    A method for estimating software reliability for nuclear safety software is proposed in this paper. This method is based on the software reliability growth model (SRGM), where the behavior of software failure is assumed to follow a nonhomogeneous Poisson process. Two types of modeling schemes based on a particular underlying method are proposed in order to more precisely estimate and predict the number of software defects based on very rare software failure data. The Bayesian statistical inference is employed to estimate the model parameters by incorporating software test cases as a covariate into the model. It was identified that these models are capable of reasonably estimating the remaining number of software defects which directly affects the reactor trip functions. The software reliability might be estimated from these modeling equations, and one approach of obtaining software reliability value is proposed in this paper.

  19. STSE: Spatio-Temporal Simulation Environment Dedicated to Biology

    Directory of Open Access Journals (Sweden)

    Gerber Susanne

    2011-04-01

    Full Text Available Abstract Background Recently, the availability of high-resolution microscopy together with the advancements in the development of biomarkers as reporters of biomolecular interactions increased the importance of imaging methods in molecular cell biology. These techniques enable the investigation of cellular characteristics like volume, size and geometry as well as volume and geometry of intracellular compartments, and the amount of existing proteins in a spatially resolved manner. Such detailed investigations opened up many new areas of research in the study of spatial, complex and dynamic cellular systems. One of the crucial challenges for the study of such systems is the design of a well stuctured and optimized workflow to provide a systematic and efficient hypothesis verification. Computer Science can efficiently address this task by providing software that facilitates handling, analysis, and evaluation of biological data to the benefit of experimenters and modelers. Results The Spatio-Temporal Simulation Environment (STSE is a set of open-source tools provided to conduct spatio-temporal simulations in discrete structures based on microscopy images. The framework contains modules to digitize, represent, analyze, and mathematically model spatial distributions of biochemical species. Graphical user interface (GUI tools provided with the software enable meshing of the simulation space based on the Voronoi concept. In addition, it supports to automatically acquire spatial information to the mesh from the images based on pixel luminosity (e.g. corresponding to molecular levels from microscopy images. STSE is freely available either as a stand-alone version or included in the linux live distribution Systems Biology Operational Software (SB.OS and can be downloaded from http://www.stse-software.org/. The Python source code as well as a comprehensive user manual and video tutorials are also offered to the research community. We discuss main concepts

  20. Agile distributed software development

    DEFF Research Database (Denmark)

    Persson, John Stouby; Mathiassen, Lars; Aaen, Ivan

    2012-01-01

    While face-to-face interaction is fundamental in agile software development, distributed environments must rely extensively on mediated interactions. Practicing agile principles in distributed environments therefore poses particular control challenges related to balancing fixed vs. evolving quality...... requirements and people vs. process-based collaboration. To investigate these challenges, we conducted an in-depth case study of a successful agile distributed software project with participants from a Russian firm and a Danish firm. Applying Kirsch’s elements of control framework, we offer an analysis of how...

  1. Processeringsoptimering med Canons software

    DEFF Research Database (Denmark)

    Precht, Helle

    2009-01-01

    . Muligheder i software optimering blev studeret i relation til optimal billedkvalitet og kontrol optagelser, for at undersøge om det var muligt at acceptere diagnostisk billedkvalitet og derved tage afsæt i ALARA. Metode og materialer Et kvantitativt eksperimentelt studie baseret på forsøg med teknisk og...... humant fantom. CD Rad fantom anvendes som teknisk fantom, hvor billederne blev analyseret med CD Rad software, og resultatet var en objektiv IQF værdi. Det humane fantom var et lamme pelvis med femur, der via NRPB’ er sammenlignelig med absorptionen ved et femårigt barn. De humane forsøgsbilleder blev...

  2. Software product quality control

    CERN Document Server

    Wagner, Stefan

    2013-01-01

    Quality is not a fixed or universal property of software; it depends on the context and goals of its stakeholders. Hence, when you want to develop a high-quality software system, the first step must be a clear and precise specification of quality. Yet even if you get it right and complete, you can be sure that it will become invalid over time. So the only solution is continuous quality control: the steady and explicit evaluation of a product's properties with respect to its updated quality goals.This book guides you in setting up and running continuous quality control in your environment. Star

  3. Agile software development

    CERN Document Server

    Stober, Thomas

    2009-01-01

    Software Development is moving towards a more agile and more flexible approach. It turns out that the traditional 'waterfall' model is not supportive in an environment where technical, financial and strategic constraints are changing almost every day. But what is agility? What are today's major approaches? And especially: What is the impact of agile development principles on the development teams, on project management and on software architects? How can large enterprises become more agile and improve their business processes, which have been existing since many, many years? What are the limit

  4. Machine Tool Software

    Science.gov (United States)

    1988-01-01

    A NASA-developed software package has played a part in technical education of students who major in Mechanical Engineering Technology at William Rainey Harper College. Professor Hack has been using (APT) Automatically Programmed Tool Software since 1969 in his CAD/CAM Computer Aided Design and Manufacturing curriculum. Professor Hack teaches the use of APT programming languages for control of metal cutting machines. Machine tool instructions are geometry definitions written in APT Language to constitute a "part program." The part program is processed by the machine tool. CAD/CAM students go from writing a program to cutting steel in the course of a semester.

  5. Green in software engineering

    CERN Document Server

    Calero Munoz, Coral

    2015-01-01

    This is the first book that presents a comprehensive overview of sustainability aspects in software engineering. Its format follows the structure of the SWEBOK and covers the key areas involved in the incorporation of green aspects in software engineering, encompassing topics from requirement elicitation to quality assurance and maintenance, while also considering professional practices and economic aspects. The book consists of thirteen chapters, which are structured in five parts. First the "Introduction" gives an overview of the primary general concepts related to Green IT, discussing wha

  6. Agile Software Development

    OpenAIRE

    Stewart, Rhonda

    2009-01-01

    One of the most noticeable changes to software process thinking in the last ten years has been the appearance of the word ‘agile’ (Fowler, 2005). In the Information Technology (IT) industry Agile Software Development, or simply Agile is used to refer to a family of lightweight development approaches that share a common set of values and principles1 focused around adapting to change and putting people first (Fowler, 2005). Such Agile methods2 provide an alternative to the well-established Wate...

  7. Software Testing as Science

    Directory of Open Access Journals (Sweden)

    Ingrid Gallesdic

    2013-06-01

    Full Text Available The most widespread opinion among people who have some connection with software testing is that this activity is an art. In fact, books have been published widely whose titles refer to it as art, role or process. But because software complexity is increasing every year, this paper proposes a new approach, conceiving the test as a science. This is because the processes by which they are applied are the steps of the scientific method: inputs, processes, outputs. The contents of this paper examines the similarities and test characteristics as science.

  8. The PANIC software system

    Science.gov (United States)

    Ibáñez Mengual, José M.; Fernández, Matilde; Rodríguez Gómez, Julio F.; García Segura, Antonio J.; Storz, Clemens

    2010-07-01

    PANIC is the Panoramic Near Infrared Camera for the 2.2m and 3.5m telescopes at Calar Alto observatory. The aim of the project is to build a wide-field general purpose NIR camera. In this paper we describe the software system of the instrument, which comprises four main packages: GEIRS for the instrument control and the data acquisition; the Observation Tool (OT), the software used for detailed definition and pre-planning the observations, developed in Java; the Quick Look tool (PQL) for easy inspection of the data in real-time and a scientific pipeline (PAPI), both based on the Python programming language.

  9. Six Sigma software development

    CERN Document Server

    Tayntor, Christine B

    2002-01-01

    Since Six Sigma has had marked success in improving quality in other settings, and since the quality of software remains poor, it seems a natural evolution to apply the concepts and tools of Six Sigma to system development and the IT department. Until now however, there were no books available that applied these concepts to the system development process. Six Sigma Software Development fills this void and illustrates how Six Sigma concepts can be applied to all aspects of the evolving system development process. It includes the traditional waterfall model and in the support of legacy systems,

  10. Managing Distributed Software Projects

    DEFF Research Database (Denmark)

    Persson, John Stouby

    and coordination in a successful, distributed software project between a Russian and a Danish company. The case study’s control aspects were investigated, drawing on Kirsch’s (2004) elements of control framework, to analyze how control is enacted in the project. This analysis showed that informal measurement...... showed that multimodal communication can facilitate collective minding in distributed software projects and can positively impact performance. In providing an approach for investigating the impact of multimodal communication practices on virtual team performance, we can further understand and support...

  11. How can Software Packages Certification Improve Software Process

    OpenAIRE

    Pivka, Marjan; Potočan, Vojko

    1997-01-01

    Popular software assessment models such as CMM, BOOTSTRAP, SPICE or ISO 9000 ignore the impact of software product certification on software quality. The first standard for software product quality was German DIN 66285. Based on this standard, the ISO developed a international standard for quality requirements and testing procedures for software packages: ISO/IEC 12119. This paper presents our experience with classical testing models based on ISO/IEC 12119 and DIN 66285 and with our improved ...

  12. Software Risk Management Practice: Evidence From Thai Software Industry

    OpenAIRE

    Tharwon Arnuphaptrairong

    2014-01-01

    Software risk management has been around at least since it was introduced in mainstream of software management process, in 1989 [1]-[3] but little has been reported about its industrial practice [4]-[6]. This paper reports the current software risk management practice in Thai software industry. A questionnaire survey was designed to capture the information of the software project risk management practice. The questionnaire was sent to 141 companies and received a response rate 28 percent. The...

  13. Dynamic data-driven sensor network adaptation for border control

    Science.gov (United States)

    Bein, Doina; Madan, Bharat B.; Phoha, Shashi; Rajtmajer, Sarah; Rish, Anna

    2013-06-01

    Given a specific scenario for the border control problem, we propose a dynamic data-driven adaptation of the associated sensor network via embedded software agents which make sensor network control, adaptation and collaboration decisions based on the contextual information value of competing data provided by different multi-modal sensors. We further propose the use of influence diagrams to guide data-driven decision making in selecting the appropriate action or course of actions which maximize a given utility function by designing a sensor embedded software agent that uses an influence diagram to make decisions about whether to engage or not engage higher level sensors for accurately detecting human presence in the region. The overarching goal of the sensor system is to increase the probability of target detection and classification and reduce the rate of false alarms. The proposed decision support software agent is validated experimentally on a laboratory testbed for multiple border control scenarios.

  14. Digital 'faces' of synthetic biology.

    Science.gov (United States)

    Friedrich, Kathrin

    2013-06-01

    In silicio design plays a fundamental role in the endeavour to synthesise biological systems. In particular, computer-aided design software enables users to manage the complexity of biological entities that is connected to their construction and reconfiguration. The software's graphical user interface bridges the gap between the machine-readable data on the algorithmic subface of the computer and its human-amenable surface represented by standardised diagrammatic elements. Notations like the Systems Biology Graphical Notation (SBGN), together with interactive operations such as drag & drop, allow the user to visually design and simulate synthetic systems as 'bio-algorithmic signs'. Finally, the digital programming process should be extended to the wet lab to manufacture the designed synthetic biological systems. By exploring the different 'faces' of synthetic biology, I argue that in particular computer-aided design (CAD) is pushing the idea to automatically produce de novo objects. Multifaceted software processes serve mutually aesthetic, epistemic and performative purposes by simultaneously black-boxing and bridging different data sources, experimental operations and community-wide standards. So far, synthetic biology is mainly a product of digital media technologies that structurally mimic the epistemological challenge to take both qualitative as well as quantitative aspects of biological systems into account in order to understand and produce new and functional entities.

  15. Model Driven Language Engineering

    OpenAIRE

    Patrascoiu, Octavian

    2005-01-01

    Modeling is a most important exercise in software engineering and development and one of the current practices is object-oriented (OO) modeling. The Object Management Group (OMG) has defined a standard object-oriented modeling language the Unified Modeling Language (UML). The OMG is not only interested in modeling languages; its primary aim is to enable easy integration of software systems and components using vendor-neutral technologies. This thesis investigates the possibilities for designi...

  16. Bug Localization in Test-Driven Development

    Directory of Open Access Journals (Sweden)

    Massimo Ficco

    2011-01-01

    Full Text Available Software development teams that use agile methodologies are increasingly adopting the test-driven development practice (TDD. TDD allows to produce software by iterative and incremental work cycle, and with a strict control over the process, favouring an early detection of bugs. However, when applied to large and complex systems, TDD benefits are not so obvious; manually locating and fixing bugs introduced during the iterative development steps is a nontrivial task. In such systems, the propagation chains following the bugs activation can be unacceptably long and intricate, and the size of the code to be analyzed is often too large. In this paper, a bug localization technique specifically tailored to TDD is presented. The technique is embedded in the TDD cycle, and it aims to improve developers' ability to locate bugs as soon as possible. It is implemented in a tool and experimentally evaluated on newly developed Java programs.

  17. The fallacy of Software Patents

    CERN Document Server

    CERN. Geneva

    2015-01-01

    Software patents are usually used as argument for innovation but do they really promote innovation? Who really benefits from software patents? This talk attempts to show the problems with software patents and how they can actually harm innovation having little value for software users and our society in general.

  18. Evaluating Commercial Game System Software

    OpenAIRE

    Quinn, Kelly; クイン, ケリー

    2009-01-01

    This paper describes the TOEIC test DS Training software published by Obunsha for the Nintendo DS game system. This paper describes the different features of the software, the advantages and disadvantages of the software and the results of a survey of students' reactions to the software and using the DS as a platform for studying English.

  19. Impact of Evolution of Concerns in the Model-Driven Architecture Design Approach

    NARCIS (Netherlands)

    Tekinerdogan, Bedir; Aksit, Mehmet; Henninger, Francis

    2007-01-01

    Separation of concerns is an important principle for designing high quality software systems and is both applied in the Model-Driven Architecture (MDA) and Aspect-Oriented Software Development (AOSD). The AOSD and MDA techniques seem to be complementary to each other; historically AOSD has focused o

  20. The MDE Diploma: First International Postgraduate Specialization in Model-Driven Engineering

    Science.gov (United States)

    Cabot, Jordi; Tisi, Massimo

    2011-01-01

    Model-Driven Engineering (MDE) is changing the way we build, operate, and maintain our software-intensive systems. Several projects using MDE practices are reporting significant improvements in quality and performance but, to be able to handle these projects, software engineers need a set of technical and interpersonal skills that are currently…

  1. Patterns for Parallel Software Design

    CERN Document Server

    Ortega-Arjona, Jorge Luis

    2010-01-01

    Essential reading to understand patterns for parallel programming Software patterns have revolutionized the way we think about how software is designed, built, and documented, and the design of parallel software requires you to consider other particular design aspects and special skills. From clusters to supercomputers, success heavily depends on the design skills of software developers. Patterns for Parallel Software Design presents a pattern-oriented software architecture approach to parallel software design. This approach is not a design method in the classic sense, but a new way of managin

  2. The Art of Software Testing

    CERN Document Server

    Myers, Glenford J; Badgett, Tom

    2011-01-01

    The classic, landmark work on software testing The hardware and software of computing have changed markedly in the three decades since the first edition of The Art of Software Testing, but this book's powerful underlying analysis has stood the test of time. Whereas most books on software testing target particular development techniques, languages, or testing methods, The Art of Software Testing, Third Edition provides a brief but powerful and comprehensive presentation of time-proven software testing approaches. If your software development project is mission critical, this book is an investme

  3. Software testing concepts and operations

    CERN Document Server

    Mili, Ali

    2015-01-01

    Explores and identifies the main issues, concepts, principles and evolution of software testing, including software quality engineering and testing concepts, test data generation, test deployment analysis, and software test managementThis book examines the principles, concepts, and processes that are fundamental to the software testing function. This book is divided into five broad parts. Part I introduces software testing in the broader context of software engineering and explores the qualities that testing aims to achieve or ascertain, as well as the lifecycle of software testing. Part II c

  4. Writing testable software requirements

    Energy Technology Data Exchange (ETDEWEB)

    Knirk, D. [Sandia National Labs., Albuquerque, NM (United States)

    1997-11-01

    This tutorial identifies common problems in analyzing requirements in the problem and constructing a written specification of what the software is to do. It deals with two main problem areas: identifying and describing problem requirements, and analyzing and describing behavior specifications.

  5. Global Software Development

    DEFF Research Database (Denmark)

    Søderberg, Anne-Marie; Krishna, S.; Bjørn, Pernille

    2013-01-01

    accounts of close collaboration processes in two large and complex projects, where off-shoring of software development is moved to a strategic level, we found that the vendor was able to establish a strategic partnership through long-term engagement with the field of banking and insurance as well...

  6. Software for noise measurements

    International Nuclear Information System (INIS)

    The CURS program library comprising 38 fortran-programs, designed for processing descrete experimental data in the form of random or determined periodic processes is described. The library is based on the modular construction principle which allows one to create on its base any sets of programs to solve tasks related to NPP operation, and to develop special software

  7. Software Carpentry: Lessons Learned

    CERN Document Server

    Wilson, Greg

    2013-01-01

    Over the last 15 years, Software Carpentry has evolved from a week-long training course at the US national laboratories into a worldwide volunteer effort to raise standards in scientific computing. This article explains what we have learned along the way the challenges we now face, and our plans for the future.

  8. Software engineering tools.

    Science.gov (United States)

    Wear, L L; Pinkert, J R

    1994-01-01

    We have looked at general descriptions and illustrations of several software development tools, such as tools for prototyping, developing DFDs, testing, and maintenance. Many others are available, and new ones are being developed. However, you have at least seen some examples of powerful CASE tools for systems development.

  9. Iterative software kernels

    Energy Technology Data Exchange (ETDEWEB)

    Duff, I.

    1994-12-31

    This workshop focuses on kernels for iterative software packages. Specifically, the three speakers discuss various aspects of sparse BLAS kernels. Their topics are: `Current status of user lever sparse BLAS`; Current status of the sparse BLAS toolkit`; and `Adding matrix-matrix and matrix-matrix-matrix multiply to the sparse BLAS toolkit`.

  10. Generic Kalman Filter Software

    Science.gov (United States)

    Lisano, Michael E., II; Crues, Edwin Z.

    2005-01-01

    The Generic Kalman Filter (GKF) software provides a standard basis for the development of application-specific Kalman-filter programs. Historically, Kalman filters have been implemented by customized programs that must be written, coded, and debugged anew for each unique application, then tested and tuned with simulated or actual measurement data. Total development times for typical Kalman-filter application programs have ranged from months to weeks. The GKF software can simplify the development process and reduce the development time by eliminating the need to re-create the fundamental implementation of the Kalman filter for each new application. The GKF software is written in the ANSI C programming language. It contains a generic Kalman-filter-development directory that, in turn, contains a code for a generic Kalman filter function; more specifically, it contains a generically designed and generically coded implementation of linear, linearized, and extended Kalman filtering algorithms, including algorithms for state- and covariance-update and -propagation functions. The mathematical theory that underlies the algorithms is well known and has been reported extensively in the open technical literature. Also contained in the directory are a header file that defines generic Kalman-filter data structures and prototype functions and template versions of application-specific subfunction and calling navigation/estimation routine code and headers. Once the user has provided a calling routine and the required application-specific subfunctions, the application-specific Kalman-filter software can be compiled and executed immediately. During execution, the generic Kalman-filter function is called from a higher-level navigation or estimation routine that preprocesses measurement data and post-processes output data. The generic Kalman-filter function uses the aforementioned data structures and five implementation- specific subfunctions, which have been developed by the user on

  11. Evaluation & Optimization of Software Engineering

    OpenAIRE

    Asaduzzaman Noman; Atik Ahmed Sourav; Shakh Md. Alimuzjaman Alim

    2016-01-01

    The term is made of two words, software and engineering. Software is more than just a program code. A program is an executable code, which serves some computational purpose. Software is considered to be collection of executable programming code, associated libraries and documentations. Software, when made for a specific requirement is called software product. Engineering on the other hand, is all about developing products, using well-defined, scientific principles and methods. The outcome ...

  12. Self-assembling software generator

    Science.gov (United States)

    Bouchard, Ann M.; Osbourn, Gordon C.

    2011-11-25

    A technique to generate an executable task includes inspecting a task specification data structure to determine what software entities are to be generated to create the executable task, inspecting the task specification data structure to determine how the software entities will be linked after generating the software entities, inspecting the task specification data structure to determine logic to be executed by the software entities, and generating the software entities to create the executable task.

  13. Numerical software: science or alchemy

    Energy Technology Data Exchange (ETDEWEB)

    Gear, C.W.

    1979-06-01

    This is a summary of the Forsythe lecture presented at the Computer Science Conference, Dayton, Ohio, in February 1979. It examines the activity called Numerical Software, first to see what distinguishes numerical software from any other form of software and why numerical software is so much more difficult. Then it examines the scientific basis of such software and discusses that is lacking in that basis.

  14. Flight Software Math Library

    Science.gov (United States)

    McComas, David

    2013-01-01

    The flight software (FSW) math library is a collection of reusable math components that provides typical math utilities required by spacecraft flight software. These utilities are intended to increase flight software quality reusability and maintainability by providing a set of consistent, well-documented, and tested math utilities. This library only has dependencies on ANSI C, so it is easily ported. Prior to this library, each mission typically created its own math utilities using ideas/code from previous missions. Part of the reason for this is that math libraries can be written with different strategies in areas like error handling, parameters orders, naming conventions, etc. Changing the utilities for each mission introduces risks and costs. The obvious risks and costs are that the utilities must be coded and revalidated. The hidden risks and costs arise in miscommunication between engineers. These utilities must be understood by both the flight software engineers and other subsystem engineers (primarily guidance navigation and control). The FSW math library is part of a larger goal to produce a library of reusable Guidance Navigation and Control (GN&C) FSW components. A GN&C FSW library cannot be created unless a standardized math basis is created. This library solves the standardization problem by defining a common feature set and establishing policies for the library s design. This allows the libraries to be maintained with the same strategy used in its initial development, which supports a library of reusable GN&C FSW components. The FSW math library is written for an embedded software environment in C. This places restrictions on the language features that can be used by the library. Another advantage of the FSW math library is that it can be used in the FSW as well as other environments like the GN&C analyst s simulators. This helps communication between the teams because they can use the same utilities with the same feature set and syntax.

  15. Framework of Software Quality Management Using Object oriented Software Agent

    Directory of Open Access Journals (Sweden)

    Anand Pandey

    2013-01-01

    Full Text Available Development of software is a scientific and economic problem, particularly the design of complex systems whichrequire evolving methods and approaches. Agent technology is currently one of the most active and vibrant areas of IT research and development. Object-oriented Software Engineering (OOSE has become an active area of research in recent years. In this paper, we review the framework of software quality management using object- oriented methodology concepts for software agents.The software specification acts as a bridge between customers, architects, software developers and testers. Using object-oriented concept of software agent and its standard it may offer benefits even if the system is implemented without an object-based language or framework . We propose and discuss a software agent framework, specifically to support software quality management. Although still in its initial phases, research indicates some promise in enabling software developers to meet market expectations and produce projects timeously, within budget and to users satisfaction. However, the software quality management environment has also changed and is continuously evolving. Currently software projects are developed and deployed in distributed, pervasive and collaborative environments and its quality should be managed by applying its best standard. From the point of view of software engineering this framework and its standards are applying for developing the software projects.We discuss the standard and benefits that can be gained by using object-oriented concepts, and where the concepts require further development.

  16. ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry

    Directory of Open Access Journals (Sweden)

    Ramos Hector

    2011-03-01

    Full Text Available Abstract Background Since its inception, proteomics has essentially operated in a discovery mode with the goal of identifying and quantifying the maximal number of proteins in a sample. Increasingly, proteomic measurements are also supporting hypothesis-driven studies, in which a predetermined set of proteins is consistently detected and quantified in multiple samples. Selected reaction monitoring (SRM is a targeted mass spectrometric technique that supports the detection and quantification of specific proteins in complex samples at high sensitivity and reproducibility. Here, we describe ATAQS, an integrated software platform that supports all stages of targeted, SRM-based proteomics experiments including target selection, transition optimization and post acquisition data analysis. This software will significantly facilitate the use of targeted proteomic techniques and contribute to the generation of highly sensitive, reproducible and complete datasets that are particularly critical for the discovery and validation of targets in hypothesis-driven studies in systems biology. Result We introduce a new open source software pipeline, ATAQS (Automated and Targeted Analysis with Quantitative SRM, which consists of a number of modules that collectively support the SRM assay development workflow for targeted proteomic experiments (project management and generation of protein, peptide and transitions and the validation of peptide detection by SRM. ATAQS provides a flexible pipeline for end-users by allowing the workflow to start or end at any point of the pipeline, and for computational biologists, by enabling the easy extension of java algorithm classes for their own algorithm plug-in or connection via an external web site. This integrated system supports all steps in a SRM-based experiment and provides a user-friendly GUI that can be run by any operating system that allows the installation of the Mozilla Firefox web browser. Conclusions Targeted

  17. Model-based robustness testing for avionics-embedded software

    Institute of Scientific and Technical Information of China (English)

    Yang Shunkun; Liu Bin; Wang Shihai; Lu Minyan

    2013-01-01

    Robustness testing for safety-critical embedded software is still a challenge in its nascent stages.In this paper,we propose a practical methodology and implement an environment by employing model-based robustness testing for embedded software systems.It is a system-level black-box testing approach in which the fault behaviors of embedded software is triggered with the aid of modelbased fault injection by the support of an executable model-driven hardware-in-loop (HIL) testing environment.The prototype implementation of the robustness testing environment based on the proposed approach is experimentally discussed and illustrated by industrial case studies based on several avionics-embedded software systems.The results show that our proposed and implemented robustness testing method and environment are effective to find more bugs,and reduce burdens of testing engineers to enhance efficiency of testing tasks,especially for testing complex embedded systems.

  18. Lab Companion : A software for laboratory management

    Directory of Open Access Journals (Sweden)

    S.Marla

    2010-12-01

    Full Text Available The complete sequencing of various plant and animal genomes (http://www.ncbi.nlm.nih.gov/genomeprj and the advances in transcriptomics, proteomics and metabolomics have resulted in a virtual explosion in biotechnology and molecular biological studies.These studies involve large scale and complex experimentation. Keeping this in view we have developed a tool Lab Companion whichserves to automate the maintenance of molecular biology and biotechnology laboratories. A relational database Lab Companion software was constructed. The backend was created using Microsoft SQL server 2005 and front end was created using Microsoft visual studio 2005 framework 2.0. The developed tool will serve to automate the management of stock inventory of the biotechnology and molecular biology laboratories.

  19. Passive and Driven Trends in the Evolution of Complexity

    CERN Document Server

    Yaeger, Larry; Sporns, Olaf

    2011-01-01

    The nature and source of evolutionary trends in complexity is difficult to assess from the fossil record, and the driven vs. passive nature of such trends has been debated for decades. There are also questions about how effectively artificial life software can evolve increasing levels of complexity. We extend our previous work demonstrating an evolutionary increase in an information theoretic measure of neural complexity in an artificial life system (Polyworld), and introduce a new technique for distinguishing driven from passive trends in complexity. Our experiments show that evolution can and does select for complexity increases in a driven fashion, in some circumstances, but under other conditions it can also select for complexity stability. It is suggested that the evolution of complexity is entirely driven---just not in a single direction---at the scale of species. This leaves open the question of evolutionary trends at larger scales.

  20. Non-Equilibrium Quantum Entanglement in Biological Systems

    Institute of Scientific and Technical Information of China (English)

    LI Hong-Rong; ZHANG Pei; GAO Hong; BI Wen-Ting; ALAMRI M. D.; LI Fu-Li

    2012-01-01

    A non-equilibrium model of a classically driven quantum harmonic oscillator is proposed to explain persistent quantum entanglement in biological systems at ambient temperature. The conditions for periodic entanglement generation are derived. Our results support the evidence that biological systems may have quantum entanglement at biological temperatures.%A non-equilibrium model of a classically driven quantum harmonic oscillator is proposed to explain persistent quantum entanglement in biological systems at ambient temperature.The conditions for periodic entanglement generation are derived.Our results support the evidence that biological systems may have quantum entanglement at biological temperatures.

  1. Software Development Practices, Software Complexity, and Software Maintenance Performance: A Field Study

    OpenAIRE

    Banker, Rajiv D.; Davis, Gordon B.; Sandra A. Slaughter

    1998-01-01

    Software maintenance claims a large proportion of organizational resources. It is thought that many maintenance problems derive from inadequate software design and development practices. Poor design choices can result in complex software that is costly to support and difficult to change. However, it is difficult to assess the actual maintenance performance effects of software development practices because their impact is realized over the software life cycle. To estimate the impact of develop...

  2. A software engineering process for safety-critical software application.

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Byung Heon; Kim, Hang Bae; Chang, Hoon Seon; Jeon, Jong Sun [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1995-02-01

    Application of computer software to safety-critical systems in on the increase. To be successful, the software must be designed and constructed to meet the functional and performance requirements of the system. For safety reason, the software must be demonstrated not only to meet these requirements, but also to operate safely as a component within the system. For longer-term cost consideration, the software must be designed and structured to ease future maintenance and modifications. This paper presents a software engineering process for the production of safety-critical software for a nuclear power plant. The presentation is expository in nature of a viable high quality safety-critical software development. It is based on the ideas of a rational design process and on the experience of the adaptation of such process in the production of the safety-critical software for the shutdown system number two of Wolsung 2, 3 and 4 nuclear power generation plants. This process is significantly different from a conventional process in terms of rigorous software development phases and software design techniques, The process covers documentation, design, verification and testing using mathematically precise notations and highly reviewable tabular format to specify software requirements and software requirements and software requirements and code against software design using static analysis. The software engineering process described in this paper applies the principle of information-hiding decomposition in software design using a modular design technique so that when a change is required or an error is detected, the affected scope can be readily and confidently located. it also facilitates a sense of high degree of confidence in the `correctness` of the software production, and provides a relatively simple and straightforward code implementation effort. 1 figs., 10 refs. (Author).

  3. A software engineering process for safety-critical software application

    International Nuclear Information System (INIS)

    Application of computer software to safety-critical systems in on the increase. To be successful, the software must be designed and constructed to meet the functional and performance requirements of the system. For safety reason, the software must be demonstrated not only to meet these requirements, but also to operate safely as a component within the system. For longer-term cost consideration, the software must be designed and structured to ease future maintenance and modifications. This paper presents a software engineering process for the production of safety-critical software for a nuclear power plant. The presentation is expository in nature of a viable high quality safety-critical software development. It is based on the ideas of a rational design process and on the experience of the adaptation of such process in the production of the safety-critical software for the shutdown system number two of Wolsung 2, 3 and 4 nuclear power generation plants. This process is significantly different from a conventional process in terms of rigorous software development phases and software design techniques, The process covers documentation, design, verification and testing using mathematically precise notations and highly reviewable tabular format to specify software requirements and software requirements and software requirements and code against software design using static analysis. The software engineering process described in this paper applies the principle of information-hiding decomposition in software design using a modular design technique so that when a change is required or an error is detected, the affected scope can be readily and confidently located. it also facilitates a sense of high degree of confidence in the 'correctness' of the software production, and provides a relatively simple and straightforward code implementation effort. 1 figs., 10 refs. (Author)

  4. From raw data to biological discoveries: a computational analysis pipeline for mass spectrometry-based proteomics.

    Science.gov (United States)

    Lavallée-Adam, Mathieu; Park, Sung Kyu Robin; Martínez-Bartolomé, Salvador; He, Lin; Yates, John R

    2015-11-01

    In the last two decades, computational tools for mass spectrometry-based proteomics data analysis have evolved from a few stand-alone software solutions serving specific goals, such as the identification of amino acid sequences based on mass spectrometry spectra, to large-scale complex pipelines integrating multiple computer programs to solve a collection of problems. This software evolution has been mostly driven by the appearance of novel technologies that allowed the community to tackle complex biological problems, such as the identification of proteins that are differentially expressed in two samples under different conditions. The achievement of such objectives requires a large suite of programs to analyze the intricate mass spectrometry data. Our laboratory addresses complex proteomics questions by producing and using algorithms and software packages. Our current computational pipeline includes, among other things, tools for mass spectrometry raw data processing, peptide and protein identification and quantification, post-translational modification analysis, and protein functional enrichment analysis. In this paper, we describe a suite of software packages we have developed to process mass spectrometry-based proteomics data and we highlight some of the new features of previously published programs as well as tools currently under development. Graphical Abstract ᅟ.

  5. From Raw Data to Biological Discoveries: A Computational Analysis Pipeline for Mass Spectrometry-Based Proteomics

    Science.gov (United States)

    Lavallée-Adam, Mathieu; Park, Sung Kyu Robin; Martínez-Bartolomé, Salvador; He, Lin; Yates, John R.

    2015-11-01

    In the last two decades, computational tools for mass spectrometry-based proteomics data analysis have evolved from a few stand-alone software solutions serving specific goals, such as the identification of amino acid sequences based on mass spectrometry spectra, to large-scale complex pipelines integrating multiple computer programs to solve a collection of problems. This software evolution has been mostly driven by the appearance of novel technologies that allowed the community to tackle complex biological problems, such as the identification of proteins that are differentially expressed in two samples under different conditions. The achievement of such objectives requires a large suite of programs to analyze the intricate mass spectrometry data. Our laboratory addresses complex proteomics questions by producing and using algorithms and software packages. Our current computational pipeline includes, among other things, tools for mass spectrometry raw data processing, peptide and protein identification and quantification, post-translational modification analysis, and protein functional enrichment analysis. In this paper, we describe a suite of software packages we have developed to process mass spectrometry-based proteomics data and we highlight some of the new features of previously published programs as well as tools currently under development.

  6. Biological computation

    CERN Document Server

    Lamm, Ehud

    2011-01-01

    Introduction and Biological BackgroundBiological ComputationThe Influence of Biology on Mathematics-Historical ExamplesBiological IntroductionModels and Simulations Cellular Automata Biological BackgroundThe Game of Life General Definition of Cellular Automata One-Dimensional AutomataExamples of Cellular AutomataComparison with a Continuous Mathematical Model Computational UniversalitySelf-Replication Pseudo Code Evolutionary ComputationEvolutionary Biology and Evolutionary ComputationGenetic AlgorithmsExample ApplicationsAnalysis of the Behavior of Genetic AlgorithmsLamarckian Evolution Genet

  7. The Driven Spinning Top

    Science.gov (United States)

    Grosu, Ioan; Featonby, David

    2016-01-01

    This driven top is quite a novelty and can, with some trials, be made using the principles outlined here. This new top has many applications in developing both understanding and skills and these are detailed in the article. Depending on reader's available time and motivation they may feel an urge to make one themselves, or simply invest a few…

  8. Software Architecture Design Reasoning

    Science.gov (United States)

    Tang, Antony; van Vliet, Hans

    Despite recent advancements in software architecture knowledge management and design rationale modeling, industrial practice is behind in adopting these methods. The lack of empirical proofs and the lack of a practical process that can be easily incorporated by practitioners are some of the hindrance for adoptions. In particular, the process to support systematic design reasoning is not available. To rectify this issue, we propose a design reasoning process to help architects cope with an architectural design environment where design concerns are cross-cutting and diversified.We use an industrial case study to validate that the design reasoning process can help improve the quality of software architecture design. The results have indicated that associating design concerns and identifying design options are important steps in design reasoning.

  9. Chemical recognition software

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, J.S.; Trahan, M.W.; Nelson, W.E.; Hargis, P.H. Jr.; Tisone, G.C.

    1994-06-01

    We have developed a capability to make real time concentration measurements of individual chemicals in a complex mixture using a multispectral laser remote sensing system. Our chemical recognition and analysis software consists of three parts: (1) a rigorous multivariate analysis package for quantitative concentration and uncertainty estimates, (2) a genetic optimizer which customizes and tailors the multivariate algorithm for a particular application, and (3) an intelligent neural net chemical filter which pre-selects from the chemical database to find the appropriate candidate chemicals for quantitative analyses by the multivariate algorithms, as well as providing a quick-look concentration estimate and consistency check. Detailed simulations using both laboratory fluorescence data and computer synthesized spectra indicate that our software can make accurate concentration estimates from complex multicomponent mixtures, even when the mixture is noisy and contaminated with unknowns.

  10. Chemical recognition software

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, J.S.; Trahan, M.W.; Nelson, W.E.; Hargis, P.J. Jr.; Tisone, G.C.

    1994-12-01

    We have developed a capability to make real time concentration measurements of individual chemicals in a complex mixture using a multispectral laser remote sensing system. Our chemical recognition and analysis software consists of three parts: (1) a rigorous multivariate analysis package for quantitative concentration and uncertainty estimates, (2) a genetic optimizer which customizes and tailors the multivariate algorithm for a particular application, and (3) an intelligent neural net chemical filter which pre-selects from the chemical database to find the appropriate candidate chemicals for quantitative analyses by the multivariate algorithms, as well as providing a quick-look concentration estimate and consistency check. Detailed simulations using both laboratory fluorescence data and computer synthesized spectra indicate that our software can make accurate concentration estimates from complex multicomponent mixtures. even when the mixture is noisy and contaminated with unknowns.

  11. Implementing Software Defined Radio

    CERN Document Server

    Grayver, Eugene

    2013-01-01

    Software Defined Radio makes wireless communications easier, more efficient, and more reliable. This book bridges the gap between academic research and practical implementation. When beginning a project, practicing engineers, technical managers, and graduate students can save countless hours by considering the concepts presented in these pages. The author covers the myriad options and trade-offs available when selecting an appropriate hardware architecture. As demonstrated here, the choice between hardware- and software-centric architecture can mean the difference between meeting an aggressive schedule and bogging down in endless design iterations. Because of the author’s experience overseeing dozens of failed and successful developments, he is able to present many real-life examples. Some of the key concepts covered are: Choosing the right architecture for the market – laboratory, military, or commercial Hardware platforms – FPGAs, GPPs, specialized and hybrid devices Standardization efforts to ens...

  12. TOUGH2 software qualification

    International Nuclear Information System (INIS)

    TOUGH2 is a numerical simulation code for multi-dimensional coupled fluid and heat flow of multiphase, multicomponent fluid mixtures in porous and fractured media. It belongs to the MULKOM (open-quotes MULti-KOMponentclose quotes) family of codes and is a more general version of the TOUGH simulator. The MULKOM family of codes was originally developed with a focus on geothermal reservoir simulation. They are suited to modeling systems which contain different fluid mixtures, with applications to flow problems arising in the context of high-level nuclear waste isolation, oil and gas recovery and storage, and groundwater resource protection. TOUGH2 is essentially a subset of MULKOM, consisting of a selection of the better tested and documented MULKOM program modules. The purpose of this package of reports is to provide all software baseline documents necessary for the software qualification of TOUGH2

  13. TOUGH2 software qualification

    Energy Technology Data Exchange (ETDEWEB)

    Pruess, K.; Simmons, A.; Wu, Y.S.; Moridis, G.

    1996-02-01

    TOUGH2 is a numerical simulation code for multi-dimensional coupled fluid and heat flow of multiphase, multicomponent fluid mixtures in porous and fractured media. It belongs to the MULKOM ({open_quotes}MULti-KOMponent{close_quotes}) family of codes and is a more general version of the TOUGH simulator. The MULKOM family of codes was originally developed with a focus on geothermal reservoir simulation. They are suited to modeling systems which contain different fluid mixtures, with applications to flow problems arising in the context of high-level nuclear waste isolation, oil and gas recovery and storage, and groundwater resource protection. TOUGH2 is essentially a subset of MULKOM, consisting of a selection of the better tested and documented MULKOM program modules. The purpose of this package of reports is to provide all software baseline documents necessary for the software qualification of TOUGH2.

  14. Applications in computer-assisted biology

    NARCIS (Netherlands)

    Nijveen, H.

    2013-01-01

    Biology is becoming a data-rich science driven by the development of high-throughput technologies like next-generation DNA sequencing. This is fundamentally changing biological research. The genome sequences of many species are becoming available, as well as the genetic variation within a species, a

  15. GEMBASSY: an EMBOSS associated software package for comprehensive genome analyses

    OpenAIRE

    Itaya, Hidetoshi; Oshita, Kazuki; Arakawa, Kazuharu; Tomita, Masaru

    2013-01-01

    The popular European Molecular Biology Open Software Suite (EMBOSS) currently contains over 400 tools used in various bioinformatics researches, equipped with sophisticated development frameworks for interoperability and tool discoverability as well as rich documentations and various user interfaces. In order to further strengthen EMBOSS in the fields of genomics, we here present a novel EMBOSS associated software (EMBASSY) package named GEMBASSY, which adds more than 50 analysis tools from t...

  16. Analysis of Whole Transcriptome Sequencing Data: Workflow and Software.

    Science.gov (United States)

    Yang, In Seok; Kim, Sangwoo

    2015-12-01

    RNA is a polymeric molecule implicated in various biological processes, such as the coding, decoding, regulation, and expression of genes. Numerous studies have examined RNA features using whole transcriptome sequencing (RNA-seq) approaches. RNA-seq is a powerful technique for characterizing and quantifying the transcriptome and accelerates the development of bioinformatics software. In this review, we introduce routine RNA-seq workflow together with related software, focusing particularly on transcriptome reconstruction and expression quantification. PMID:26865842

  17. The ATLAS data management software engineering process

    International Nuclear Information System (INIS)

    Rucio is the next-generation data management system of the ATLAS experiment. The software engineering process to develop Rucio is fundamentally different to existing software development approaches in the ATLAS distributed computing community. Based on a conceptual design document, development takes place using peer-reviewed code in a test-driven environment. The main objectives are to ensure that every engineer understands the details of the full project, even components usually not touched by them, that the design and architecture are coherent, that temporary contributors can be productive without delay, that programming mistakes are prevented before being committed to the source code, and that the source is always in a fully functioning state. This contribution will illustrate the workflows and products used, and demonstrate the typical development cycle of a component from inception to deployment within this software engineering process. Next to the technological advantages, this contribution will also highlight the social aspects of an environment where every action is subject to detailed scrutiny.

  18. The ATLAS data management software engineering process

    Science.gov (United States)

    Lassnig, M.; Garonne, V.; Stewart, G. A.; Barisits, M.; Beermann, T.; Vigne, R.; Serfon, C.; Goossens, L.; Nairz, A.; Molfetas, A.; Atlas Collaboration

    2014-06-01

    Rucio is the next-generation data management system of the ATLAS experiment. The software engineering process to develop Rucio is fundamentally different to existing software development approaches in the ATLAS distributed computing community. Based on a conceptual design document, development takes place using peer-reviewed code in a test-driven environment. The main objectives are to ensure that every engineer understands the details of the full project, even components usually not touched by them, that the design and architecture are coherent, that temporary contributors can be productive without delay, that programming mistakes are prevented before being committed to the source code, and that the source is always in a fully functioning state. This contribution will illustrate the workflows and products used, and demonstrate the typical development cycle of a component from inception to deployment within this software engineering process. Next to the technological advantages, this contribution will also highlight the social aspects of an environment where every action is subject to detailed scrutiny.

  19. ThermalTracker Software

    Energy Technology Data Exchange (ETDEWEB)

    2016-08-10

    The software processes recorded thermal video and detects the flight tracks of birds and bats that passed through the camera's field of view. The output is a set of images that show complete flight tracks for any detections, with the direction of travel indicated and the thermal image of the animal delineated. A report of the descriptive features of each detected track is also output in the form of a comma-separated value text file.

  20. Standard software for CAMAC

    International Nuclear Information System (INIS)

    The NIM Committee (National Instrumentation Methods Committee) of the U.S. Department of Energy and the ESONE Committee of European Laboratories have jointly specified standard software for use with CAMAC. Three general approaches were followed: the definition of a language called IML for use in CAMAC systems, the definition of a standard set of subroutine calls, and real-time extensions to the BASIC language. This paper summarizes the results of these efforts. 1 table