WorldWideScience

Sample records for biology driven software

  1. Systems biology driven software design for the research enterprise

    Directory of Open Access Journals (Sweden)

    Killcoyne Sarah

    2008-06-01

    Full Text Available Abstract Background In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature of systems biology, and its association with high throughput experimental platforms, there is an additional need to continually integrate new technologies. As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools. Results We illustrate an approach, through the discussion of a purpose built software architecture, which allows disparate groups to reuse tools and access data sources in a common manner. The architecture allows for: the rapid development of distributed applications; interoperability, so it can be used by a wide variety of developers and computational biologists; development using standard tools, so that it is easy to maintain and does not require a large development effort; extensibility, so that new technologies and data types can be incorporated; and non intrusive development, insofar as researchers need not to adhere to a pre-existing object model. Conclusion By using a relatively simple integration strategy, based upon a common identity system and dynamically discovered interoperable services, a light-weight software architecture can become the focal point through which scientists can both get access to and analyse the plethora of experimentally derived data.

  2. 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

  3. 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

  4. 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

  5. Metrics for Event Driven Software

    Directory of Open Access Journals (Sweden)

    Neha Chaudhary

    2016-01-01

    Full Text Available The evaluation of Graphical User Interface has significant role to improve its quality. Very few metrics exists for the evaluation of Graphical User Interface. The purpose of metrics is to obtain better measurements in terms of risk management, reliability forecast, project scheduling, and cost repression. In this paper structural complexity metrics is proposed for the evaluation of Graphical User Interface. Structural complexity of Graphical User Interface is considered as an indicator of complexity. The goal of identifying structural complexity is to measure the GUI testability. In this testability evaluation the process of measuring the complexity of the user interface from testing perspective is proposed. For the GUI evaluation and calculating structural complexity an assessment process is designed which is based on types of events. A fuzzy model is developed to evaluate the structural complexity of GUI. This model takes five types of events as input and return structural complexity of GUI as output. Further a relationship is established between structural complexity and testability of event driven software. Proposed model is evaluated with four different applications. It is evident from the results that higher the complexities lower the testability of application.

  6. Quality Attribute Driven Software Architecture Reconstruction

    Science.gov (United States)

    2016-06-21

    3890 Quality Attribute Driven Software Architecture Reconstruction SATURN Workshop April 7, 2005 Liam O’Brien © 2005 by Carnegie Mellon University...Version 1.0 QADSAR – SATURN 2005 - page 2 Motivation - 1 • Software architectures are critical to implement an organization’s business goals and critical...Attribute Driven Software Architecture Reconstruction 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER

  7. 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.

  8. 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

  9. Static Checking of Interrupt-driven Software

    DEFF Research Database (Denmark)

    Brylow, Dennis; Damgaard, Niels; Palsberg, Jens

    2001-01-01

    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...

  10. Model Driven Software Development for Agricultural Robotics

    DEFF Research Database (Denmark)

    Larsen, Morten

    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...

  11. Model-driven evolution of software architectures

    OpenAIRE

    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 costs associated with the evolution of software architectures. Automation and abstraction are two basic software engineering techniques to deal with complexity. In this thesis we investigate the appli...

  12. 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

  13. Traceability for Model Driven, Software Product Line Engineering

    NARCIS (Netherlands)

    Anquetil, N.; Grammel, B.; Galvao Lourenco da Silva, I.; Noppen, J.A.R.; Shakil Khan, S.; Arboleda, H.; Rashid, A.; Garcia, A.

    2008-01-01

    Traceability is an important challenge for software organizations. This is true for traditional software development and even more so in new approaches that introduce more variety of artefacts such as Model Driven development or Software Product Lines. In this paper we look at some aspect of the int

  14. 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

  15. 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

  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. 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.

  18. Small is beautiful: customer driven software development

    DEFF Research Database (Denmark)

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

    1999-01-01

    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......, professional associations and software houses. The paper presents a case study of the product development for a Danish owned software house.......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...

  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. Constraint driven software design: an escape from the waterfall model

    NARCIS (Netherlands)

    Hoog, de Robert; Jong, de Ton; Vries, de Frits

    1994-01-01

    This paper presents the principles of a development methodology for software design. The methodology is based on a nonlinear, product-driven approach that integrates quality aspects. The principles are made more concrete in two examples: one for developing educational simulations and one for develop

  1. 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.

  2. 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.

  3. 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.

  4. Constraint driven software design: an escape from the waterfall model

    OpenAIRE

    Hoog, de, C.; Jong, De, Cornelis; Vries, de, B.

    1994-01-01

    This paper presents the principles of a development methodology for software design. The methodology is based on a nonlinear, product-driven approach that integrates quality aspects. The principles are made more concrete in two examples: one for developing educational simulations and one for developing expert systems. It is shown that the flexibility needed for building high quality systems leads to integrated development environments in which methodology, product and tools are closely attune...

  5. Aspect-Oriented Model-Driven Software Product Line Engineering

    Science.gov (United States)

    Groher, Iris; Voelter, Markus

    Software product line engineering aims to reduce development time, effort, cost, and complexity by taking advantage of the commonality within a portfolio of similar products. The effectiveness of a software product line approach directly depends on how well feature variability within the portfolio is implemented and managed throughout the development lifecycle, from early analysis through maintenance and evolution. This article presents an approach that facilitates variability implementation, management, and tracing by integrating model-driven and aspect-oriented software development. Features are separated in models and composed of aspect-oriented composition techniques on model level. Model transformations support the transition from problem to solution space models. Aspect-oriented techniques enable the explicit expression and modularization of variability on model, template, and code level. The presented concepts are illustrated with a case study of a home automation system.

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. Software for systems biology: from tools to integrated platforms.

    Science.gov (United States)

    Ghosh, Samik; Matsuoka, Yukiko; Asai, Yoshiyuki; Hsin, Kun-Yi; Kitano, Hiroaki

    2011-11-03

    Understanding complex biological systems requires extensive support from software tools. Such tools are needed at each step of a systems biology computational workflow, which typically consists of data handling, network inference, deep curation, dynamical simulation and model analysis. In addition, there are now efforts to develop integrated software platforms, so that tools that are used at different stages of the workflow and by different researchers can easily be used together. This Review describes the types of software tools that are required at different stages of systems biology research and the current options that are available for systems biology researchers. We also discuss the challenges and prospects for modelling the effects of genetic changes on physiology and the concept of an integrated platform.

  11. Observation-Driven Configuration of Complex Software Systems

    CERN Document Server

    Sage, Aled

    2010-01-01

    The ever-increasing complexity of software systems makes them hard to comprehend, predict and tune due to emergent properties and non-deterministic behaviour. Complexity arises from the size of software systems and the wide variety of possible operating environments: the increasing choice of platforms and communication policies leads to ever more complex performance characteristics. In addition, software systems exhibit different behaviour under different workloads. Many software systems are designed to be configurable so that policies can be chosen to meet the needs of various stakeholders. For complex software systems it can be difficult to accurately predict the effects of a change and to know which configuration is most appropriate. This thesis demonstrates that it is useful to run automated experiments that measure a selection of system configurations. Experiments can find configurations that meet the stakeholders' needs, find interesting behavioural characteristics, and help produce predictive models of...

  12. 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…

  13. 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.

  14. 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.

  15. 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 ...

  16. 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.

  17. 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.

  18. Software that goes with the flow in systems biology

    Directory of Open Access Journals (Sweden)

    Le Novère Nicolas

    2010-11-01

    Full Text Available Abstract A recent article in BMC Bioinformatics describes new advances in workflow systems for computational modeling in systems biology. Such systems can accelerate, and improve the consistency of, modeling through automation not only at the simulation and results-production stages, but also at the model-generation stage. Their work is a harbinger of the next generation of more powerful software for systems biologists. See research article: http://www.biomedcentral.com/1471-2105/11/582/abstract/ Ever since the rise of systems biology at the end of the last century, mathematical representations of biological systems and their activities have flourished. They are being used to describe everything from biomolecular networks, such as gene regulation, metabolic processes and signaling pathways, at the lowest biological scales, to tissue growth and differentiation, drug effects, environmental interactions, and more. A very active area in the field has been the development of techniques that facilitate the construction, analysis and dissemination of computational models. The heterogeneous, distributed nature of most data resources today has increased not only the opportunities for, but also the difficulties of, developing software systems to support these tasks. The work by Li et al. 1 published in BMC Bioinformatics represents a promising evolutionary step forward in this area. They describe a workflow system - a visual software environment enabling a user to create a connected set of operations to be performed sequentially using seperate tools and resources. Their system uses third-party data resources accessible over the Internet to elaborate and parametrize (that is, assign parameter values to computational models in a semi-automated manner. In Li et al.'s work, the authors point towards a promising future for computational modeling and simultaneously highlight some of the difficulties that need to be overcome before we get there.

  19. 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.

  20. 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

    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...... a mixed development approach.......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...

  1. 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.

  2. 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...

  3. 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.

  4. Pegasys: software for executing and integrating analyses of biological sequences

    Directory of Open Access Journals (Sweden)

    Lett Drew

    2004-04-01

    Full Text Available Abstract Background We present Pegasys – a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools. Results The Pegasys system includes numerous tools for pair-wise and multiple sequence alignment, ab initio gene prediction, RNA gene detection, masking repetitive sequences in genomic DNA as well as filters for database formatting and processing raw output from various analysis tools. We introduce a novel data structure for creating workflows of sequence analyses and a unified data model to store its results. The software allows users to dynamically create analysis workflows at run-time by manipulating a graphical user interface. All non-serial dependent analyses are executed in parallel on a compute cluster for efficiency of data generation. The uniform data model and backend relational database management system of Pegasys allow for results of heterogeneous programs included in the workflow to be integrated and exported into General Feature Format for further analyses in GFF-dependent tools, or GAME XML for import into the Apollo genome editor. The modularity of the design allows for new tools to be added to the system with little programmer overhead. The database application programming interface allows programmatic access to the data stored in the backend through SQL queries. Conclusions The Pegasys system enables biologists and bioinformaticians to create and manage sequence analysis workflows. The software is released under the Open Source GNU General Public License. All source code and documentation is available for download at http://bioinformatics.ubc.ca/pegasys/.

  5. 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.

  6. 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.

  7. 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.

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

    Science.gov (United States)

    Shamir, Lior; Delaney, John D; Orlov, Nikita; Eckley, D Mark; Goldberg, Ilya G

    2010-11-24

    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.

  9. The CECAM Electronic Structure Library: community-driven development of software libraries for electronic structure simulations

    Science.gov (United States)

    Oliveira, Micael

    The CECAM Electronic Structure Library (ESL) is a community-driven effort to segregate shared pieces of software as libraries that could be contributed and used by the community. Besides allowing to share the burden of developing and maintaining complex pieces of software, these can also become a target for re-coding by software engineers as hardware evolves, ensuring that electronic structure codes remain at the forefront of HPC trends. In a series of workshops hosted at the CECAM HQ in Lausanne, the tools and infrastructure for the project were prepared, and the first contributions were included and made available online (http://esl.cecam.org). In this talk I will present the different aspects and aims of the ESL and how these can be useful for the electronic structure community.

  10. 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.

  11. 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.

  12. 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.

    . An event driven software package was developed for the above database. The Graphical User Interface (GUI) software using 'C' language helps to retrieve the required parameter at a particular place/station. This is very helpful to search for the data of a...

  13. The Case for "Story-Driven" Biology Education

    Science.gov (United States)

    Schattner, Peter

    2015-01-01

    Can learning molecular biology and genetics be enjoyable? Of course it can. Biologists know their field is exciting and fascinating and that learning how cells and molecules shape the living world is extraordinarily interesting. But can students who are not already inclined towards science also be convinced that learning molecular biology is…

  14. 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…

  15. Web-based software tool for constraint-based design specification of synthetic biological systems.

    Science.gov (United States)

    Oberortner, Ernst; Densmore, Douglas

    2015-06-19

    miniEugene provides computational support for solving combinatorial design problems, enabling users to specify and enumerate designs for novel biological systems based on sets of biological constraints. This technical note presents a brief tutorial for biologists and software engineers in the field of synthetic biology on how to use miniEugene. After reading this technical note, users should know which biological constraints are available in miniEugene, understand the syntax and semantics of these constraints, and be able to follow a step-by-step guide to specify the design of a classical synthetic biological system-the genetic toggle switch.1 We also provide links and references to more information on the miniEugene web application and the integration of the miniEugene software library into sophisticated Computer-Aided Design (CAD) tools for synthetic biology ( www.eugenecad.org ).

  16. 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.

  17. Practical use of BiNoM: a biological network manager software.

    Science.gov (United States)

    Bonnet, Eric; Calzone, Laurence; Rovera, Daniel; Stoll, Gautier; Barillot, Emmanuel; Zinovyev, Andrei

    2013-01-01

    The Biological Network Manager (BiNoM) is a software tool for the manipulation and analysis of biological networks. It facilitates the import and conversion of a set of well-established systems biology file formats. It also provides a large set of graph-based algorithms that allow users to analyze and extract relevant subnetworks from large molecular maps. It has been successfully used in several projects related to the analysis of large and complex biological data, or networks from databases. In this tutorial, we present a detailed and practical case study of how to use BiNoM to analyze biological networks.

  18. 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.

  19. Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab

    Directory of Open Access Journals (Sweden)

    Michael R. Crusoe

    2016-11-01

    Full Text Available The khmer software project provides both research and production functionality for largescale nucleic-acid sequence analysis. The software implements several novel data structures and algorithms that perform data pre-filtering for common bioinformatics tasks, including sequence mapping and de novo assembly. Development is driven by a small lab with one full-time developer (MRC, as well as several graduate students and a professor (CTB who contribute regularly to research features. Here we describe our efforts to bring better design, testing, and more open development to the khmer software project as of version 1.1. The khmer software is developed openly at http://github.com/dib-lab/khmer/.

  20. 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.

  1. 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...

  2. 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...

  3. 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...

  4. 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.

  5. 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…

  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. Metric Evolution Maps : Multidimensional Attribute-driven Exploration of Software Repositories

    NARCIS (Netherlands)

    Rodrigues Oliveira da Silva, Renato; Faccin Vernier, Eduardo; Rauber, Paulo; Comba, J. L. D.; Minghim, Rosane; Telea, Alexandru

    2016-01-01

    Understanding how software entities in a repository evolve over time is challenging, as an entity has many aspects that undergo such changes. We cast this problem in a multidimensional visualization context: First, we capture change by extracting quality metrics from all software entities in all rev

  8. 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.

  9. 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.

  10. Model-driven robot-software design using template-based target descriptions

    NARCIS (Netherlands)

    Broenink, Jan F.; Groothuis, Marcel A.; Visser, Peter M.; Bezemer, M.M.; Kubus, D.; Nilsson, K.; Johansson, R.

    2010-01-01

    This paper is about using templates and passing model-specific information between tools via parameterized tokens in the generated, high-level code, to get a better separation of design steps. This allows for better quality of the models and more reuse, thus enhancing the efficiency of model-driven

  11. 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

  12. Examples of testing global identifiability of biological and biomedical models with the DAISY software.

    Science.gov (United States)

    Saccomani, Maria Pia; Audoly, Stefania; Bellu, Giuseppina; D'Angiò, Leontina

    2010-04-01

    DAISY (Differential Algebra for Identifiability of SYstems) is a recently developed computer algebra software tool which can be used to automatically check global identifiability of (linear and) nonlinear dynamic models described by differential equations involving polynomial or rational functions. Global identifiability is a fundamental prerequisite for model identification which is important not only for biological or medical systems but also for many physical and engineering systems derived from first principles. Lack of identifiability implies that the parameter estimation techniques may not fail but any obtained numerical estimates will be meaningless. The software does not require understanding of the underlying mathematical principles and can be used by researchers in applied fields with a minimum of mathematical background. We illustrate the DAISY software by checking the a priori global identifiability of two benchmark nonlinear models taken from the literature. The analysis of these two examples includes comparison with other methods and demonstrates how identifiability analysis is simplified by this tool. Thus we illustrate the identifiability analysis of other two examples, by including discussion of some specific aspects related to the role of observability and knowledge of initial conditions in testing identifiability and to the computational complexity of the software. The main focus of this paper is not on the description of the mathematical background of the algorithm, which has been presented elsewhere, but on illustrating its use and on some of its more interesting features. DAISY is available on the web site http://www.dei.unipd.it/ approximately pia/.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. Software design for a database driven system for accelerator magnet measurements

    Energy Technology Data Exchange (ETDEWEB)

    Brown, B.C.; Bleadon, M.E.; Glass, H.D.; Glosson, R.; Hanft, R.W.; Harding, D.J.; Mazur, P.O.; Pachnik, J.E.; Sim, J.W.; Trombly-Freytag, K.; Walbridge, D.G.

    1991-05-01

    Measurements of more than 1000 new magnets are needed for the Main Injector Project at Fermilab. In order to achieve efficiency and accuracy in measurements, we chose a database driven design for control of the measurement system. We will use a relational database to describe the measurement subjects and equipment. A logbook system defined in the database will provide for prescription of measurements to be carried out, description of measurements as they are carried out, and a comment database for less structured information. The operator interface will be built on X-windows. This paper will describe our system design. 2 refs.

  18. 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.

  19. 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%...

  20. 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.

  1. 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

  2. GOAL: A software tool for assessing biological significance of genes groups

    Directory of Open Access Journals (Sweden)

    Famili Fazel

    2010-05-01

    Full Text Available Abstract Background Modern high throughput experimental techniques such as DNA microarrays often result in large lists of genes. Computational biology tools such as clustering are then used to group together genes based on their similarity in expression profiles. Genes in each group are probably functionally related. The functional relevance among the genes in each group is usually characterized by utilizing available biological knowledge in public databases such as Gene Ontology (GO, KEGG pathways, association between a transcription factor (TF and its target genes, and/or gene networks. Results We developed GOAL: Gene Ontology AnaLyzer, a software tool specifically designed for the functional evaluation of gene groups. GOAL implements and supports efficient and statistically rigorous functional interpretations of gene groups through its integration with available GO, TF-gene association data, and association with KEGG pathways. In order to facilitate more specific functional characterization of a gene group, we implement three GO-tree search strategies rather than one as in most existing GO analysis tools. Furthermore, GOAL offers flexibility in deployment. It can be used as a standalone tool, a plug-in to other computational biology tools, or a web server application. Conclusion We developed a functional evaluation software tool, GOAL, to perform functional characterization of a gene group. GOAL offers three GO-tree search strategies and combines its strength in function integration, portability and visualization, and its flexibility in deployment. Furthermore, GOAL can be used to evaluate and compare gene groups as the output from computational biology tools such as clustering algorithms.

  3. Ideas and perspectives: climate-relevant marine biologically driven mechanisms in Earth system models

    Science.gov (United States)

    Hense, Inga; Stemmler, Irene; Sonntag, Sebastian

    2017-01-01

    The current generation of marine biogeochemical modules in Earth system models (ESMs) considers mainly the effect of marine biota on the carbon cycle. We propose to also implement other biologically driven mechanisms in ESMs so that more climate-relevant feedbacks are captured. We classify these mechanisms in three categories according to their functional role in the Earth system: (1) biogeochemical pumps, which affect the carbon cycling; (2) biological gas and particle shuttles, which affect the atmospheric composition; and (3) biogeophysical mechanisms, which affect the thermal, optical, and mechanical properties of the ocean. To resolve mechanisms from all three classes, we find it sufficient to include five functional groups: bulk phyto- and zooplankton, calcifiers, and coastal gas and surface mat producers. We strongly suggest to account for a larger mechanism diversity in ESMs in the future to improve the quality of climate projections.

  4. 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…

  5. Atlas-builder software and the eNeuro atlas: resources for developmental biology and neuroscience.

    Science.gov (United States)

    Heckscher, Ellie S; Long, Fuhui; Layden, Michael J; Chuang, Chein-Hui; Manning, Laurina; Richart, Jourdain; Pearson, Joseph C; Crews, Stephen T; Peng, Hanchuan; Myers, Eugene; Doe, Chris Q

    2014-06-01

    A major limitation in understanding embryonic development is the lack of cell type-specific markers. Existing gene expression and marker atlases provide valuable tools, but they typically have one or more limitations: a lack of single-cell resolution; an inability to register multiple expression patterns to determine their precise relationship; an inability to be upgraded by users; an inability to compare novel patterns with the database patterns; and a lack of three-dimensional images. Here, we develop new 'atlas-builder' software that overcomes each of these limitations. A newly generated atlas is three-dimensional, allows the precise registration of an infinite number of cell type-specific markers, is searchable and is open-ended. Our software can be used to create an atlas of any tissue in any organism that contains stereotyped cell positions. We used the software to generate an 'eNeuro' atlas of the Drosophila embryonic CNS containing eight transcription factors that mark the major CNS cell types (motor neurons, glia, neurosecretory cells and interneurons). We found neuronal, but not glial, nuclei occupied stereotyped locations. We added 75 new Gal4 markers to the atlas to identify over 50% of all interneurons in the ventral CNS, and these lines allowed functional access to those interneurons for the first time. We expect the atlas-builder software to benefit a large proportion of the developmental biology community, and the eNeuro atlas to serve as a publicly accessible hub for integrating neuronal attributes - cell lineage, gene expression patterns, axon/dendrite projections, neurotransmitters--and linking them to individual neurons.

  6. Model for biological communication in a nanofabricated cell-mimic driven by stochastic resonance

    Energy Technology Data Exchange (ETDEWEB)

    Karig, David K [ORNL; Siuti, Piro [ORNL; Dar, Roy D. [University of Tennessee, Knoxville (UTK); Retterer, Scott T [ORNL; Doktycz, Mitchel John [ORNL; Simpson, Michael L [ORNL

    2011-01-01

    Cells offer natural examples of highly efficient networks of nanomachines. Accordingly, both intracellular and intercellular communication mechanisms in nature are looked to as a source of inspiration and instruction for engineered nanocommunication. Harnessing biological functionality in this manner requires an interdisciplinary approach that integrates systems biology, synthetic biology, and nanofabrication. Recent years have seen the amassing of a tremendous wealth of data from the sequencing of new organisms and from high throughput expression experiments. At the same time, a deeper fundamental understanding of individual cell function has been developed, as exemplified by the growth of fields such as noise biology, which seeks to characterize the role of noise in gene expression. The availability of well characterized biological components coupled with a deeper understanding of cell function has led to efforts to engineer both living cells and to create bio-like functionality in non-living substrates in the field of synthetic biology. Here, we present a model system that exemplifies the synergism between these realms of research. We propose a synthetic gene network for operation in a nanofabricated cell mimic array that propagates a biomolecular signal over long distances using the phenomenon of stochastic resonance. Our system consists of a bacterial quorum sensing signal molecule, a bistable genetic switch triggered by this signal, and an array of nanofabricated cell mimic wells that contain the genetic system. An optimal level of noise in the system helps to propagate a time-varying AHL signal over long distances through the array of mimics. This noise level is determined both by the system volume and by the parameters of the genetic network. Our proposed genetically driven stochastic resonance system serves as a testbed for exploring the potential harnessing of gene expression noise to aid in the transmission of a time-varying molecular signal.

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

    Directory of Open Access Journals (Sweden)

    Balsa-Canto Eva

    2009-06-01

    Full Text Available 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. Dynamic optimization can solve many important problems in systems biology, including optimal control for obtaining a desired biological performance, the analysis of network designs and computer aided design of biological units. Results Here, we present a software toolbox, DOTcvpSB, which uses a rich ensemble of state-of-the-art numerical methods for solving continuous and mixed-integer dynamic optimization (MIDO problems. The toolbox has been written in MATLAB and provides an easy and user friendly environment, including a graphical user interface, while ensuring a good numerical performance. Problems are easily stated thanks to the compact input definition. The toolbox also offers the possibility of importing SBML models, thus enabling it as a powerful optimization companion to modelling packages in systems biology. It serves as a means of handling generic black-box models as well. Conclusion Here we illustrate the capabilities and performance of DOTcvpSB by solving several challenging optimization problems related with bioreactor optimization, optimal drug infusion to a patient and the minimization of intracellular oscillations. The results illustrate how the suite of solvers available allows the efficient solution of a wide class of dynamic optimization problems, including challenging multimodal ones. The toolbox is freely available for academic use.

  8. Biological knowledge-driven analysis of epistasis in human GWAS with application to lipid traits.

    Science.gov (United States)

    Ma, Li; Keinan, Alon; Clark, Andrew G

    2015-01-01

    While the importance of epistasis is well established, specific gene-gene interactions have rarely been identified in human genome-wide association studies (GWAS), mainly due to low power associated with such interaction tests. In this chapter, we integrate biological knowledge and human GWAS data to reveal epistatic interactions underlying quantitative lipid traits, which are major risk factors for coronary artery disease. To increase power to detect interactions, we only tested pairs of SNPs filtered by prior biological knowledge, including GWAS results, protein-protein interactions (PPIs), and pathway information. Using published GWAS and 9,713 European Americans (EA) from the Atherosclerosis Risk in Communities (ARIC) study, we identified an interaction between HMGCR and LIPC affecting high-density lipoprotein cholesterol (HDL-C) levels. We then validated this interaction in additional multiethnic cohorts from ARIC, the Framingham Heart Study, and the Multi-Ethnic Study of Atherosclerosis. Both HMGCR and LIPC are involved in the metabolism of lipids and lipoproteins, and LIPC itself has been marginally associated with HDL-C. Furthermore, no significant interaction was detected using PPI and pathway information, mainly due to the stringent significance level required after correcting for the large number of tests conducted. These results suggest the potential of biological knowledge-driven approaches to detect epistatic interactions in human GWAS, which may hold the key to exploring the role gene-gene interactions play in connecting genotypes and complex phenotypes in future GWAS.

  9. 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.

  10. Human urinary biomarkers of dioxin exposure: analysis by metabolomics and biologically driven data dimensionality reduction.

    Science.gov (United States)

    Jeanneret, Fabienne; Boccard, Julien; Badoud, Flavia; Sorg, Olivier; Tonoli, David; Pelclova, Daniela; Vlckova, Stepanka; Rutledge, Douglas N; Samer, Caroline F; Hochstrasser, Denis; Saurat, Jean-Hilaire; Rudaz, Serge

    2014-10-15

    Untargeted metabolomic approaches offer new opportunities for a deeper understanding of the molecular events related to toxic exposure. This study proposes a metabolomic investigation of biochemical alterations occurring in urine as a result of dioxin toxicity. Urine samples were collected from Czech chemical workers submitted to severe dioxin occupational exposure in a herbicide production plant in the late 1960s. Experiments were carried out with ultra-high pressure liquid chromatography (UHPLC) coupled to high-resolution quadrupole time-of-flight (QTOF) mass spectrometry. A chemistry-driven feature selection was applied to focus on steroid-related metabolites. Supervised multivariate data analysis allowed biomarkers, mainly related to bile acids, to be highlighted. These results supported the hypothesis of liver damage and oxidative stress for long-term dioxin toxicity. As a second step of data analysis, the information gained from the urine analysis of Victor Yushchenko after his poisoning was examined. A subset of relevant urinary markers of acute dioxin toxicity from this extreme phenotype, including glucuro- and sulfo-conjugated endogenous steroid metabolites and bile acids, was assessed for its ability to detect long-term effects of exposure. The metabolomic strategy presented in this work allowed the determination of metabolic patterns related to dioxin effects in human and the discovery of highly predictive subsets of biologically meaningful and clinically relevant compounds. These results are expected to provide valuable information for a deeper understanding of the molecular events related to dioxin toxicity. Furthermore, it presents an original methodology of data dimensionality reduction by using extreme phenotype as a guide to select relevant features prior to data modeling (biologically driven data reduction).

  11. 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.

  12. 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

    2016-01-04

    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.

  13. Respondent driven sampling for HIV biological and behavioral surveillance in Latin America and the Caribbean.

    Science.gov (United States)

    Montealegre, Jane R; Johnston, Lisa G; Murrill, Christopher; Monterroso, Edgar

    2013-09-01

    Since 2005, respondent driven sampling (RDS) has been widely used for HIV biological and behavioral surveillance surveys (BBSS) in Latin America and the Caribbean (LAC). In this manuscript, we provide a focused review of RDS among hard-to-reach high-risk populations in LAC and describe their principal operational, design, and analytical considerations. We reviewed published and unpublished reports, protocols, and manuscripts for RDS studies conducted in LAC between January 1, 2005 and December 31, 2011. We abstracted key operational information and generated summary statistics across all studies. Between 2005 and 2011, 87 RDS studies were conducted in 15 countries in LAC (68 % in South America, 18 % in Mexico and Central America, and 14 % in the Caribbean). The target populations were primarily men who have sex with men (43 %), sex workers (29 %), and drug users (26 %). Study considerations included establishing clear eligibility criteria, measuring social network sizes, collecting specimens for biological testing, among others. Most of the reviewed studies are the first in their respective countries to collect data on hard-to-reach populations and the first attempt to use a probability-based sampling method. These RDS studies allowed researchers and public health practitioners in LAC to access hard-to-reach HIV high-risk populations and collect valuable data on the prevalence of HIV and other infections, as well as related risk behaviors.

  14. Documentation Driven Software Development

    Science.gov (United States)

    2010-06-01

    Information Assurance Workshop, June21-23, 2006. 26 Lange, Douglas . “PAL Boot Camp: Acquiring, Training, and Deploying Systems with Learning... McGregor , D, Brutzman, D, Blais, C, Arnold, A, Falash, M, Pollak, E, “DIS-XML: Moving to Open Data Exchange Standards”, Proceedings of the Simulation

  15. 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

  16. Biologically driven neural platform invoking parallel electrophoretic separation and urinary metabolite screening.

    Science.gov (United States)

    Page, Tessa; Nguyen, Huong Thi Huynh; Hilts, Lindsey; Ramos, Lorena; Hanrahan, Grady

    2012-06-01

    This work reveals a computational framework for parallel electrophoretic separation of complex biological macromolecules and model urinary metabolites. More specifically, the implementation of a particle swarm optimization (PSO) algorithm on a neural network platform for multiparameter optimization of multiplexed 24-capillary electrophoresis technology with UV detection is highlighted. Two experimental systems were examined: (1) separation of purified rabbit metallothioneins and (2) separation of model toluene urinary metabolites and selected organic acids. Results proved superior to the use of neural networks employing standard back propagation when examining training error, fitting response, and predictive abilities. Simulation runs were obtained as a result of metaheuristic examination of the global search space with experimental responses in good agreement with predicted values. Full separation of selected analytes was realized after employing optimal model conditions. This framework provides guidance for the application of metaheuristic computational tools to aid in future studies involving parallel chemical separation and screening. Adaptable pseudo-code is provided to enable users of varied software packages and modeling framework to implement the PSO algorithm for their desired use.

  17. 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…

  18. Decision peptide-driven: a free software tool for accurate protein quantification using gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry.

    Science.gov (United States)

    Santos, Hugo M; Reboiro-Jato, Miguel; Glez-Peña, Daniel; Nunes-Miranda, J D; Fdez-Riverola, Florentino; Carvallo, R; Capelo, J L

    2010-09-15

    The decision peptide-driven tool implements a software application for assisting the user in a protocol for accurate protein quantification based on the following steps: (1) protein separation through gel electrophoresis; (2) in-gel protein digestion; (3) direct and inverse (18)O-labeling and (4) matrix assisted laser desorption ionization time of flight mass spectrometry, MALDI analysis. The DPD software compares the MALDI results of the direct and inverse (18)O-labeling experiments and quickly identifies those peptides with paralleled loses in different sets of a typical proteomic workflow. Those peptides are used for subsequent accurate protein quantification. The interpretation of the MALDI data from direct and inverse labeling experiments is time-consuming requiring a significant amount of time to do all comparisons manually. The DPD software shortens and simplifies the searching of the peptides that must be used for quantification from a week to just some minutes. To do so, it takes as input several MALDI spectra and aids the researcher in an automatic mode (i) to compare data from direct and inverse (18)O-labeling experiments, calculating the corresponding ratios to determine those peptides with paralleled losses throughout different sets of experiments; and (ii) allow to use those peptides as internal standards for subsequent accurate protein quantification using (18)O-labeling. In this work the DPD software is presented and explained with the quantification of protein carbonic anhydrase.

  19. An Hypothesis-Driven, Molecular Phylogenetics Exercise for College Biology Students

    Science.gov (United States)

    Parker, Joel D.; Ziemba, Robert E.; Cahan, Sara Helms; Rissing, Steven W.

    2004-01-01

    This hypothesis-driven laboratory exercise teaches how DNA evidence can be used to investigate an organism's evolutionary history while providing practical modeling of the fundamental processes of gene transcription and translation. We used an inquiry-based approach to construct a laboratory around a nontrivial, open-ended evolutionary question…

  20. Interactive learning in biology with PhotoCD and associated software

    Directory of Open Access Journals (Sweden)

    Linda Baggott

    1995-12-01

    Full Text Available PhotoCD is a novel electronic format which uses digital technology to scan colour or monochrome photographs, store them on compact discs, and then display them as highquality images on a TV or on a monitor screen. A technical description of this technology can be found in Beisner (1993, Bowers (1994 and Chen (1993. Supporting software is available to access and manipulate the images for use in interactive learning.

  1. Mapping Transcriptional Networks in Plants: Data-Driven Discovery of Novel Biological Mechanisms.

    Science.gov (United States)

    Gaudinier, Allison; Brady, Siobhan M

    2016-04-29

    In plants, systems biology approaches have led to the generation of a variety of large data sets. Many of these data are created to elucidate gene expression profiles and their corresponding transcriptional regulatory mechanisms across a range of tissue types, organs, and environmental conditions. In an effort to map the complexity of this transcriptional regulatory control, several types of experimental assays have been used to map transcriptional regulatory networks. In this review, we discuss how these methods can be best used to identify novel biological mechanisms by focusing on the appropriate biological context. Translating network biology back to gene function in the plant, however, remains a challenge. We emphasize the need for validation and insight into the underlying biological processes to successfully exploit systems approaches in an effort to determine the emergent properties revealed by network analyses.

  2. 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…

  3. 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.

  4. 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

  5. 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....

  6. 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.

  7. Evidence of market-driven size-selective fishing and the mediating effects of biological and institutional factors

    Science.gov (United States)

    Reddy, Sheila M. W.; Wentz, Allison; Aburto-Oropeza, Octavio; Maxey, Martin; Nagavarapu, Sriniketh; Leslie, Heather M.

    2014-01-01

    Market demand is often ignored or assumed to lead uniformly to the decline of resources. Yet little is known about how market demand influences natural resources in particular contexts, or the mediating effects of biological or institutional factors. Here, we investigate this problem by examining the Pacific red snapper (Lutjanus peru) fishery around La Paz, Mexico, where medium or “plate-sized” fish are sold to restaurants at a premium price. If higher demand for plate-sized fish increases the relative abundance of the smallest (recruit size class) and largest (most fecund) fish, this may be a market mechanism to increase stocks and fishermen’s revenues. We tested this hypothesis by estimating the effect of prices on the distribution of catch across size classes using daily records of prices and catch. We linked predictions from this economic choice model to a staged-based model of the fishery to estimate the effects on the stock and revenues from harvest. We found that the supply of plate-sized fish increased by 6%, while the supply of large fish decreased by 4% as a result of a 13% price premium for plate-sized fish. This market-driven size selection increased revenues (14%) but decreased total fish biomass (−3%). However, when market-driven size selection was combined with limited institutional constraints, both fish biomass (28%) and fishermen’s revenue (22%) increased. These results show that the direction and magnitude of the effects of market demand on biological populations and human behavior can depend on both biological attributes and institutional constraints. Fisheries management may capitalize on these conditional effects by implementing size-based regulations when economic and institutional incentives will enhance compliance, as in the case we describe here, or by creating compliance enhancing conditions for existing regulations. PMID:23865225

  8. Fluctuation-Driven Transport in Biological Nanopores. A 3D Poisson–Nernst–Planck Study

    Directory of Open Access Journals (Sweden)

    Marcel Aguilella-Arzo

    2017-03-01

    Full Text Available Living systems display a variety of situations in which non-equilibrium fluctuations couple to certain protein functions yielding astonishing results. Here we study the bacterial channel OmpF under conditions similar to those met in vivo, where acidic resistance mechanisms are known to yield oscillations in the electric potential across the cell membrane. We use a three-dimensional structure-based theoretical approach to assess the possibility of obtaining fluctuation-driven transport. Our calculations show that remarkably high voltages would be necessary to observe the actual transport of ions against their concentration gradient. The reasons behind this are the mild selectivity of this bacterial pore and the relatively low efficiencies of the oscillating signals characteristic of membrane cells (random telegraph noise and thermal noise.

  9. Development of interactive hypermedia software for high school biology: A research and development study

    Science.gov (United States)

    Alturki, Uthman T.

    The goal of this research was to research, design, and develop a hypertext program for students who study biology. The Ecology Hypertext Program was developed using Research and Development (R&D) methodology. The purpose of this study was to place the final "product", a CD-ROM for learning biology concepts, in the hands of teachers and students to help them in learning and teaching process. The product was created through a cycle of literature review, needs assessment, development, and a cycle of field tests and revisions. I applied the ten steps of R&D process suggested by Borg and Gall (1989) which, consisted of: (1) Literature review, (2) Needs assessment, (3) Planning, (4) Develop preliminary product, (5) Preliminary field-testing, (6) Preliminary revision, (7) Main field-testing, (8) Main revision, (9) Final field-testing, and (10) Final product revision. The literature review and needs assessment provided a support and foundation for designing the preliminary product---the Ecology Hypertext Program. Participants in the needs assessment joined a focus group discussion. They were a group of graduate students in education who suggested the importance for designing this product. For the preliminary field test, the participants were a group of high school students studying biology. They were the potential user of the product. They reviewed the preliminary product and then filled out a questionnaire. Their feedback and suggestions were used to develop and improve the product in a step called preliminary revision. The second round of field tasting was the main field test in which the participants joined a focus group discussion. They were the same group who participated in needs assessment task. They reviewed the revised product and then provided ideas and suggestions to improve the product. Their feedback were categorized and implemented to develop the product as in the main revision task. Finally, a group of science teachers participated in this study by reviewing

  10. Software para la nomenclatura de las sustancias en la especialidad biología-química

    Directory of Open Access Journals (Sweden)

    Guillermo Houari Mesa Briñas

    2015-04-01

    Full Text Available El aprendizaje de los contenidos de Química trasciende social y significativamente, si se considera el rol que su enseñanza juega en el acercamiento de los estudiantes en su aplicación cotidiana en diferentes contextos de la vida. La nomenclatura y la notación química, como parte esencial de su lenguaje, constituyen conocimientos que permiten profundizar en esa dirección. El artículo, presenta el resultado acerca de cómo contribuir con el dominio de la nomenclatura y la notación de las sustancias en estudiantes de la especialidad pedagógica Biología-Química. Como resultado, se ofrece un software de alternativa didáctica para la relación entre la nomenclatura y notación química con la aplicación de las sustancias en la vida. El estudio, se centró en el empleo de las tecnologías de la información y la comunicación en la enseñanza-aprendizaje de estos contenidos y su aplicación para la vida en tres contextos: doméstico, social e industrial. Los resultados, impactaron positivamente en el dominio de los contenidos y su contextualización. El software fue introducido en la práctica educativa, lo que demostró su efectividad en la solución del problema investigado y contribuyó con la profesionalización de los futuros profesores de Biología- Química

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

    Science.gov (United States)

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

    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. In this revised curriculum, students begin with a traditional set of biology, chemistry, physics, and mathematics major core-requirements, a geographic information systems (GIS) course, a choice of an instrumental analysis course or a statistical analysis systems (SAS) programming course, and then, students can add major-electives that further add depth and value to their future post-graduate specialty areas. Open-sourced georeferenced census, health and health disparity data were coupled with GIS and SAS tools, in a public health surveillance system project, based on US county zip-codes, to develop use-cases for chronic adult obesity where income, poverty status, health insurance coverage, education, and age were categorical variables. Across the 48 contiguous states, obesity rates are found to be directly proportional to high poverty and inversely proportional to median income and educational achievement. For the State of Delaware, age and educational attainment were found to be limiting obesity risk-factors in its adult population. Furthermore, the 2004-2010 obesity trends showed that for two of the less densely populated Delaware counties; Sussex and Kent, the rates of adult obesity were found to be progressing at much higher proportions when compared to the national average.

  12. 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

  13. 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

  14. 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

  15. Biology-Driven Gene-Gene Interaction Analysis of Age-Related Cataract in the eMERGE Network

    Science.gov (United States)

    Hall, Molly A; Verma, Shefali S; Wallace, John; Lucas, Anastasia; Berg, Richard L; Connolly, John; Crawford, Dana C; Crosslin, David R; de Andrade, Mariza; Doheny, Kimberly F; Haines, Jonathan L; Harley, John B; Jarvik, Gail P; Kitchner, Terrie; Kuivaniemi, Helena; Larson, Eric B; Carrell, David S; Tromp, Gerard; Vrabec, Tamara R; Pendergrass, Sarah A; McCarty, Catherine A; Ritchie, Marylyn D

    2015-01-01

    Bioinformatics approaches to examine gene-gene models provide a means to discover interactions between multiple genes that underlie complex disease. Extensive computational demands and adjusting for multiple testing make uncovering genetic interactions a challenge. Here, we address these issues using our knowledge-driven filtering method, Biofilter, to identify putative single nucleotide polymorphism (SNP) interaction models for cataract susceptibility, thereby reducing the number of models for analysis. Models were evaluated in 3,377 European Americans (1,185 controls, 2,192 cases) from the Marshfield Clinic, a study site of the Electronic Medical Records and Genomics (eMERGE) Network, using logistic regression. All statistically significant models from the Marshfield Clinic were then evaluated in an independent dataset of 4,311 individuals (742 controls, 3,569 cases), using independent samples from additional study sites in the eMERGE Network: Mayo Clinic, Group Health/University of Washington, Vanderbilt University Medical Center, and Geisinger Health System. Eighty-three SNP-SNP models replicated in the independent dataset at likelihood ratio test P < 0.05. Among the most significant replicating models was rs12597188 (intron of CDH1)–rs11564445 (intron of CTNNB1). These genes are known to be involved in processes that include: cell-to-cell adhesion signaling, cell-cell junction organization, and cell-cell communication. Further Biofilter analysis of all replicating models revealed a number of common functions among the genes harboring the 83 replicating SNP-SNP models, which included signal transduction and PI3K-Akt signaling pathway. These findings demonstrate the utility of Biofilter as a biology-driven method, applicable for any genome-wide association study dataset. PMID:25982363

  16. 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

  17. 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.

  18. A biology-driven approach identifies the hypoxia gene signature as a predictor of the outcome of neuroblastoma patients

    Directory of Open Access Journals (Sweden)

    Fardin Paolo

    2010-07-01

    Full Text Available Abstract Background Hypoxia is a condition of low oxygen tension occurring in the tumor microenvironment and it is related to poor prognosis in human cancer. To examine the relationship between hypoxia and neuroblastoma, we generated and tested an in vitro derived hypoxia gene signature for its ability to predict patients' outcome. Results We obtained the gene expression profile of 11 hypoxic neuroblastoma cell lines and we derived a robust 62 probesets signature (NB-hypo taking advantage of the strong discriminating power of the l1-l2 feature selection technique combined with the analysis of differential gene expression. We profiled gene expression of the tumors of 88 neuroblastoma patients and divided them according to the NB-hypo expression values by K-means clustering. The NB-hypo successfully stratifies the neuroblastoma patients into good and poor prognosis groups. Multivariate Cox analysis revealed that the NB-hypo is a significant independent predictor after controlling for commonly used risk factors including the amplification of MYCN oncogene. NB-hypo increases the resolution of the MYCN stratification by dividing patients with MYCN not amplified tumors in good and poor outcome suggesting that hypoxia is associated with the aggressiveness of neuroblastoma tumor independently from MYCN amplification. Conclusions Our results demonstrate that the NB-hypo is a novel and independent prognostic factor for neuroblastoma and support the view that hypoxia is negatively correlated with tumors' outcome. We show the power of the biology-driven approach in defining hypoxia as a critical molecular program in neuroblastoma and the potential for improvement in the current criteria for risk stratification.

  19. 基于FSM和事件驱动的卫星管理软件设计%Design of Satellite Management Software Based on FSM and Event-driven

    Institute of Scientific and Technical Information of China (English)

    张合生; 金玉红; 李杰; 盖建宁

    2009-01-01

    随着航天飞行器结构的复杂和软件规模的膨胀,软件的结构成为软件设计的关键技术,针对该问题,提出以有限状态机为模型的软件模块化设计方法.该设计按事件产生、消息(事件)队列维护、事件响应的处理流程,建立事件驱动机制,构建软件系统结构.实验结果表明,该设讣提高了软件的可靠性和开发效率,使其更易于维护和扩展,并降低了失效风险.%With the structure of aerospace craft increasingly becoming complex and its software scale being more and more inflated, the design of software framework becomes the key technology of the software design. Aiming at this problem, this paper proposes a software modularized design method based on Finite State Machine(FSM) model. It establishes event-driven mechanism and constructs system structure of the software according to the process flow which is event generating, event queue maintaining and event answering. Experimental result indicates that the design improves the reliability and developing efficiency of software, makes it easier vindicating and expanding, and reduces the disabled risk,

  20. Developer Driven and User Driven Usability Evaluations

    DEFF Research Database (Denmark)

    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....... The four primary findings from my studies are: 1) The developer driven approach reveals a high level of thoroughness and downstream utility. 2) The user driven approach has higher performance regarding validity 3) The level of reliability is comparable between the two approaches. 4) The user driven...

  1. 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.

  2. 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.

  3. 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

  4. High biological productivity in the central Arabian Sea during the summer monsoon driven by Ekman pumping and lateral advection

    Digital Repository Service at National Institute of Oceanography (India)

    PrasannaKumar, S.; Madhupratap, M.; DileepKumar, M.; Muraleedharan, P.M.; DeSouza, S.N.; Gauns, M.; Sarma, V.V.S.S.

    in light of the physical forcing and prevailing chemical fields. In the northern part of the central Arabian Sea, north of the axis of the Findlater Jet, upward Ekman pumping and entrainment driven by basin-wide winds along with advection of upwelled waters...

  5. 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.

  6. 应用领域驱动设计实现大坝安全监测复杂业务%Application of Domain Driven Design in Complex Business of Dam Safety Monitoring Software

    Institute of Scientific and Technical Information of China (English)

    易广军; 朱赵辉; 孙建会

    2015-01-01

    Through the domain driven design, reasonable separation of domain knowledge, the article uses a uniifed model that software developers and domain experts can understand to express the business logic. Compared with the traditional pattern of data driven development, it makes the core business of dam safety monitoring software clear thread, easy to extend and maintain. Effect of practical application proves the domain model of the method designed is able to adapt to the change of demand and the increase of the new features, advantageous to realize the automation of complex business processing.%通过领域驱动设计,合理地分离领域知识,用软件开发人员和领域专家都能理解的统一模型表达业务逻辑,相比传统的数据驱动开发模式,使大坝安全监测软件中的核心业务脉络清晰,易于扩展和维护。实际应用效果证明该方法设计的领域模型能够很好地适应需求的变更和新功能的增加,有利于实现大坝安全监测复杂业务的自动化处理。

  7. All biology is computational biology

    Science.gov (United States)

    2017-01-01

    Here, I argue that computational thinking and techniques are so central to the quest of understanding life that today all biology is computational biology. Computational biology brings order into our understanding of life, it makes biological concepts rigorous and testable, and it provides a reference map that holds together individual insights. The next modern synthesis in biology will be driven by mathematical, statistical, and computational methods being absorbed into mainstream biological training, turning biology into a quantitative science. PMID:28278152

  8. The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community.

    Science.gov (United States)

    Aebersold, Ruedi; Bader, Gary D; Edwards, Aled M; van Eyk, Jennifer E; Kussmann, Martin; Qin, Jun; Omenn, Gilbert S

    2013-01-04

    The biology and disease oriented branch of the Human Proteome Project (B/D-HPP) was established by the Human Proteome Organization (HUPO) with the main goal of supporting the broad application of state-of the-art measurements of proteins and proteomes by life scientists studying the molecular mechanisms of biological processes and human disease. This will be accomplished through the generation of research and informational resources that will support the routine and definitive measurement of the process or disease relevant proteins. The B/D-HPP is highly complementary to the C-HPP and will provide datasets and biological characterization useful to the C-HPP teams. In this manuscript we describe the goals, the plans, and the current status of the of the B/D-HPP.

  9. HIV among injecting drug users: current epidemiology, biologic markers, respondent-driven sampling, and supervised-injection facilities

    Science.gov (United States)

    Des Jarlais, Don C.; Arasteh, Kamyar; Semaan, Salaam; Wood, Evan

    2017-01-01

    Purpose of review To describe recent research done primarily during the past 12 months (i.e., primarily in 2008) on the epidemiology of HIV infection among injecting drug users (IDUs). Recent findings Major research developments include a global assessment of HIV infection among IDUs and evidence of a transition from epidemics concentrated among IDUs to generalized, heterosexual epidemics in eastern Europe and Asia. Intervention research also includes several studies of supervised-injecting facilities. Methodological research includes respondent-driven sampling and the use of hepatitis C virus and herpes simplex virus-2 as biomarkers for injecting and sexual risk. Summary There have been important advances in research during the past year, but HIV infection continues to spread rapidly across many areas of the world among IDUs and their nondrug-using sex partners. PMID:19532069

  10. 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.

  11. 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.

  12. 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)

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

    Directory of Open Access Journals (Sweden)

    N. Restrepo-Coupe

    2015-12-01

    Full Text Available 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

  14. MODIS vegetation products as proxies of photosynthetic potential along a gradient of meteorologically and biologically driven ecosystem productivity

    Science.gov (United States)

    Restrepo-Coupe, Natalia; Huete, Alfredo; Davies, Kevin; Cleverly, James; Beringer, Jason; Eamus, Derek; van Gorsel, Eva; Hutley, Lindsay B.; Meyer, Wayne S.

    2016-10-01

    A direct relationship between gross ecosystem productivity (GEP) estimated 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 and temperate 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 GEP and four measures of photosynthetic potential, derived via parameterization of the light response curve: ecosystem light use efficiency (LUE), photosynthetic capacity (Pc), GEP at saturation (GEPsat), and quantum yield (α), 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 biophysical 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 GEP. Our results show that in primarily meteorological-driven (e.g. photosynthetic active radiation, air temperature, and/or precipitation) and relatively aseasonal 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

  15. Teaching Methods Exploration of Software Process Improvement with Story-Driven%案例驱动的软件过程改进教学方法探讨

    Institute of Scientific and Technical Information of China (English)

    王安生; 傅湘玲

    2011-01-01

    围绕软件过程改进的教学已经成为软件学院研究生和高年本科生的重要工作.如何在短时间内让学生理解、掌握软件过程改进的原理和方法,缩短学生承担企业角色和提升企业能力,是软件学院教学的重点之一.本文首先回顾了我国软件学院针对软件过程改进相关教学的情况.综述了国内外相关书籍和教材的情况,讨论了国际上具有代表性的软件过程改进的教学方法,以及早期我国进行软件工程化教育的工作.论述了以案例驱动的过程改进教材结构、教学内容剪裁、教学方法以及教学难点.总结了该教材在两个院校多批次的使用效果.%Software Process Improvement (SPI) for postgraduates and undergraduated students in software schools is an very important class. One of the question is how students could master principles of SPI in short time and have abilities to play in enterprise's roles and improve the engineering capability of corporations in the future. This paper firstly reviews history about SPI teaching, then, summarize and discuss the related text books and references and the representative teaching methods of SPI in international, as well as education on engineering of software development early in China. The paper describes the structures of our SPI textbook which include not only SPI methods, but also stories from a massive-scale project and several corporations of China. Afterwards, we discuss the tailoring of textbooks contents, teaching methods, and important and difficult points on teaching of our methods. In the end, the experiences and lesson-learned from several classes in two software schools are concluded.

  16. 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.

  17. 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.

  18. EVALUATING THE ECOLOGICAL RESILIENT DRIVEN PERFORMANCE OF A TROPICAL WASTE STABILIZATION POND SYSTEM USING ECOLOGICAL SIGNATURE OF BIOLOGICAL INTEGRITY

    Directory of Open Access Journals (Sweden)

    Susmita Lahiri Ganguly

    2015-06-01

    Full Text Available Using ecological signature of biological integrity as a measure of performance, the reclamation efficiency of waste stabilization ponds was evaluated over a period of four years in a tropical sewage treatment plant – cum fish culture consisting of two anaerobic, two facultative and four maturation ponds located serially across the sewage effluent gradient. The four maturation ponds were used for batch culture of fish. Samples of surface and bottom water as well as surface sediment were collected twice a month from different ponds of the system and examined for some nutrient cycling bacteria, primary production, chlorophyll content of micro-algae, phytoplankton, zooplankton abundance, fish growth and water quality parameters. Computation of ecological signature using aerobic mineralization index for heterotrophic and ammonifying bacteria revealed steady increase across the sewage effluent gradient. The heterotrophic and ammonifying bacterial populations appeared to have a direct function with the concentrations of chemical oxygen demand of water. The sum of total scores for different optimal conditions for fish growth increased as a function of the distance from the source of effluent implying that ecological resilience of the waste stabilization ponds has been accomplished by the sedimentation, chelation, and biological functional attributes mediated through redundancy of different subsystems, self- purification capacity of the system as a whole.

  19. 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.

  20. 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

  1. Workstation software framework

    Science.gov (United States)

    Andolfato, L.; Karban, R.

    2008-08-01

    The Workstation Software Framework (WSF) is a state machine model driven development toolkit designed to generate event driven applications based on ESO VLT software. State machine models are used to generate executables. The toolkit provides versatile code generation options and it supports Mealy, Moore and hierarchical state machines. Generated code is readable and maintainable since it combines well known design patterns such as the State and the Template patterns. WSF promotes a development process that is based on model reusability through the creation of a catalog of state machine patterns.

  2. 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.

  3. 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。

  4. 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

  5. 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)

  6. 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.

  7. 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。

  8. 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

  9. 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

  10. 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

    2017-02-01

    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.

  11. 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.

  12. Research on the Project-driven Teaching Method of“Software Engineering”%项目驱动的《软件工程》教学法初探

    Institute of Scientific and Technical Information of China (English)

    陈海燕; 张育平; 臧洌; 沈国华

    2013-01-01

      《软件工程》是我校计算机专业本科阶段唯一一门综合性课程,除了介绍软件开发的过程、原理、方法,还需综合运用多方面的专业知识。抽象的理论知识和高度的实践性使之成为老师难教、学生难学的课程。文章提出采用项目驱动教学法来解决目前软件工程教学中存在的问题,将项目开发贯穿于教学过程,设计了各阶段教学内容、实践内容和实施步骤。教学实践表明,该方法能全面提高学生的动手能力,加深对理论知识的理解。%“Software engineering”is the only comprehensive curriculum for undergraduates of our college. In this curriculum, the process,principles and methods of software development are introduced,furthermore,a wide range of expertise are much needed simultaneously. Abstract theoretical knowledge and high degree of practicality make this curriculum difficult for teachers to teach and for students to grasp. This paper proposes applying the project-driven teaching methods to solve the problems existing in the current“software engineering”teaching,In this method,project development activities will go throughout the whole teaching process. Teaching content,practical content and implementation steps of each stage are designed. The practice shows that the method can improve students' practical ability and deepen the understanding of the theoretical knowledge.

  13. A Requirement-Driven Software Trustworthiness Evaluation and Evolution Model%一种需求驱动的软件可信性评估及演化模型

    Institute of Scientific and Technical Information of China (English)

    丁帅; 鲁付俊; 杨善林; 夏承遗

    2011-01-01

    Software trustworthiness evaluation model is built upon the accurately eliciting of trustworthy requirements and the reasonable establish ment of indicator system in the domain special application. Toward software which has huge architecture and complex non-functional demands,trustworthy requirements become changing with software operational state transition. The stability of trustworthiness evaluation indicator system will be affected by trustworthy requirement dynamic evolution. The software trustworthiness evaluation and evolution problem are attracting wide attention in the field of trustworthy software. In this paper, a novel requirement-driven software trustworthiness evaluation and evolution model is designed. Firstly, several key technologies adopted in the process of software trustworthiness evaluation are analyzed and summarized, such as requirements analysis and indicators extraction, trustworthy evidence acquisition and conversion, etc.And the problem of trustworthiness evaluation adaptive solution under the requirements evolution is discussed. Secondly, incidence matrix is used to achieve correlation analysis between trustworthy attributes and then the variation rule of relative weight is revealed. On this basis, adaptive reconstruction device, which can analyze and solve the software trustworthiness evaluation indicator system of self-reconfiguration, is designed based on incidence matrix. Finally, a complete framework of trustworthiness evaluation evolution and evolution model is proposed. Experimental results show the rationality and validity of the model.%软件可信性评估模型的构建依赖于对特定应用领域中可信需求的准确提取和指标系统的合理建立.对于体系结构庞大、非功能性需求复杂的软件而言,可信需求往往随着软件运行状态的转移而不断发生变化.由于可信需求的动态演化将直接影响指标系统的稳定性,因此引起了可信软件研究领域专家的广泛关

  14. 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.

  15. 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.

  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...

  17. 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.

  18. Two problems in multiphase biological flows: Blood flow and particulate transport in microvascular network, and pseudopod-driven motility of amoeboid cells

    Science.gov (United States)

    Bagchi, Prosenjit

    2016-11-01

    In this talk, two problems in multiphase biological flows will be discussed. The first is the direct numerical simulation of whole blood and drug particulates in microvascular networks. Blood in microcirculation behaves as a dense suspension of heterogeneous cells. The erythrocytes are extremely deformable, while inactivated platelets and leukocytes are nearly rigid. A significant progress has been made in recent years in modeling blood as a dense cellular suspension. However, many of these studies considered the blood flow in simple geometry, e.g., straight tubes of uniform cross-section. In contrast, the architecture of a microvascular network is very complex with bifurcating, merging and winding vessels, posing a further challenge to numerical modeling. We have developed an immersed-boundary-based method that can consider blood cell flow in physiologically realistic and complex microvascular network. In addition to addressing many physiological issues related to network hemodynamics, this tool can be used to optimize the transport properties of drug particulates for effective organ-specific delivery. Our second problem is pseudopod-driven motility as often observed in metastatic cancer cells and other amoeboid cells. We have developed a multiscale hydrodynamic model to simulate such motility. We study the effect of cell stiffness on motility as the former has been considered as a biomarker for metastatic potential. Funded by the National Science Foundation.

  19. Sustainable Software Decisions for Long-term Projects (Invited)

    Science.gov (United States)

    Shepherd, A.; Groman, R. C.; Chandler, C. L.; Gaylord, D.; Sun, M.

    2013-12-01

    Adopting new, emerging technologies can be difficult for established projects that are positioned to exist for years to come. In some cases the challenge lies in the pre-existing software architecture. In others, the challenge lies in the fluctuation of resources like people, time and funding. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) was created in late 2006 by combining the data management offices for the U.S. GLOBEC and U.S. JGOFS programs to publish data for researchers funded by the National Science Foundation (NSF). Since its inception, BCO-DMO has been supporting access and discovery of these data through web-accessible software systems, and the office has worked through many of the challenges of incorporating new technologies into its software systems. From migrating human readable, flat file metadata storage into a relational database, and now, into a content management system (Drupal) to incorporating controlled vocabularies, new technologies can radically affect the existing software architecture. However, through the use of science-driven use cases, effective resource management, and loosely coupled software components, BCO-DMO has been able to adapt its existing software architecture to adopt new technologies. One of the latest efforts at BCO-DMO revolves around applying metadata semantics for publishing linked data in support of data discovery. This effort primarily affects the metadata web interface software at http://bco-dmo.org and the geospatial interface software at http://mapservice.bco-dmo.org/. With guidance from science-driven use cases and consideration of our resources, implementation decisions are made using a strategy to loosely couple the existing software systems to the new technologies. The results of this process led to the use of REST web services and a combination of contributed and custom Drupal modules for publishing BCO-DMO's content using the Resource Description Framework (RDF) via an instance of

  20. 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.

  1. 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)

  2. Ontology Driven Piecemeal Development of Smart Spaces

    Science.gov (United States)

    Ovaska, Eila

    Software development is facing new challenges due to transformation from product based software engineering towards integration and collaboration based software engineering that embodies high degree of dynamism both at design time and run time. Short time-to-markets require cost reduction by maximizing software reuse; openness for new innovations presumes a flexible innovation platform and agile software development; and user satisfaction assumes high quality in a situation based manner. How to deal with these contradictory requirements in software engineering? The main contribution of this paper is a novel approach that is influenced by business innovation, human centered design, model driven development and ontology oriented design. The approach is called Ontology driven Piecemeal Software Engineering (OPSE). OPSE facilitates incremental software development based on software pieces that follow the design principles defined by means of ontologies. Its key elements are abstraction, aggregation and adaptivity. The approach is intended for and applied to the development of smart spaces.

  3. 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

  4. 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 ...

  5. 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

  6. 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.

  7. 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.

  8. 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

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

    OpenAIRE

    Azanza Sesé, Maider

    2011-01-01

    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. 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)

  11. 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)

  12. 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....

  13. Reusable Software.

    Science.gov (United States)

    1984-03-01

    overseeing reusable software, the Reusable Software Organization ( RUSO ). This author does not feel at this time that establishment of such a specific...49] have not been accompanied by establishment of RUSO -like activities. There is need, however, for assurance that functions which a RUSO might be...assurance 6. establishment and maintenance of reuse archival facilities and activities. Actual establishment of a RUSO is best dictated by size of the

  14. 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.

  15. MIAWARE Software

    DEFF Research Database (Denmark)

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

    2008-01-01

    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...... 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...... is automatically generated. Furthermore, MIAWARE software is accompanied with an intelligent search engine for medical reports, based on the relations between parts of the lungs. A logical structure of the lungs is introduced to the search algorithm through the specially developed ontology. As a result...

  16. 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 sim...

  17. 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

  18. [Software version and medical device software supervision].

    Science.gov (United States)

    Peng, Liang; Liu, Xiaoyan

    2015-01-01

    The importance of software version in the medical device software supervision does not cause enough attention at present. First of all, the effect of software version in the medical device software supervision is discussed, and then the necessity of software version in the medical device software supervision is analyzed based on the discussion of the misunderstanding of software version. Finally the concrete suggestions on software version naming rules, software version supervision for the software in medical devices, and software version supervision scheme are proposed.

  19. 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.

  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. 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…

  2. 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)

  3. 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

  4. Software Patents.

    Science.gov (United States)

    Burke, Edmund B.

    1994-01-01

    Outlines basic patent law information that pertains to computer software programs. Topics addressed include protection in other countries; how to obtain patents; kinds of patents; duration; classes of patentable subject matter, including machines and processes; patentability searches; experimental use prior to obtaining a patent; and patent…

  5. Educational Software.

    Science.gov (United States)

    Northwest Regional Educational Lab., Portland, OR.

    The third session of IT@EDU98 consisted of five papers on educational software and was chaired by Tran Van Hao (University of Education, Ho Chi Minh City, Vietnam). "Courseware Engineering" (Nguyen Thanh Son, Ngo Ngoc Bao Tran, Quan Thanh Tho, Nguyen Hong Lam) briefly describes the use of courseware. "Machine Discovery Theorems in Geometry: A…

  6. An Empirical Study of a Free Software Company

    OpenAIRE

    Pakusch, Cato

    2010-01-01

    Free software has matured well into the commercial software market, yet little qualitative research exists which accurately describes the state of commercial free software today. For this thesis, an instrumental case study was performed on a prominent free software company in Norway. The study found that the commercial free software market is largely driven by social networks, which have a social capital in its own that attracts more people, which in turn become members of the ...

  7. 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.

  8. Formative research to optimize respondent-driven sampling surveys among hard-to-reach populations in HIV behavioral and biological surveillance: lessons learned from four case studies.

    Science.gov (United States)

    Johnston, Lisa Grazina; Whitehead, Sara; Simic-Lawson, Milena; Kendall, Carl

    2010-06-01

    Respondent-driven sampling (RDS) is widely adopted as a method to assess HIV and other sexually transmitted infection prevalence and risk factors among hard-to-reach populations. Failures to properly implement RDS in several settings could potentially have been avoided, had formative research been conducted. However, to date there is no published literature addressing the use of formative research in preparing for RDS studies. This paper uses examples from Banja Luka, Bosnia and Herzegovina; Bangkok, Thailand; Podgorica, Montenegro; and St Vincent's and Grenadine Islands, Eastern Caribbean; among populations of men who have sex with men, female sex workers, and injecting drug users to describe how formative research was used to plan, implement, and predict outcomes of RDS surveys and to provide a template of RDS-specific questions for conducting formative research in preparation for RDS surveys. We outline case studies to illustrate how formative research may help researchers to determine whether RDS methodology is appropriate for a particular population and sociocultural context, and to decide on implementation details that lead to successful study outcomes.

  9. EPIQR software

    Energy Technology Data Exchange (ETDEWEB)

    Flourentzos, F. [Federal Institute of Technology, Lausanne (Switzerland); Droutsa, K. [National Observatory of Athens, Athens (Greece); Wittchen, K.B. [Danish Building Research Institute, Hoersholm (Denmark)

    1999-11-01

    The support of the EPIQR method is a multimedia computer program. Several modules help the users of the method to treat the data collected during a diagnosis survey, to set up refurbishment scenario and calculate their cost or energy performance, and finally to visualize the results in a comprehensive way and to prepare quality reports. This article presents the structure and the main features of the software. (au)

  10. 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.

  11. Concise review: putting a finger on stem cell biology: zinc finger nuclease-driven targeted genetic editing in human pluripotent stem cells.

    Science.gov (United States)

    Collin, Joseph; Lako, Majlinda

    2011-07-01

    Human pluripotent stem cells (hPSCs) encompassing human embryonic stem cells and human induced pluripotent stem cells (hiPSCs) have a wide appeal for numerous basic biology studies and for therapeutic applications because of their potential to give rise to almost any cell type in the human body and immense ability to self-renew. Much attention in the stem cell field is focused toward the study of gene-based anomalies relating to the causative affects of human disease and their correction with the potential for patient-specific therapies using gene corrected hiPSCs. Therefore, the genetic manipulation of stem cells is clearly important for the development of future medicine. Although successful targeted genetic engineering in hPSCs has been reported, these cases are surprisingly few because of inherent technical limitations with the methods used. The development of more robust and efficient means by which to achieve specific genomic modifications in hPSCs has far reaching implications for stem cell research and its applications. Recent proof-of-principle reports have shown that genetic alterations with minimal toxicity are now possible through the use of zinc finger nucleases (ZFNs) and the inherent DNA repair mechanisms within the cell. In light of recent comprehensive reviews that highlight the applications, methodologies, and prospects of ZFNs, this article focuses on the application of ZFNs to stem cell biology, discussing the published work to date, potential problems, and future uses for this technology both experimentally and therapeutically.

  12. 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.

  13. A Software Development Platform for Mechatronic Systems

    DEFF Research Database (Denmark)

    Guan, Wei

    present a challenge to the practitioners who adopt conventional software development approach. An effective approach towards industrial production of software for mechatronic systems is needed. This approach requires a disciplined engineering process that encompasses model-driven engineering and component......-based software engineering, whereby we enable incremental software development using component models to address the essential design issues of real-time embedded systems. To this end, this dissertation presents a software development platform that provides an incremental model-driven development process based...... rigorous construction of systems. The incremental development process separates the development activities into prefabrication of reusable components, conguration and generation of applications using validated components, and elimination of design errors using model-based analysis and verfication methods...

  14. 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

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

    Directory of Open Access Journals (Sweden)

    Jason Gunther Lomnitz

    2016-07-01

    Full Text Available 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 3 stable states by transient stimulation through one of two input channels: a positive channel that increases

  16. 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

  17. 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

  18. 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.

  19. SIGffRid: A tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics

    Directory of Open Access Journals (Sweden)

    Kucherov Gregory

    2008-01-01

    Full Text Available Abstract Background Many programs have been developed to identify transcription factor binding sites. However, most of them are not able to infer two-word motifs with variable spacer lengths. This case is encountered for RNA polymerase Sigma (σ Factor Binding Sites (SFBSs usually composed of two boxes, called -35 and -10 in reference to the transcription initiation point. Our goal is to design an algorithm detecting SFBS by using combinational and statistical constraints deduced from biological observations. Results We describe a new approach to identify SFBSs by comparing two related bacterial genomes. The method, named SIGffRid (SIGma Factor binding sites Finder using R'MES to select Input Data, performs a simultaneous analysis of pairs of promoter regions of orthologous genes. SIGffRid uses a prior identification of over-represented patterns in whole genomes as selection criteria for potential -35 and -10 boxes. These patterns are then grouped using pairs of short seeds (of which one is possibly gapped, allowing a variable-length spacer between them. Next, the motifs are extended guided by statistical considerations, a feature that ensures a selection of motifs with statistically relevant properties. We applied our method to the pair of related bacterial genomes of Streptomyces coelicolor and Streptomyces avermitilis. Cross-check with the well-defined SFBSs of the SigR regulon in S. coelicolor is detailed, validating the algorithm. SFBSs for HrdB and BldN were also found; and the results suggested some new targets for these σ factors. In addition, consensus motifs for BldD and new SFBSs binding sites were defined, overlapping previously proposed consensuses. Relevant tests were carried out also on bacteria with moderate GC content (i.e. Escherichia coli/Salmonella typhimurium and Bacillus subtilis/Bacillus licheniformis pairs. Motifs of house-keeping σ factors were found as well as other SFBSs such as that of SigW in Bacillus strains

  20. 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.

  1. 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

  2. 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. Graphical Abstract ᅟ.

  3. 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.

  4. 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].

  5. Minerva: User-Centered Science Operations Software Capability for Future Human Exploration

    Science.gov (United States)

    Deans, Matthew; Marquez, Jessica J.; Cohen, Tamar; Miller, Matthew J.; Deliz, Ivonne; Hillenius, Steven; Hoffman, Jeffrey; Lee, Yeon Jin; Lees, David; Norheim, Johannes; Lim, Darlene S. S.

    2017-01-01

    In June of 2016, the Biologic Analog Science Associated with Lava Terrains (BASALT) research project conducted its first field deployment, which we call BASALT-1. BASALT-1 consisted of a science-driven field campaign in a volcanic field in Idaho as a simulated human mission to Mars. Scientists and mission operators were provided a suite of ground software tools that we refer to collectively as Minerva to carry out their work. Minerva provides capabilities for traverse planning and route optimization, timeline generation and display, procedure management, execution monitoring, data archiving, visualization, and search. This paper describes the Minerva architecture, constituent components, use cases, and some preliminary findings from the BASALT-1 campaign.

  6. Sandia software guidelines: Software quality planning

    Energy Technology Data Exchange (ETDEWEB)

    1987-08-01

    This volume is one in a series of Sandia Software Guidelines intended for use in producing quality software within Sandia National Laboratories. In consonance with the IEEE Standard for Software Quality Assurance Plans, this volume identifies procedures to follow in producing a Software Quality Assurance Plan for an organization or a project, and provides an example project SQA plan. 2 figs., 4 tabs.

  7. 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.

  8. 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

  9. Software Metrics to Estimate Software Quality using Software Component Reusability

    Directory of Open Access Journals (Sweden)

    Prakriti Trivedi

    2012-03-01

    Full Text Available Today most of the applications developed using some existing libraries, codes, open sources etc. As a code is accessed in a program, it is represented as the software component. Such as in java beans and in .net ActiveX controls are the software components. These components are ready to use programming code or controls that excel the code development. A component based software system defines the concept of software reusability. While using these components the main question arise is whether to use such components is beneficial or not. In this proposed work we are trying to present the answer for the same question. In this work we are presenting a set of software matrix that will check the interconnection between the software component and the application. How strong this relation defines the software quality after using this software component. The overall metrics will return the final result in terms of the boundless of the component with application.

  10. Toward effective software solutions for big biology

    NARCIS (Netherlands)

    Prins, Pjotr; de Ligt, Joep; Tarasov, Artem; Jansen, Ritsert C; Cuppen, Edwin; Bourne, Philip E

    2015-01-01

    Leading scientists tell us that the problem of large data and data integration, referred to as 'big data', is acute and hurting research. Recently, Snijder et al.1 suggested a culture change in which scientists would aim to share high-dimensional data among laboratories. It is important to realize t

  11. 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

  12. 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

  13. 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.

  14. The Mars Exploration Rover Surface Mobility Flight Software: Driving Ambition

    Science.gov (United States)

    Biesiadecki, Jeffrey J.; Maimone, Mark W.

    2006-01-01

    In this paper we describe the software that has driven these rovers more than a combined 11,000 meters over the Martian surface, including its design and implementation, and summarize current mobility performance results from Mars.

  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. 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

  18. 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.

  19. Controlling Software Piracy.

    Science.gov (United States)

    King, Albert S.

    1992-01-01

    Explains what software manufacturers are doing to combat software piracy, recommends how managers should deal with this problem, and provides a role-playing exercise to help students understand the issues in software piracy. (SR)

  20. 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.

  1. 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

  2. Muscle-driven nanogenerators

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhong L. (Marietta, GA); Yang, Rusen (Atlanta, GA)

    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.

  3. Improved optically driven microrotors

    Science.gov (United States)

    Asavei, Theodor; Loke, Vincent L. Y.; Nieminen, Timo A.; Heckenberg, Norman R.; Rubinsztein-Dunlop, Halina

    2008-08-01

    Two-photon polymerization of optically curing resins is a powerful method to fabricate micron sized objects which can be used as tools to measure properties at small scales. These microdevices can be driven by means of externally applied focused laser beams (optical tweezers) through angular momentum exchange, giving rise to a net torque. The advantage of the optical drive is that no contact is required, therefore making the microdevices suited to non-invasive biological applications. The fabrication method is versatile and allows building objects of any 3D shape. We discuss the design and modelling of various optically driven rotors. In particular, we consider fabrication of microspheres with an internal shape birefringence in order to obtain rotation in an optical trap. The reason for fabricating this type of object is that they are well-suited for studies of mechanical properties of single biomolecules such as the torsional stiffness of DNA or torque generated by molecular motors. The microspheres fabricated are able to transduce torques of 2000 pNnm with optical powers of 500 mW and could be rotated with frequencies up to 40 Hz in circularly polarized light.

  4. 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.

  5. 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.

  6. 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...

  7. 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.

  8. 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…

  9. 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.

  10. 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.

  11. 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.

  12. Software Metrics for Identifying Software Size in Software Development Projects

    Directory of Open Access Journals (Sweden)

    V.S.P Vidanapathirana

    2015-11-01

    Full Text Available Measurements are fundamental any engineering discipline. They indicate the amount, extent, dimension or capacity of an attribute or a product, in a quantitative manner. The analyzed results of the measured data can be given as the basic idea of metrics. It is a quantitative representation of the measurements of the degree to which a system, component, or process possesses a given attribute. When it comes to software, the metrics are a wide scope of measurements of computer programming. The size oriented metrics takes a main role in it since they can be used as the key for better estimations, to improve trust and confidence, and to have a better control over the software products. Software professionals traditionally have been measuring the size of software applications by using several methods. In this paper the researchers discuss about the software size metrics for identifying software size and it is mainly focused on the software development projects in today’s Information Technology (IT industry.

  13. Molecular dynamics for irradiation driven chemistry

    DEFF Research Database (Denmark)

    Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

    2016-01-01

    that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... capable to operate with a large library of classical potentials, many-body force fields and their combinations. IDMD opens a broad range of possibilities for modelling of irradiation driven modifications and chemistry of complex molecular systems ranging from radiotherapy cancer treatments to the modern...... technologies such as focused electron beam deposition (FEBID). As an example, the new methodology is applied for studying the irradiation driven chemistry caused by FEBID of tungsten hexacarbonyl W(CO)6 precursor molecules on a hydroxylated SiO2 surface. It is demonstrated that knowing the interaction...

  14. 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.

  15. Payload software technology: Software technology development plan

    Science.gov (United States)

    1977-01-01

    Programmatic requirements for the advancement of software technology are identified for meeting the space flight requirements in the 1980 to 1990 time period. The development items are described, and software technology item derivation worksheets are presented along with the cost/time/priority assessments.

  16. 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.

  17. EMMA: A New Paradigm in Configurable Software

    Energy Technology Data Exchange (ETDEWEB)

    Nogiec, J. M. [Fermilab; Trombly-Freytag, K. [Fermilab

    2016-10-05

    EMMA is a framework designed to create a family of configurable software systems, with emphasis on extensibility and flexibility. It is based on a loosely coupled, event driven architecture. The EMMA framework has been built upon the premise of composing software systems from independent components. It opens up opportunities for reuse of components and their functionality and composing them together in many different ways. It provides the developer of test and measurement applications with a lightweight alternative to microservices, while sharing their various advantages, including composability, loose coupling, encapsulation, and reuse.

  18. Modular software-controlled electrochemical system

    Science.gov (United States)

    Hagan, D.; Spivey, J.; Niculescu, V. A.

    1987-03-01

    A modular microcomputer-controlled three-electrode potentiostat configured with graphics is presented. The system is designed for metallic surface characterization and is capable of performing in different modes of operation including single sweep voltammetry, cyclic voltammetry, and chronoamperometry. An integrated and flexible software system for control, data taking, data storage, and transfer is described. Data analysis software for the IBM-PC computer including two- and three-dimensional plotting as well as menu-driven theoretical modeling, simulation, and curvefitting has been developed.

  19. 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

  20. Commercial Data Mining Software

    Science.gov (United States)

    Zhang, Qingyu; Segall, Richard S.

    This chapter discusses selected commercial software for data mining, supercomputing data mining, text mining, and web mining. The selected software are compared with their features and also applied to available data sets. The software for data mining are SAS Enterprise Miner, Megaputer PolyAnalyst 5.0, PASW (formerly SPSS Clementine), IBM Intelligent Miner, and BioDiscovery GeneSight. The software for supercomputing are Avizo by Visualization Science Group and JMP Genomics from SAS Institute. The software for text mining are SAS Text Miner and Megaputer PolyAnalyst 5.0. The software for web mining are Megaputer PolyAnalyst and SPSS Clementine . Background on related literature and software are presented. Screen shots of each of the selected software are presented, as are conclusions and future directions.

  1. 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.

  2. Pragmatic Software Innovation

    DEFF Research Database (Denmark)

    Aaen, Ivan; Jensen, Rikke Hagensby

    2014-01-01

    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......, 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...

  3. Paladin Software Support Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The Paladin Software Support Environment (SSE) occupies 2,241 square-feet. It contains the hardware and software tools required to support the Paladin Automatic Fire...

  4. 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.

  5. 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....

  6. 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

  7. 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.

  8. 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.

  9. Software Engineering for Portability.

    Science.gov (United States)

    Stanchev, Ivan

    1990-01-01

    Discussion of the portability of educational software focuses on the software design and development process. Topics discussed include levels of portability; the user-computer dialog; software engineering principles; design techniques for student performance records; techniques of courseware programing; and suggestions for further research and…

  10. 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

  11. 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,…

  12. 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

  13. Funding Research Software Development

    Science.gov (United States)

    Momcheva, Ivelina G.

    2017-01-01

    Astronomical software is used by each and every member of our scientific community. Purpose-build software is becoming ever more critical as we enter the regime of large datasets and simulations of increasing complexity. However, financial investments in building, maintaining and renovating the software infrastructure have been uneven. In this talk I will summarize past and current funding sources for astronomical software development, discuss other models of funding and introduce a new initiative for supporting community software at STScI. The purpose of this talk is to prompt discussion about how we allocate resources to this vital infrastructure.

  14. 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

  15. 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

  16. Designing the Cloud-based DOE Systems Biology Knowledgebase

    Energy Technology Data Exchange (ETDEWEB)

    Lansing, Carina S.; Liu, Yan; Yin, Jian; Corrigan, Abigail L.; Guillen, Zoe C.; Kleese van Dam, Kerstin; Gorton, Ian

    2011-09-01

    Systems Biology research, even more than many other scientific domains, is becoming increasingly data-intensive. Not only have advances in experimental and computational technologies lead to an exponential increase in scientific data volumes and their complexity, but increasingly such databases themselves are providing the basis for new scientific discoveries. To engage effectively with these community resources, integrated analyses, synthesis and simulation software is needed, regularly supported by scientific workflows. In order to provide a more collaborative, community driven research environment for this heterogeneous setting, the Department of Energy (DOE) has decided to develop a federated, cloud based cyber infrastructure - the Systems Biology Knowledgebase (Kbase). Pacific Northwest National Laboratory (PNNL) with its long tradition in data intensive science lead two of the five initial pilot projects, these two focusing on defining and testing the basic federated cloud-based system architecture and develop a prototype implementation. Hereby the community wide accessibility of biological data and the capability to integrate and analyze this data within its changing research context were seen as key technical functionalities the Kbase needed to enable. In this paper we describe the results of our investigations into the design of a cloud based federated infrastructure for: (1) Semantics driven data discovery, access and integration; (2) Data annotation, publication and sharing; (3) Workflow enabled data analysis; and (4) Project based collaborative working. We describe our approach, exemplary use cases and our prototype implementation that demonstrates the feasibility of this approach.

  17. Software Certification - Coding, Code, and Coders

    Science.gov (United States)

    Havelund, Klaus; Holzmann, Gerard J.

    2011-01-01

    We describe a certification approach for software development that has been adopted at our organization. JPL develops robotic spacecraft for the exploration of the solar system. The flight software that controls these spacecraft is considered to be mission critical. We argue that the goal of a software certification process cannot be the development of "perfect" software, i.e., software that can be formally proven to be correct under all imaginable and unimaginable circumstances. More realistically, the goal is to guarantee a software development process that is conducted by knowledgeable engineers, who follow generally accepted procedures to control known risks, while meeting agreed upon standards of workmanship. We target three specific issues that must be addressed in such a certification procedure: the coding process, the code that is developed, and the skills of the coders. The coding process is driven by standards (e.g., a coding standard) and tools. The code is mechanically checked against the standard with the help of state-of-the-art static source code analyzers. The coders, finally, are certified in on-site training courses that include formal exams.

  18. 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....

  19. 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...

  20. 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...

  1. NASA software documentation standard software engineering program

    Science.gov (United States)

    1991-01-01

    The NASA Software Documentation Standard (hereinafter referred to as Standard) can be applied to the documentation of all NASA software. This Standard is limited to documentation format and content requirements. It does not mandate specific management, engineering, or assurance standards or techniques. This Standard defines the format and content of documentation for software acquisition, development, and sustaining engineering. Format requirements address where information shall be recorded and content requirements address what information shall be recorded. This Standard provides a framework to allow consistency of documentation across NASA and visibility into the completeness of project documentation. This basic framework consists of four major sections (or volumes). The Management Plan contains all planning and business aspects of a software project, including engineering and assurance planning. The Product Specification contains all technical engineering information, including software requirements and design. The Assurance and Test Procedures contains all technical assurance information, including Test, Quality Assurance (QA), and Verification and Validation (V&V). The Management, Engineering, and Assurance Reports is the library and/or listing of all project reports.

  2. 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.

  3. 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...

  4. 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.

  5. 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.

  6. COTS software selection process.

    Energy Technology Data Exchange (ETDEWEB)

    Watkins, William M. (Strike Wire Technologies, Louisville, CO); Lin, Han Wei; McClelland, Kelly (U.S. Security Associates, Livermore, CA); Ullrich, Rebecca Ann; Khanjenoori, Soheil; Dalton, Karen; Lai, Anh Tri; Kuca, Michal; Pacheco, Sandra; Shaffer-Gant, Jessica

    2006-05-01

    Today's need for rapid software development has generated a great interest in employing Commercial-Off-The-Shelf (COTS) software products as a way of managing cost, developing time, and effort. With an abundance of COTS software packages to choose from, the problem now is how to systematically evaluate, rank, and select a COTS product that best meets the software project requirements and at the same time can leverage off the current corporate information technology architectural environment. This paper describes a systematic process for decision support in evaluating and ranking COTS software. Performed right after the requirements analysis, this process provides the evaluators with more concise, structural, and step-by-step activities for determining the best COTS software product with manageable risk. In addition, the process is presented in phases that are flexible to allow for customization or tailoring to meet various projects' requirements.

  7. Social software in global software development

    DEFF Research Database (Denmark)

    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...

  8. 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.

  9. 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

  10. 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.

  11. Software systems for astronomy

    CERN Document Server

    Conrad, Albert R

    2014-01-01

    This book covers the use and development of software for astronomy. It describes the control systems used to point the telescope and operate its cameras and spectrographs, as well as the web-based tools used to plan those observations. In addition, the book also covers the analysis and archiving of astronomical data once it has been acquired. Readers will learn about existing software tools and packages, develop their own software tools, and analyze real data sets.

  12. 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)

  13. Solar Asset Management Software

    Energy Technology Data Exchange (ETDEWEB)

    Iverson, Aaron [Ra Power Management, Inc., Oakland, CA (United States); Zviagin, George [Ra Power Management, Inc., Oakland, CA (United States)

    2016-09-30

    Ra Power Management (RPM) has developed a cloud based software platform that manages the financial and operational functions of third party financed solar projects throughout their lifecycle. RPM’s software streamlines and automates the sales, financing, and management of a portfolio of solar assets. The software helps solar developers automate the most difficult aspects of asset management, leading to increased transparency, efficiency, and reduction in human error. More importantly, our platform will help developers save money by improving their operating margins.

  14. 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...

  15. 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

  16. 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.

  17. Lean software development

    OpenAIRE

    Hefnerová, Lucie

    2011-01-01

    The main goal of this bachelor thesis is the emergence of the clear Czech written material concerning the concept of Lean Software Development, which has been gaining significant attention in the field of software development, recently. Another goal of this thesis is to summarize the possible approaches of categorizing the concept and to summarize the possible approaches of defining the relationship between Lean and Agile software development. The detailed categorization of the tools potentia...

  18. Parallel Software Model Checking

    Science.gov (United States)

    2015-01-08

    JAN 2015 2. REPORT TYPE N/A 3. DATES COVERED 4. TITLE AND SUBTITLE Parallel Software Model Checking 5a. CONTRACT NUMBER 5b. GRANT NUMBER...AND ADDRESS(ES) Software Engineering Institute Carnegie Mellon University Pittsburgh, PA 15213 8. PERFORMING ORGANIZATION REPORT NUMBER 9...3: ∧ ≥ 10 ∧ ≠ 10 ⇒ : Parallel Software Model Checking Team Members Sagar Chaki, Arie Gurfinkel

  19. 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...

  20. 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).

  1. Global Software Engineering

    DEFF Research Database (Denmark)

    Ebert, Christof; Kuhrmann, Marco; Prikladnicki, Rafael

    2016-01-01

    Professional software products and IT systems and services today are developed mostly by globally distributed teams, projects, and companies. Successfully orchestrating Global Software Engineering (GSE) has become the major success factor both for organizations and practitioners. Yet, more than...... and experience reported at the IEEE International Conference on Software Engineering (ICGSE) series. The outcomes of our analysis show GSE as a field highly attached to industry and, thus, a considerable share of ICGSE papers address the transfer of Software Engineering concepts and solutions to the global stage...

  2. 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

  3. 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....

  4. 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

  5. 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

  6. 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

  7. Software Thread Integration and Synthesis for Real-Time Applications

    OpenAIRE

    Dean, Alexander G.

    2005-01-01

    Submitted on behalf of EDAA (http://www.edaa.com/); International audience; Software Thread Integration (STI) and Asynchronous STI (ASTI) are compiler techniques which interleave functions from separate program threads at the assembly language level, creating implicitly multithreaded functions which provide low-cost concurrency on generic hardware. This extends the reach of software and reduces the need to rely upon dedicated hardware. STI and ASTI are driven by two types of timing requiremen...

  8. Teaching Social Software with Social Software

    Science.gov (United States)

    Mejias, Ulises

    2006-01-01

    Ulises Mejias examines how social software--information and communications technologies that facilitate the collaboration and exchange of ideas--enables students to participate in distributed research, an approach to learning in which knowledge is collectively constructed and shared. During Fall 2005, Mejias taught a graduate seminar that provided…

  9. 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.

  10. Driven optical matter (Conference Presentation)

    Science.gov (United States)

    Figliozzi, Patrick; Sule, Nishant; Yan, Zijie; Vaikuntanathan, Suriyanarayanan; Rice, Stuart A.; Scherer, Norbert F.

    2016-09-01

    Optical trapping has enabled studying a wide variety of questions and systems in chemistry, biology, physics, and materials science. For example, optical trapping has been used to understand hydrodynamic interactions in dilute and dense colloidal fluids and discover connections to granular materials. In this presentation we show that shaped optical fields and gradients can be used to study the electrodynamic interactions amongst nanoparticles (NPs) and drive them into new ordered states. We demonstrate the formation and use of NP-based optical matter to study a range of nonequilibrium phenomena in solution; field-driven barrier crossing phenomena and noise-driven ordering. Optical matter, a material that forms only in the presence of an optical field, involves NP interactions by optical scattering and interference. Metal NPs can be formed into regular arrangements in minimally shaped fields; e.g., in focused Gaussian beams, line traps, and optical ring traps. Inter-particle interactions and motions are also affected when the optical matter is driven. Particles recirculate in an optical ring vortex trap allowing long term measurements to examine rare events. In particular, particles can hop between optical binding sites, move past electrodynamic obstacles or pass each other while moving around the ring. The polarization state of the optical beam can be used to produce periodic variations of the NP electrodynamic interactions. As particles circulate this "noise" causes NP clusters to be less stable as if the temperature of the system is increased. Conversely, we observe noise-driven ordering in dense systems. We will explain these phenomena using simulations and theory.

  11. 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...

  12. Software cost estimation

    NARCIS (Netherlands)

    Heemstra, F.J.

    1992-01-01

    The paper gives an overview of the state of the art of software cost estimation (SCE). The main questions to be answered in the paper are: (1) What are the reasons for overruns of budgets and planned durations? (2) What are the prerequisites for estimating? (3) How can software development effort be

  13. Software engineering ethics

    Science.gov (United States)

    Bown, Rodney L.

    1991-01-01

    Software engineering ethics is reviewed. The following subject areas are covered: lack of a system viewpoint; arrogance of PC DOS software vendors; violation od upward compatibility; internet worm; internet worm revisited; student cheating and company hiring interviews; computing practitioners and the commodity market; new projects and old programming languages; schedule and budget; and recent public domain comments.

  14. 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.

  15. 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.

  16. Software Quality Metrics

    Science.gov (United States)

    1991-07-01

    March 1979, pp. 121-128. Gorla, Narasimhaiah, Alan C. Benander, and Barbara A. Benander, "Debugging Effort Estimation Using Software Metrics", IEEE...Society, IEEE Guide for the Use of IEEE Standard Dictionary of Measures to Produce Reliable Software, IEEE Std 982.2-1988, June 1989. Jones, Capers

  17. Cactus: Software Priorities

    Science.gov (United States)

    Hyde, Hartley

    2009-01-01

    The early eighties saw a period of rapid change in computing and teachers lost control of how they used computers in their classrooms. Software companies produced computer tools that looked so good that teachers forgot about writing their own classroom materials and happily purchased software--that offered much more than teachers needed--from…

  18. 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.

  19. 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...

  20. 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.

  1. 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.

  2. 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.

  3. 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....... The software architect must modify multiple elements of the architecture manually, which risks introducing inconsistencies. This chapter provides an overview, comparison and detailed treatment of the various state-of-the-art approaches to describing and evolving software architectures. Furthermore, we discuss...... 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...

  4. 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...... makes these countries an attractive host for software companies. Often, high-quality engineering and excellent quality of products, e.g., machinery and equipment, are mentioned. Yet, the question is: Can such arguments be also found for the software industry? We aim at investigating the degree...... of professionalism and systematization of software development to draw a map of strengths and weaknesses. To this end, we conducted as a first step an exploratory survey in Germany, presented in this paper. In this survey, we focused on the perceived importance of the two general software engineering process areas...

  5. Trends in software testing

    CERN Document Server

    Mohanty, J; Balakrishnan, Arunkumar

    2017-01-01

    This book is focused on the advancements in the field of software testing and the innovative practices that the industry is adopting. Considering the widely varied nature of software testing, the book addresses contemporary aspects that are important for both academia and industry. There are dedicated chapters on seamless high-efficiency frameworks, automation on regression testing, software by search, and system evolution management. There are a host of mathematical models that are promising for software quality improvement by model-based testing. There are three chapters addressing this concern. Students and researchers in particular will find these chapters useful for their mathematical strength and rigor. Other topics covered include uncertainty in testing, software security testing, testing as a service, test technical debt (or test debt), disruption caused by digital advancement (social media, cloud computing, mobile application and data analytics), and challenges and benefits of outsourcing. The book w...

  6. Revisiting software ecosystems research

    DEFF Research Database (Denmark)

    Manikas, Konstantinos

    2016-01-01

    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...... 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....

  7. 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.

  8. Software-Reconfigurable Processors for Spacecraft

    Science.gov (United States)

    Farrington, Allen; Gray, Andrew; Bell, Bryan; Stanton, Valerie; Chong, Yong; Peters, Kenneth; Lee, Clement; Srinivasan, Jeffrey

    2005-01-01

    A report presents an overview of an architecture for a software-reconfigurable network data processor for a spacecraft engaged in scientific exploration. When executed on suitable electronic hardware, the software performs the functions of a physical layer (in effect, acts as a software radio in that it performs modulation, demodulation, pulse-shaping, error correction, coding, and decoding), a data-link layer, a network layer, a transport layer, and application-layer processing of scientific data. The software-reconfigurable network processor is undergoing development to enable rapid prototyping and rapid implementation of communication, navigation, and scientific signal-processing functions; to provide a long-lived communication infrastructure; and to provide greatly improved scientific-instrumentation and scientific-data-processing functions by enabling science-driven in-flight reconfiguration of computing resources devoted to these functions. This development is an extension of terrestrial radio and network developments (e.g., in the cellular-telephone industry) implemented in software running on such hardware as field-programmable gate arrays, digital signal processors, traditional digital circuits, and mixed-signal application-specific integrated circuits (ASICs).

  9. Scientific Software Component Technology

    Energy Technology Data Exchange (ETDEWEB)

    Kohn, S.; Dykman, N.; Kumfert, G.; Smolinski, B.

    2000-02-16

    We are developing new software component technology for high-performance parallel scientific computing to address issues of complexity, re-use, and interoperability for laboratory software. Component technology enables cross-project code re-use, reduces software development costs, and provides additional simulation capabilities for massively parallel laboratory application codes. The success of our approach will be measured by its impact on DOE mathematical and scientific software efforts. Thus, we are collaborating closely with library developers and application scientists in the Common Component Architecture forum, the Equation Solver Interface forum, and other DOE mathematical software groups to gather requirements, write and adopt a variety of design specifications, and develop demonstration projects to validate our approach. Numerical simulation is essential to the science mission at the laboratory. However, it is becoming increasingly difficult to manage the complexity of modern simulation software. Computational scientists develop complex, three-dimensional, massively parallel, full-physics simulations that require the integration of diverse software packages written by outside development teams. Currently, the integration of a new software package, such as a new linear solver library, can require several months of effort. Current industry component technologies such as CORBA, JavaBeans, and COM have all been used successfully in the business domain to reduce software development costs and increase software quality. However, these existing industry component infrastructures will not scale to support massively parallel applications in science and engineering. In particular, they do not address issues related to high-performance parallel computing on ASCI-class machines, such as fast in-process connections between components, language interoperability for scientific languages such as Fortran, parallel data redistribution between components, and massively

  10. 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.

  11. Query Driven Visualization

    CERN Document Server

    Buddelmeijer, Hugo

    2011-01-01

    The request driven way of deriving data in Astro-WISE is extended to a query driven way of visualization. This allows scientists to focus on the science they want to perform, because all administration of their data is automated. This can be done over an abstraction layer that enhances control and flexibility for the scientist.

  12. Network Motifs in Object-Oriented Software Systems

    CERN Document Server

    Ma, Yutao; Liu, Jing

    2008-01-01

    Nowadays, software has become a complex piece of work that may be beyond our control. Understanding how software evolves over time plays an important role in controlling software development processes. Recently, a few researchers found the quantitative evidence of structural duplication in software systems or web applications, which is similar to the evolutionary trend found in biological systems. To investigate the principles or rules of software evolution, we introduce the relevant theories and methods of complex networks into structural evolution and change of software systems. According to the results of our experiment on network motifs, we find that the stability of a motif shows positive correlation with its abundance and a motif with high Z score tends to have stable structure. These findings imply that the evolution of software systems is based on functional cloning as well as structural duplication and tends to be structurally stable. So, the work presented in this paper will be useful for the analys...

  13. Building Models of Installations to Recommend Applications in IoT Software Ecosystems

    DEFF Research Database (Denmark)

    Tomlein, Matus; Grønbæk, Kaj

    2016-01-01

    Internet of Things devices are driven by applications. To stimulate innovation on their platforms, manufacturers of embedded products are creating software ecosystems that enable third-parties develop applications for their devices. Since such applications are developed externally, their seamless...

  14. 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.

  15. 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.

  16. Error Free Software

    Science.gov (United States)

    1985-01-01

    A mathematical theory for development of "higher order" software to catch computer mistakes resulted from a Johnson Space Center contract for Apollo spacecraft navigation. Two women who were involved in the project formed Higher Order Software, Inc. to develop and market the system of error analysis and correction. They designed software which is logically error-free, which, in one instance, was found to increase productivity by 600%. USE.IT defines its objectives using AXES -- a user can write in English and the system converts to computer languages. It is employed by several large corporations.

  17. 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

  18. 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.

  19. Calidad de componentes software

    OpenAIRE

    2010-01-01

    En los últimos años se constata una tendencia creciente por parte de las organizaciones a desarrollar sus sistemas software mediante la combinación de componentes, en lugar de desarrollar dichos sistemas partiendo de cero. Esta tendencia es debida a varios factores. Entre ellos cabe destacar: la necesidad de las organizaciones de reducir los costes y el tiempo dedicados al desarrollo de los sistemas software; el crecimiento del mercado de componentes software; la reducción de la distancia ent...

  20. 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...

  1. 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.

  2. 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.

  3. CNEOST Control Software System

    Science.gov (United States)

    Wang, X.; Zhao, H. B.; Xia, Y.; Lu, H.; Li, B.

    2015-03-01

    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 message passing mechanism via WebSocket protocol, and improves its flexibility, expansibility, and scalability. The user interface with responsive web design realizes the remote operating under both desktop and mobile devices. The stable operating of 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.

  4. "IBSAR" Software 4.0

    Directory of Open Access Journals (Sweden)

    2004-06-01

    Full Text Available A review for Arabic software entitled "IBSAR" software assigned to help blinds in usage of the computer, the software pronounces the commands and the contents of screens and applications browsed by users, this review includes general introduction about the software, the components and commands of the software , system requirements , and its functions with Windows operating system and Microsoft Word.

  5. 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.

  6. A Novel Software Evolution Model Based on Software Networks

    Science.gov (United States)

    Pan, Weifeng; Li, Bing; Ma, Yutao; Liu, Jing

    Many published papers analyzed the forming mechanisms and evolution laws of OO software systems from software reuse, software pattern, etc. There, however, have been fewer models so far merely built on the software components such as methods, classes, etc. and their interactions. In this paper, a novel Software Evolution Model based on Software Networks (called SEM-SN) is proposed. It uses software network at class level to represent software systems, and uses software network’s dynamical generating process to simulate activities in real software development process such as new classes’ dynamical creations and their dynamical interactions with already existing classes. It also introduces the concept of node/edge ageing to describe the decaying of classes with time. Empirical results on eight open-source Object-Oriented (OO) software systems demonstrate that SCM-SN roughly describes the evolution process of software systems and the emergence of their complex network characteristics.

  7. 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

  8. 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

  9. 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…

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

    DEFF Research Database (Denmark)

    Guo, Yu

    2010-01-01

    as well as application models in a computer-aided software engineering environment. Furthermore, component models have been realized following carefully developed design patterns, which provide for an efficient and reusable implementation. The components have been ultimately implemented as prefabricated...... executable objects that can be linked together into an executable application. The development of embedded software using the COMDES framework is supported by the associated integrated engineering environment consisting of a number of tools, which support basic functionalities, such as system modelling......, validation, and executable code generation for specific hardware platforms. Developing such an environment and the associated tools is a highly complex engineering task. Therefore, this thesis has investigated key design issues and analysed existing platforms supporting model-driven software development...

  11. TMT common software update

    Science.gov (United States)

    Gillies, Kim; Brighton, Allan; Buur, Hanne

    2016-08-01

    TMT Common Software (CSW). CSW consists of software services and library code that is used by developers to create the subsystems and components that participate in the software system. CSW also defines the types of components that can be constructed and their functional roles in the software system. TMT CSW has recently passed its preliminary design review. The unique features of CSW include its use of multiple, open-source products as the basis for services, and an approach that works to reduce the amount of CSW-provided infrastructure code. Considerable prototyping was completed during this phase to mitigate risk with results that demonstrate the validity of this design approach and the selected service implementation products. This paper describes the latest design of TMT CSW, key features, and results from the prototyping effort.

  12. Software citation principles

    Directory of Open Access Journals (Sweden)

    Arfon M. Smith

    2016-09-01

    Full Text Available Software is a critical part of modern research and yet there is little support across the scholarly ecosystem for its acknowledgement and citation. Inspired by the activities of the FORCE11 working group focused on data citation, this document summarizes the recommendations of the FORCE11 Software Citation Working Group and its activities between June 2015 and April 2016. Based on a review of existing community practices, the goal of the working group was to produce a consolidated set of citation principles that may encourage broad adoption of a consistent policy for software citation across disciplines and venues. Our work is presented here as a set of software citation principles, a discussion of the motivations for developing the principles, reviews of existing community practice, and a discussion of the requirements these principles would place upon different stakeholders. Working examples and possible technical solutions for how these principles can be implemented will be discussed in a separate paper.

  13. 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.

  14. Collaborative software development

    NARCIS (Netherlands)

    Jonge, M. de; Visser, E.; Visser, J.M.W.

    2001-01-01

    We present an approach to collaborative software development where obtaining components and contributing components across organizational boundaries are explicit phases in the development process. A lightweight generative infrastructure supports this approach with an online package base, and several

  15. Error-Free Software

    Science.gov (United States)

    1989-01-01

    001 is an integrated tool suited for automatically developing ultra reliable models, simulations and software systems. Developed and marketed by Hamilton Technologies, Inc. (HTI), it has been applied in engineering, manufacturing, banking and software tools development. The software provides the ability to simplify the complex. A system developed with 001 can be a prototype or fully developed with production quality code. It is free of interface errors, consistent, logically complete and has no data or control flow errors. Systems can be designed, developed and maintained with maximum productivity. Margaret Hamilton, President of Hamilton Technologies, also directed the research and development of USE.IT, an earlier product which was the first computer aided software engineering product in the industry to concentrate on automatically supporting the development of an ultrareliable system throughout its life cycle. Both products originated in NASA technology developed under a Johnson Space Center contract.

  16. 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...

  17. Software For Genetic Algorithms

    Science.gov (United States)

    Wang, Lui; Bayer, Steve E.

    1992-01-01

    SPLICER computer program is genetic-algorithm software tool used to solve search and optimization problems. Provides underlying framework and structure for building genetic-algorithm application program. Written in Think C.

  18. Tier2 Submit Software

    Science.gov (United States)

    Download this tool for Windows or Mac, which helps facilities prepare a Tier II electronic chemical inventory report. The data can also be exported into the CAMEOfm (Computer-Aided Management of Emergency Operations) emergency planning software.

  19. 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...... række danske software-, elektronik- og IT-virksomheder....

  20. 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...

  1. 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.

  2. 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.

  3. 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.

  4. Project Portfolio Management Software

    Directory of Open Access Journals (Sweden)

    Paul POCATILU

    2006-01-01

    Full Text Available 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.

  5. Astronomical Software Directory Service

    Science.gov (United States)

    Hanisch, Robert J.; Payne, Harry; Hayes, Jeffrey

    1997-01-01

    With the support of NASA's Astrophysics Data Program (NRA 92-OSSA-15), we have developed the Astronomical Software Directory Service (ASDS): a distributed, searchable, WWW-based database of software packages and their related documentation. ASDS provides integrated access to 56 astronomical software packages, with more than 16,000 URLs indexed for full-text searching. Users are performing about 400 searches per month. A new aspect of our service is the inclusion of telescope and instrumentation manuals, which prompted us to change the name to the Astronomical Software and Documentation Service. ASDS was originally conceived to serve two purposes: to provide a useful Internet service in an area of expertise of the investigators (astronomical software), and as a research project to investigate various architectures for searching through a set of documents distributed across the Internet. Two of the co-investigators were then installing and maintaining astronomical software as their primary job responsibility. We felt that a service which incorporated our experience in this area would be more useful than a straightforward listing of software packages. The original concept was for a service based on the client/server model, which would function as a directory/referral service rather than as an archive. For performing the searches, we began our investigation with a decision to evaluate the Isite software from the Center for Networked Information Discovery and Retrieval (CNIDR). This software was intended as a replacement for Wide-Area Information Service (WAIS), a client/server technology for performing full-text searches through a set of documents. Isite had some additional features that we considered attractive, and we enjoyed the cooperation of the Isite developers, who were happy to have ASDS as a demonstration project. We ended up staying with the software throughout the project, making modifications to take advantage of new features as they came along, as well as

  6. Investing in Software Sustainment

    Science.gov (United States)

    2015-04-30

    recognize this need in a timely fashion has the potential to increase sustainment costs and, at the same time, degrade system performance. The decisions...corresponding funding decisions. The model allows decision-makers to analyze multiple allocation strategies in response to changes from mission...Engineering Institute (SEI). He works primarily on software measurement and estimation. He spent 30 years in the industry as a software developer and

  7. 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.

  8. ISEES: an institute for sustainable software to accelerate environmental science

    Science.gov (United States)

    Jones, M. B.; Schildhauer, M.; Fox, P. A.

    2013-12-01

    Software is essential to the full science lifecycle, spanning data acquisition, processing, quality assessment, data integration, analysis, modeling, and visualization. Software runs our meteorological sensor systems, our data loggers, and our ocean gliders. Every aspect of science is impacted by, and improved by, software. Scientific advances ranging from modeling climate change to the sequencing of the human genome have been rendered possible in the last few decades due to the massive improvements in the capabilities of computers to process data through software. This pivotal role of software in science is broadly acknowledged, while simultaneously being systematically undervalued through minimal investments in maintenance and innovation. As a community, we need to embrace the creation, use, and maintenance of software within science, and address problems such as code complexity, openness,reproducibility, and accessibility. We also need to fully develop new skills and practices in software engineering as a core competency in our earth science disciplines, starting with undergraduate and graduate education and extending into university and agency professional positions. The Institute for Sustainable Earth and Environmental Software (ISEES) is being envisioned as a community-driven activity that can facilitate and galvanize activites around scientific software in an analogous way to synthesis centers such as NCEAS and NESCent that have stimulated massive advances in ecology and evolution. We will describe the results of six workshops (Science Drivers, Software Lifecycles, Software Components, Workforce Development and Training, Sustainability and Governance, and Community Engagement) that have been held in 2013 to envision such an institute. We will present community recommendations from these workshops and our strategic vision for how ISEES will address the technical issues in the software lifecycle, sustainability of the whole software ecosystem, and the critical

  9. Towards research on software cybernetics

    OpenAIRE

    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.

  10. 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.

  11. Laser-Driven Fusion.

    Science.gov (United States)

    Gibson, A. F.

    1980-01-01

    Discusses the present status and future prospects of laser-driven fusion. Current research (which is classified under three main headings: laser-matter interaction processes, compression, and laser development) is also presented. (HM)

  12. [Research progress of cardiac systems biology].

    Science.gov (United States)

    Wang, Juan; Shang, Tong

    2009-04-01

    Systems Biology is one of the most widely discussed fields among emerging post-genomic disciplines. Medical systems biology is an important component of systems biology. The goals of medical systems biology are gaining a complete understanding of human body in normal and disease states. Driven by the great importance of cardiovascular diseases, cardiac systems biology is improving rapidly. This review provides an overview of major themes in the developing field of cardiac systems biology, including some of the high-throughput experiments and strategies used to integrate the datasets, various types of computational approaches used for developing useful quantitative models, and successful examples, future directions of cardiac systems biology.

  13. 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...

  14. A practice-driven systematic review of dependency analysis solutions

    NARCIS (Netherlands)

    Callo Arias, Trosky B.; Spek, Pieter van der; Avgeriou, Paris

    2011-01-01

    When following architecture-driven strategies to develop large software-intensive systems, the analysis of the dependencies is not an easy task. In this paper, we report a systematic literature review on dependency analysis solutions. Dependency analysis concerns making dependencies due to interconn

  15. 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

  16. 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.

  17. The ACTS Center for Software Sustainability

    Energy Technology Data Exchange (ETDEWEB)

    Leroy, Drummond-Lewis [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Marques, Osni A. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2011-09-30

    This report covers the activities carried out by the project The ACTS Center for Software Sustainability, whose proposal was submitted to ASCR in 2007. These activities have their roots in the project Advanced Computational Testing Software (ACTS) Toolkit, which was part of the DOE2000 Program. Driven by the state of the software, the technology and the nature of the tools in the Toolkit, the project was reformulated in a project that better represented the goals and activities within ACTS, An Expanded Framework for the Advanced CompuTational Software (ACTS) Collection. At the heart of this project was the consolidation of lessons learned and demands from the computational science community that guided us to the creation of the now well-known DOE ACTS Collection. The goal of the project was to increase the pay-off of DOE ASCR investment in the development of the general purpose tools in the DOE ACTS Collection, reduce the duplication of efforts, and minimize the development time of high-end computer applications while maximizing the life of the codes.

  18. Toward an integrated software platform for systems pharmacology.

    Science.gov (United States)

    Ghosh, Samik; Matsuoka, Yukiko; Asai, Yoshiyuki; Hsin, Kun-Yi; Kitano, Hiroaki

    2013-12-01

    Understanding complex biological systems requires the extensive support of computational tools. This is particularly true for systems pharmacology, which aims to understand the action of drugs and their interactions in a systems context. Computational models play an important role as they can be viewed as an explicit representation of biological hypotheses to be tested. A series of software and data resources are used for model development, verification and exploration of the possible behaviors of biological systems using the model that may not be possible or not cost effective by experiments. Software platforms play a dominant role in creativity and productivity support and have transformed many industries, techniques that can be applied to biology as well. Establishing an integrated software platform will be the next important step in the field.

  19. The Ettention software package

    Energy Technology Data Exchange (ETDEWEB)

    Dahmen, Tim, E-mail: Tim.Dahmen@dfki.de [German Research Center for Artificial Intelligence GmbH (DFKI), 66123 Saarbrücken (Germany); Saarland University, 66123 Saarbrücken (Germany); Marsalek, Lukas [Eyen SE, Na Nivách 1043/16, 141 00 Praha 4 (Czech Republic); Saarland University, 66123 Saarbrücken (Germany); Marniok, Nico [Saarland University, 66123 Saarbrücken (Germany); Turoňová, Beata [Saarland University, 66123 Saarbrücken (Germany); IMPRS-CS, Max-Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken (Germany); Bogachev, Sviatoslav [Saarland University, 66123 Saarbrücken (Germany); Trampert, Patrick; Nickels, Stefan [German Research Center for Artificial Intelligence GmbH (DFKI), 66123 Saarbrücken (Germany); Slusallek, Philipp [German Research Center for Artificial Intelligence GmbH (DFKI), 66123 Saarbrücken (Germany); Saarland University, 66123 Saarbrücken (Germany)

    2016-02-15

    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. - Highlights: • Novel software package for “reconstruction from projections” in electron microscopy. • Support for high-resolution reconstructions on iterative reconstruction algorithms. • Support for CPU, GPU and Xeon Phi. • Integration in the IMOD software. • Platform for algorithm researchers: object oriented, modular design.

  20. Managing Distributed Software Projects

    DEFF Research Database (Denmark)

    Persson, John Stouby

    Increasingly, software projects are becoming geographically distributed, with limited face-toface interaction between participants. These projects face particular challenges that need careful managerial attention. This PhD study reports on how we can understand and support the management of distr......Increasingly, software projects are becoming geographically distributed, with limited face-toface interaction between participants. These projects face particular challenges that need careful managerial attention. This PhD study reports on how we can understand and support the management...... of distributed software projects, based on a literature study and a case study. The main emphasis of the literature study was on how to support the management of distributed software projects, but also contributed to an understanding of these projects. The main emphasis of the case study was on how to understand...... the management of distributed software projects, but also contributed to supporting the management of these projects. The literature study integrates what we know about risks and risk-resolution techniques, into a framework for managing risks in distributed contexts. This framework was developed iteratively...

  1. 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.

  2. Software cost/resource modeling: Software quality tradeoff measurement

    Science.gov (United States)

    Lawler, R. W.

    1980-01-01

    A conceptual framework for treating software quality from a total system perspective is developed. Examples are given to show how system quality objectives may be allocated to hardware and software; to illustrate trades among quality factors, both hardware and software, to achieve system performance objectives; and to illustrate the impact of certain design choices on software functionality.

  3. 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.

  4. 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.

  5. 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.

  6. 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…

  7. 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.

  8. 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.

  9. 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 ...

  10. libdrdc: software standards library

    Science.gov (United States)

    Erickson, David; Peng, Tie

    2008-04-01

    This paper presents the libdrdc software standards library including internal nomenclature, definitions, units of measure, coordinate reference frames, and representations for use in autonomous systems research. This library is a configurable, portable C-function wrapped C++ / Object Oriented C library developed to be independent of software middleware, system architecture, processor, or operating system. It is designed to use the automatically-tuned linear algebra suite (ATLAS) and Basic Linear Algebra Suite (BLAS) and port to firmware and software. The library goal is to unify data collection and representation for various microcontrollers and Central Processing Unit (CPU) cores and to provide a common Application Binary Interface (ABI) for research projects at all scales. The library supports multi-platform development and currently works on Windows, Unix, GNU/Linux, and Real-Time Executive for Multiprocessor Systems (RTEMS). This library is made available under LGPL version 2.1 license.

  11. Methods of Software Verification

    Directory of Open Access Journals (Sweden)

    R. E. Gurin

    2015-01-01

    Full Text Available This article is devoted to the problem of software verification (SW. Methods of software verification designed to check the software for compliance with the stated requirements such as correctness, system security and system adaptability to small changes in the environment, portability and compatibility, etc. These are various methods both by the operation process and by the way of achieving result. The article describes the static and dynamic methods of software verification and paid attention to the method of symbolic execution. In its review of static analysis are discussed and described the deductive method, and methods for testing the model. A relevant issue of the pros and cons of a particular method is emphasized. The article considers classification of test techniques for each method. In this paper we present and analyze the characteristics and mechanisms of the static analysis of dependencies, as well as their views, which can reduce the number of false positives in situations where the current state of the program combines two or more states obtained both in different paths of execution and in working with multiple object values. Dependences connect various types of software objects: single variables, the elements of composite variables (structure fields, array elements, the size of the heap areas, the length of lines, the number of initialized array elements in the verification code using static methods. The article pays attention to the identification of dependencies within the framework of the abstract interpretation, as well as gives an overview and analysis of the inference tools.Methods of dynamic analysis such as testing, monitoring and profiling are presented and analyzed. Also some kinds of tools are considered which can be applied to the software when using the methods of dynamic analysis. Based on the work a conclusion is drawn, which describes the most relevant problems of analysis techniques, methods of their solutions and

  12. A refinement driven component-based design

    DEFF Research Database (Denmark)

    Chen, Zhenbang; Liu, Zhiming; Ravn, Anders Peter;

    2007-01-01

    to integrate sophisticated checkers, generators and transformations. A feasible approach to ensuring high quality of such add-ins is to base them on sound formal foundations. This paper summarizes our research on the Refinement of Component and Object Systems (rCOS) and illustrates it with experiences from...... the work on the Common Component Modelling Example (CoCoME). This gives evidence that the formal techniques developed in rCOS can be integrated into a model-driven development process and shows where it may be integrated in computer-aided software engineering (CASE) tools for adding formally supported...

  13. 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

  14. Software Safety and Security

    CERN Document Server

    Nipkow, T; Hauptmann, B

    2012-01-01

    Recent decades have seen major advances in methods and tools for checking the safety and security of software systems. Automatic tools can now detect security flaws not only in programs of the order of a million lines of code, but also in high-level protocol descriptions. There has also been something of a breakthrough in the area of operating system verification. This book presents the lectures from the NATO Advanced Study Institute on Tools for Analysis and Verification of Software Safety and Security; a summer school held at Bayrischzell, Germany, in 2011. This Advanced Study Institute was

  15. 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,

  16. 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.

  17. TIA Software User's Manual

    Science.gov (United States)

    Cramer, K. Elliott; Syed, Hazari I.

    1995-01-01

    This user's manual describes the installation and operation of TIA, the Thermal-Imaging acquisition and processing Application, developed by the Nondestructive Evaluation Sciences Branch at NASA Langley Research Center, Hampton, Virginia. TIA is a user friendly graphical interface application for the Macintosh 2 and higher series computers. The software has been developed to interface with the Perceptics/Westinghouse Pixelpipe(TM) and PixelStore(TM) NuBus cards and the GW Instruments MacADIOS(TM) input-output (I/O) card for the Macintosh for imaging thermal data. The software is also capable of performing generic image-processing functions.

  18. 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

  19. 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...

  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. 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

  2. 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.

  3. INTEGRATING CRM SOFTWARE APPLICATIONS

    OpenAIRE

    2008-01-01

    Scientists, end users of CRM applications and producers of CRM software, all come to an agreement when talking about the idea of CRM, the CRM strategy or the term CRM. The main aspect is that CRM can be analyzed from two different points of view: CRM – the marketing strategy and CRM – the software. The first term refers to establishing some personalized relationships with the customers that can be afterwards easily managed. This way, it can determine at any time the past client relations, the...

  4. 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

  5. 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

  6. 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.

  7. 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

  8. 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

  9. Component Based Effort Estimation During Software Development: Problematic View

    Directory of Open Access Journals (Sweden)

    VINIT KUMAR

    2011-10-01

    Full Text Available Component-based software development (CBD is anemerging discipline that promises to take softwareengineering into a new era. Building on theachievements of object-oriented software construction,CBD aims to deliver software engineering from acottage industry into an industrial age for InformationTechnology, wherein software can be assembled fromcomponents, in the manner that hardware systems arecurrently constructed from kits of parts. Componentbaseddevelopment (CBD is a branch of softwareengineering that emphasizes the separation ofconcerns in respect of the wide-ranging functionalityavailable throughout a given software system. Thispractice aims to bring about an equally wide-rangingdegree of benefits in both the short-term and the longtermfor the software itself and for organizations thatsponsor such software. Software engineers regardcomponents as part of the starting platformfor service-orientation. Components play this role, for example, in Web services, and more recently, in service-oriented architectures (SOA, whereby a component is converted by the Web service into aservice and subsequently inherits further characteristics beyond that of an ordinary component. Components can produce or consume events and can be used for event driven architectures (EDA.

  10. Evaluation & Optimization of Software Engineering

    Directory of Open Access Journals (Sweden)

    Asaduzzaman Noman

    2016-06-01

    Full Text Available 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 of software engineering is an efficient and reliable software product. IEEE defines software engineering as: The application of a systematic, disciplined, quantifiable approach to the development, operation and maintenance of software; that is, the application of engineering to software.

  11. 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.

  12. The FARE Software

    Science.gov (United States)

    Pitarello, Adriana

    2015-01-01

    This article highlights the importance of immediate corrective feedback in tutorial software for language teaching in an academic learning environment. We aim to demonstrate that, rather than simply reporting on the performance of the foreign language learner, this feedback can act as a mediator of students' cognitive and metacognitive activity.…

  13. 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.

  14. Generalized Software Security Framework

    Directory of Open Access Journals (Sweden)

    Smriti Jain

    2011-01-01

    Full Text Available Security of information has become a major concern in today's digitized world. As a result, effective techniques to secure information are required. The most effective way is to incorporate security in the development process itself thereby resulting into secured product. In this paper, we propose a framework that enables security to be included in the software development process. The framework consists of three layers namely; control layer, aspect layer and development layer. The control layer illustrates the managerial control of the entire software development process with the help of governance whereas aspect layer recognizes the security mechanisms that can be incorporated during the software development to identify the various security features. The development layer helps to integrate the various security aspects as well as the controls identified in the above layers during the development process. The layers are further verified by a survey amongst the IT professionals. The professionals concluded that the developed framework is easy to use due to its layered architecture and, can be customized for various types of softwares.

  15. 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`.

  16. 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...

  17. Open Source Software Acquisition

    DEFF Research Database (Denmark)

    Holck, Jesper; Kühn Pedersen, Mogens; Holm Larsen, Michael

    2005-01-01

    Lately we have seen a growing interest from both public and private organisations to adopt OpenSource Software (OSS), not only for a few, specific applications but also on a more general levelthroughout the organisation. As a consequence, the organisations' decisions on adoption of OSS arebecoming...

  18. Software Process Improvement

    DEFF Research Database (Denmark)

    Kuhrmann, Marco; Diebold, Philipp; Münch, Jürgen

    2016-01-01

    Software process improvement (SPI) is around for decades: frameworks are proposed, success factors are studied, and experiences have been reported. However, the sheer mass of concepts, approaches, and standards published over the years overwhelms practitioners as well as researchers. What is out...

  19. Patterns in Software Development

    DEFF Research Database (Denmark)

    Corry, Aino Vonge

    the university and I entered a project to industry within Center for Object Technology (COT). I focused on promoting the pattern concept to the Danish software industry in order to help them take advantage of the benefits of applying patterns in system development. In the obligatory stay abroad, I chose to visit...

  20. Software Defined Networking

    DEFF Research Database (Denmark)

    Caba, Cosmin Marius

    resources are limited. Hence, to counteract this trend, current QoS mechanisms must become simpler to deploy and operate, in order to motivate NSPs to employ QoS techniques instead of overprovisioning. Software Defined Networking (SDN) represents a paradigm shift in the way telecommunication and data...

  1. Software for multistate analysis

    Directory of Open Access Journals (Sweden)

    Frans J. Willekens

    2014-08-01

    Full Text Available Background: The growing interest in pathways, the increased availability of life-history data,innovations in statistical and demographic techniques, and advances in softwaretechnology have stimulated the development of software packages for multistatemodeling of life histories. Objective: In the paper we list and briefly discuss several software packages for multistate analysisof life-history data. The packages cover the estimation of multistate models (transitionrates and transition probabilities, multistate life tables, multistate populationprojections, and microsimulation. Methods: Brief description of software packages in a historical and comparative perspective. Results: During the past 10 years the advances in multistate modeling software have beenimpressive. New computational tools accompany the development of new methods instatistics and demography. The statistical theory of counting processes is the preferredmethod for the estimation of multistate models and R is the preferred programmingplatform. Conclusions: Innovations in method, data, and computer technology have removed the traditionalbarriers to multistate modeling of life histories and the computation of informative lifecourseindicators. The challenge ahead of us is to model and predict individual lifehistories.

  2. Complexity, Systems, and Software

    Science.gov (United States)

    2014-08-14

    complex ( Hidden issues; dumbs down operator) 11 Complexity, Systems, and Software Sarah Sheard August 14, 2014 © 2014 Carnegie...August 14, 2014 © 2014 Carnegie Mellon University Addressing Complexity in SoSs Source: SEBOK Wiki System Con truer Strateglc Context

  3. Limits of Software Reuse

    NARCIS (Netherlands)

    Holenderski, L.

    2006-01-01

    Software reuse is considered one of the main techniques to increasesoftware productivity. We present two simple mathematical argumentsthat show some theoretical limits of reuse. It turns out that the increase of productivity due to internal reuse is at most linear, farfrom the needed exponential gr

  4. AOFlagger: RFI Software

    Science.gov (United States)

    Offringa, A. R.

    2010-10-01

    The RFI software presented here can automatically flag data and can be used to analyze the data in a measurement. The purpose of flagging is to mark samples that are affected by interfering sources such as radio stations, airplanes, electrical fences or other transmitting interferers. The tools in the package are meant for offline use. The software package contains a graphical interface ("rfigui") that can be used to visualize a measurement set and analyze mitigation techniques. It also contains a console flagger ("rficonsole") that can execute a script of mitigation functions without the overhead of a graphical environment. All tools were written in C++. The software has been tested extensively on low radio frequencies (150 MHz or lower) produced by the WSRT and LOFAR telescopes. LOFAR is the Low Frequency Array that is built in and around the Netherlands. Higher frequencies should work as well. Some of the methods implemented are the SumThreshold, the VarThreshold and the singular value decomposition (SVD) method. Included also are several surface fitting algorithms. The software is published under the GNU General Public License version 3.

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. Interface-based software testing

    Directory of Open Access Journals (Sweden)

    Aziz Ahmad Rais

    2016-10-01

    Full Text Available Software quality is determined by assessing the characteristics that specify how it should work, which are verified through testing. If it were possible to touch, see, or measure software, it would be easier to analyze and prove its quality. Unfortunately, software is an intangible asset, which makes testing complex. This is especially true when software quality is not a question of particular functions that can be tested through a graphical user interface. The primary objective of software architecture is to design quality of software through modeling and visualization. There are many methods and standards that define how to control and manage quality. However, many IT software development projects still fail due to the difficulties involved in measuring, controlling, and managing software quality. Software quality failure factors are numerous. Examples include beginning to test software too late in the development process, or failing properly to understand, or design, the software architecture and the software component structure. The goal of this article is to provide an interface-based software testing technique that better measures software quality, automates software quality testing, encourages early testing, and increases the software’s overall testability

  10. Systems biology in molecular psychiatry.

    Science.gov (United States)

    Gebicke-Haerter, P J

    2008-09-01

    The last ten to fifteen years have seen a remarkable shift of research strategies from hypothesis-driven, reductionistic to data driven, hypothesis-free approaches. This tendency has become evident after completion of the sequencing of the human genome, when publications under the label systems biology have been skyrocketing. This shift marks a gradual revision of scientific understanding of biological systems. Whilst the former has been component-oriented, precluding elements that do not belong to the hypothesis, the latter try to extract information from the whole system in the first place. Only with this information at hand, data driven strategies develop hypotheses. Data driven strategies unearth the immense complexity of biological systems and, hence, necessitate computer-aided support. Mathematical tools derived from chaos theory appear to be applicable in biological systems, but require significant improvements. The combination of high throughput data collection with in silico modelling of molecular or higher order systems can markedly extend our understanding of onset and progression of diseases. Undoubtedly, systems thinking in brain research is the greatest challenge for the years to come.

  11. Ontology-Driven Provenance Management in eScience: An Application in Parasite Research

    Science.gov (United States)

    Sahoo, Satya S.; Weatherly, D. Brent; Mutharaju, Raghava; Anantharam, Pramod; Sheth, Amit; Tarleton, Rick L.

    Provenance, from the French word "provenir", describes the lineage or history of a data entity. Provenance is critical information in scientific applications to verify experiment process, validate data quality and associate trust values with scientific results. Current industrial scale eScience projects require an end-to-end provenance management infrastructure. This infrastructure needs to be underpinned by formal semantics to enable analysis of large scale provenance information by software applications. Further, effective analysis of provenance information requires well-defined query mechanisms to support complex queries over large datasets. This paper introduces an ontology-driven provenance management infrastructure for biology experiment data, as part of the Semantic Problem Solving Environment (SPSE) for Trypanosoma cruzi (T.cruzi). This provenance infrastructure, called T.cruzi Provenance Management System (PMS), is underpinned by (a) a domain-specific provenance ontology called Parasite Experiment ontology, (b) specialized query operators for provenance analysis, and (c) a provenance query engine. The query engine uses a novel optimization technique based on materialized views called materialized provenance views (MPV) to scale with increasing data size and query complexity. This comprehensive ontology-driven provenance infrastructure not only allows effective tracking and management of ongoing experiments in the Tarleton Research Group at the Center for Tropical and Emerging Global Diseases (CTEGD), but also enables researchers to retrieve the complete provenance information of scientific results for publication in literature.

  12. 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.

  13. 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.

  14. 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…

  15. 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).

  16. 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.

  17. 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...

  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. 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.

  20. 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.

  1. 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.

  2. 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...

  3. Computer games and software engineering

    CERN Document Server

    Cooper, Kendra M L

    2015-01-01

    Computer games represent a significant software application domain for innovative research in software engineering techniques and technologies. Game developers, whether focusing on entertainment-market opportunities or game-based applications in non-entertainment domains, thus share a common interest with software engineers and developers on how to best engineer game software.Featuring contributions from leading experts in software engineering, the book provides a comprehensive introduction to computer game software development that includes its history as well as emerging research on the inte

  4. Software Systems Stockroom

    Science.gov (United States)

    2009-11-01

    mentioned, the SPP is maintained by Vanderbilt University and is distributed as open-source software via the ESCHER web portal. (Detailed, web-based SPP...user documentation is also maintained on the ESCHER site as well.) Due to this preexisting distribution mechanism, it was decided to leverage the...Contribute with data reach-back use case, and model the Stockroom SPP artifact with a URL link to the remote data payload (on the ESCHER web portal

  5. 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.

  6. Software Project Management

    Science.gov (United States)

    1989-07-01

    incorporated into the sys- Kotler88 tem. Several interesting concepts are presented, but Kotler , P. Marketing Planning: Analysis, Planning, the bulk of the...Metzger87 Mantei, M. "The Effect of Programming Team Metzger, Philip W. Managing Programming Structures on Programming Tasks." Comm. ACM People: A Personal... Philips . Software Engi- Classic approach in organization theory. neering. Englewood Cliffs, N.J.: Prentice-Hall, 1988. Shannon75 An industrial approach

  7. Avoidable Software Procurements

    Science.gov (United States)

    2012-09-01

    SET) Adobe Desktop and Server software at up to 60% off GSA TLP level 1 pricing. Autodesk Included in this award are over two dozen AutoCAD and...environmentally friendly; less CDs/DVSs, less plastic CD/DVD covers, less cardboard packaging, and less paper manuals . D. THREATS 1. Security a...pilot. There were 54 test cases which were manually executed multiple times in order to evaluate how the proposed check-in/check-out pilot system would

  8. Unified Engineering Software System

    Science.gov (United States)

    Purves, L. R.; Gordon, S.; Peltzman, A.; Dube, M.

    1989-01-01

    Collection of computer programs performs diverse functions in prototype engineering. NEXUS, NASA Engineering Extendible Unified Software system, is research set of computer programs designed to support full sequence of activities encountered in NASA engineering projects. Sequence spans preliminary design, design analysis, detailed design, manufacturing, assembly, and testing. Primarily addresses process of prototype engineering, task of getting single or small number of copies of product to work. Written in FORTRAN 77 and PROLOG.

  9. Addressing Software Security

    Science.gov (United States)

    Bailey, Brandon

    2015-01-01

    Historically security within organizations was thought of as an IT function (web sites/servers, email, workstation patching, etc.) Threat landscape has evolved (Script Kiddies, Hackers, Advanced Persistent Threat (APT), Nation States, etc.) Attack surface has expanded -Networks interconnected!! Some security posture factors Network Layer (Routers, Firewalls, etc.) Computer Network Defense (IPS/IDS, Sensors, Continuous Monitoring, etc.) Industrial Control Systems (ICS) Software Security (COTS, FOSS, Custom, etc.)

  10. Software for Spatial Statistics

    OpenAIRE

    Edzer Pebesma; Roger Bivand; Paulo Justiniano Ribeiro

    2015-01-01

    We give an overview of the papers published in this special issue on spatial statistics, of the Journal of Statistical Software. 21 papers address issues covering visualization (micromaps, links to Google Maps or Google Earth), point pattern analysis, geostatistics, analysis of areal aggregated or lattice data, spatio-temporal statistics, Bayesian spatial statistics, and Laplace approximations. We also point to earlier publications in this journal on the same topic.

  11. Software for Spatial Statistics

    Directory of Open Access Journals (Sweden)

    Edzer Pebesma

    2015-02-01

    Full Text Available We give an overview of the papers published in this special issue on spatial statistics, of the Journal of Statistical Software. 21 papers address issues covering visualization (micromaps, links to Google Maps or Google Earth, point pattern analysis, geostatistics, analysis of areal aggregated or lattice data, spatio-temporal statistics, Bayesian spatial statistics, and Laplace approximations. We also point to earlier publications in this journal on the same topic.

  12. Statistical Software Engineering

    Science.gov (United States)

    2007-11-02

    Institute acts under the responsibility given to the National Academy of Sciences by its congressional charter to be an adviser to the federal government...research in software visualization—the use of typography, graphic design, animation, and cinematography to facilitate the understanding and...components. One of its major functions is to act as the central repository for all relevant project data (statistical or nonstatistical). Thus this

  13. Spreadsheet Auditing Software

    OpenAIRE

    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 spre...

  14. Image Processing Software

    Science.gov (United States)

    1992-01-01

    To convert raw data into environmental products, the National Weather Service and other organizations use the Global 9000 image processing system marketed by Global Imaging, Inc. The company's GAE software package is an enhanced version of the TAE, developed by Goddard Space Flight Center to support remote sensing and image processing applications. The system can be operated in three modes and is combined with HP Apollo workstation hardware.

  15. Office software Individual coaching

    CERN Multimedia

    HR Department

    2010-01-01

    If one or several particular topics cause you sleepless nights, you can get the help of our trainer who will come to your workplace for a multiple of 1-hour slots . All fields in which our trainer can help are detailed in the course description in our training catalogue (Microsoft Office software, Adobe applications, i-applications etc.). Please discover these new courses in our catalogue! Tel. 74924

  16. Wildlife software: procedures for publication of computer software

    Science.gov (United States)

    Samuel, M.D.

    1990-01-01

    Computers and computer software have become an integral part of the practice of wildlife science. Computers now play an important role in teaching, research, and management applications. Because of the specialized nature of wildlife problems, specific computer software is usually required to address a given problem (e.g., home range analysis). This type of software is not usually available from commercial vendors and therefore must be developed by those wildlife professionals with particular skill in computer programming. Current journal publication practices generally prevent a detailed description of computer software associated with new techniques. In addition, peer review of journal articles does not usually include a review of associated computer software. Thus, many wildlife professionals are usually unaware of computer software that would meet their needs or of major improvements in software they commonly use. Indeed most users of wildlife software learn of new programs or important changes only by word of mouth.

  17. Calculation Software versus Illustration Software for Teaching Statistics

    DEFF Research Database (Denmark)

    Mortensen, Peter Stendahl; Boyle, Robin G.

    1999-01-01

    As personal computers have become more and more powerful, so have the software packages available to us for teaching statistics. This paper investigates what software packages are currently being used by progressive statistics instructors at university level, examines some of the deficiencies...... of such software, and indicates features that statistics instructors wish to have incorporated in software in the future. The basis of the paper is a survey of participants at ICOTS-5 (the Fifth International Conference on Teaching Statistics). These survey results, combined with the software based papers...... presented at the conference, and the experiences of the authors, give rise to certain recommendations for instructors and software developers. The main conclusions are that both calculation software and illustration software are needed in the teaching and learning process, and that no computing skills...

  18. 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

  19. FPGAs for software programmers

    CERN Document Server

    Hannig, Frank; Ziener, Daniel

    2016-01-01

    This book makes powerful Field Programmable Gate Array (FPGA) and reconfigurable technology accessible to software engineers by covering different state-of-the-art high-level synthesis approaches (e.g., OpenCL and several C-to-gates compilers). It introduces FPGA technology, its programming model, and how various applications can be implemented on FPGAs without going through low-level hardware design phases. Readers will get a realistic sense for problems that are suited for FPGAs and how to implement them from a software designer’s point of view. The authors demonstrate that FPGAs and their programming model reflect the needs of stream processing problems much better than traditional CPU or GPU architectures, making them well-suited for a wide variety of systems, from embedded systems performing sensor processing to large setups for Big Data number crunching. This book serves as an invaluable tool for software designers and FPGA design engineers who are interested in high design productivity through behavi...

  20. JPI UML Software Modeling

    Directory of Open Access Journals (Sweden)

    Cristian Vidal Silva

    2015-12-01

    Full Text Available Aspect-Oriented Programming AOP extends object-oriented programming OOP with aspects to modularize crosscutting behavior on classes by means of aspects to advise base code in the occurrence of join points according to pointcut rules definition. However, join points introduce dependencies between aspects and base code, a great issue to achieve an effective independent development of software modules. Join Point Interfaces JPI represent join points using interfaces between classes and aspect, thus these modules do not depend of each other. Nevertheless, since like AOP, JPI is a programming methodology; thus, for a complete aspect-oriented software development process, it is necessary to define JPI requirements and JPI modeling phases. Towards previous goal, this article proposes JPI UML class and sequence diagrams for modeling JPI software solutions. A purpose of these diagrams is to facilitate understanding the structure and behavior of JPI programs. As an application example, this article applies the JPI UML diagrams proposal on a case study and analyzes the associated JPI code to prove their hegemony.

  1. The ALMA software architecture

    Science.gov (United States)

    Schwarz, Joseph; Farris, Allen; Sommer, Heiko

    2004-09-01

    The software for the Atacama Large Millimeter Array (ALMA) is being developed by many institutes on two continents. The software itself will function in a distributed environment, from the 0.5-14 kmbaselines that separate antennas to the larger distances that separate the array site at the Llano de Chajnantor in Chile from the operations and user support facilities in Chile, North America and Europe. Distributed development demands 1) interfaces that allow separated groups to work with minimal dependence on their counterparts at other locations; and 2) a common architecture to minimize duplication and ensure that developers can always perform similar tasks in a similar way. The Container/Component model provides a blueprint for the separation of functional from technical concerns: application developers concentrate on implementing functionality in Components, which depend on Containers to provide them with services such as access to remote resources, transparent serialization of entity objects to XML, logging, error handling and security. Early system integrations have verified that this architecture is sound and that developers can successfully exploit its features. The Containers and their services are provided by a system-orienteddevelopment team as part of the ALMA Common Software (ACS), middleware that is based on CORBA.

  2. Terra Harvest software architecture

    Science.gov (United States)

    Humeniuk, Dave; Klawon, Kevin

    2012-06-01

    Under the Terra Harvest Program, the DIA has the objective of developing a universal Controller for the Unattended Ground Sensor (UGS) community. The mission is to define, implement, and thoroughly document an open architecture that universally supports UGS missions, integrating disparate systems, peripherals, etc. The Controller's inherent interoperability with numerous systems enables the integration of both legacy and future UGS System (UGSS) components, while the design's open architecture supports rapid third-party development to ensure operational readiness. The successful accomplishment of these objectives by the program's Phase 3b contractors is demonstrated via integration of the companies' respective plug-'n'-play contributions that include controllers, various peripherals, such as sensors, cameras, etc., and their associated software drivers. In order to independently validate the Terra Harvest architecture, L-3 Nova Engineering, along with its partner, the University of Dayton Research Institute, is developing the Terra Harvest Open Source Environment (THOSE), a Java Virtual Machine (JVM) running on an embedded Linux Operating System. The Use Cases on which the software is developed support the full range of UGS operational scenarios such as remote sensor triggering, image capture, and data exfiltration. The Team is additionally developing an ARM microprocessor-based evaluation platform that is both energy-efficient and operationally flexible. The paper describes the overall THOSE architecture, as well as the design decisions for some of the key software components. Development process for THOSE is discussed as well.

  3. Software design practice using two SCADA software packages

    DEFF Research Database (Denmark)

    Basse, K.P.; Christensen, Georg Kronborg; Frederiksen, P. K.

    1996-01-01

    Typical software development for manufacturing control is done either by specialists with consideral real-time programming experience or done by the adaptation of standard software packages for manufacturing control. After investigation and test of two commercial software packages: "InTouch" and ......Touch" and "Fix", it is argued, that a more efficient software solution can be achieved by utilising an integrated specification for SCADA and PLC-programming. Experiences gained from process control is planned investigated for descrete parts manufacturing....

  4. Proceedings Second International Workshop on Algebraic Methods in Model-based Software Engineering

    CERN Document Server

    Durán, Francisco

    2011-01-01

    Over the past years there has been quite a lot of activity in the algebraic community about using algebraic methods for providing support to model-driven software engineering. The aim of this workshop is to gather researchers working on the development and application of algebraic methods to provide rigorous support to model-based software engineering. The topics relevant to the workshop are all those related to the use of algebraic methods in software engineering, including but not limited to: formally specifying and verifying model-based software engineering concepts and related ones (MDE, UML, OCL, MOF, DSLs, ...); tool support for the above; integration of formal and informal methods; and theoretical frameworks (algebraic, rewriting-based, category theory-based, ...). The workshop's main goal is to examine, discuss, and relate the existing projects within the algebraic community that address common open-issues in model-driven software engineering.

  5. Open Source Next Generation Visualization Software for Interplanetary Missions

    Science.gov (United States)

    Trimble, Jay; Rinker, George

    2016-01-01

    Mission control is evolving quickly, driven by the requirements of new missions, and enabled by modern computing capabilities. Distributed operations, access to data anywhere, data visualization for spacecraft analysis that spans multiple data sources, flexible reconfiguration to support multiple missions, and operator use cases, are driving the need for new capabilities. NASA's Advanced Multi-Mission Operations System (AMMOS), Ames Research Center (ARC) and the Jet Propulsion Laboratory (JPL) are collaborating to build a new generation of mission operations software for visualization, to enable mission control anywhere, on the desktop, tablet and phone. The software is built on an open source platform that is open for contributions (http://nasa.github.io/openmct).

  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. Scaling up nanoscale water-driven energy conversion into evaporation-driven engines and generators

    Science.gov (United States)

    Chen, Xi; Goodnight, Davis; Gao, Zhenghan; Cavusoglu, Ahmet H.; Sabharwal, Nina; Delay, Michael; Driks, Adam; Sahin, Ozgur

    2015-06-01

    Evaporation is a ubiquitous phenomenon in the natural environment and a dominant form of energy transfer in the Earth's climate. Engineered systems rarely, if ever, use evaporation as a source of energy, despite myriad examples of such adaptations in the biological world. Here, we report evaporation-driven engines that can power common tasks like locomotion and electricity generation. These engines start and run autonomously when placed at air-water interfaces. They generate rotary and piston-like linear motion using specially designed, biologically based artificial muscles responsive to moisture fluctuations. Using these engines, we demonstrate an electricity generator that rests on water while harvesting its evaporation to power a light source, and a miniature car (weighing 0.1 kg) that moves forward as the water in the car evaporates. Evaporation-driven engines may find applications in powering robotic systems, sensors, devices and machinery that function in the natural environment.

  8. Software engineering methodologies and tools

    Science.gov (United States)

    Wilcox, Lawrence M.

    1993-01-01

    Over the years many engineering disciplines have developed, including chemical, electronic, etc. Common to all engineering disciplines is the use of rigor, models, metrics, and predefined methodologies. Recently, a new engineering discipline has appeared on the scene, called software engineering. For over thirty years computer software has been developed and the track record has not been good. Software development projects often miss schedules, are over budget, do not give the user what is wanted, and produce defects. One estimate is there are one to three defects per 1000 lines of deployed code. More and more systems are requiring larger and more complex software for support. As this requirement grows, the software development problems grow exponentially. It is believed that software quality can be improved by applying engineering principles. Another compelling reason to bring the engineering disciplines to software development is productivity. It has been estimated that productivity of producing software has only increased one to two percent a year in the last thirty years. Ironically, the computer and its software have contributed significantly to the industry-wide productivity, but computer professionals have done a poor job of using the computer to do their job. Engineering disciplines and methodologies are now emerging supported by software tools that address the problems of software development. This paper addresses some of the current software engineering methodologies as a backdrop for the general evaluation of computer assisted software engineering (CASE) tools from actual installation of and experimentation with some specific tools.

  9. The software invention cube: A classification scheme for software inventions

    NARCIS (Netherlands)

    Bergstra, J.A.; Klint, P.

    2008-01-01

    The patent system protects inventions. The requirement that a software invention should make ‘a technical contribution’ turns out to be untenable in practice and this raises the question, what constitutes an invention in the realm of software. The authors developed the Software Invention Cube (SWIC)

  10. Software requirements flow-down and preliminary software design for the G-CLEF spectrograph

    Science.gov (United States)

    Evans, Ian N.; Budynkiewicz, Jamie A.; DePonte Evans, Janet; Miller, Joseph B.; Onyuksel, Cem; Paxson, Charles; Plummer, David A.

    2016-08-01

    The Giant Magellan Telescope (GMT)-Consortium Large Earth Finder (G-CLEF) is a fiber-fed, precision radial velocity (PRV) optical echelle spectrograph that will be the first light instrument on the GMT. The G-CLEF instrument device control subsystem (IDCS) provides software control of the instrument hardware, including the active feedback loops that are required to meet the G-CLEF PRV stability requirements. The IDCS is also tasked with providing operational support packages that include data reduction pipelines and proposal preparation tools. A formal, but ultimately pragmatic approach is being used to establish a complete and correct set of requirements for both the G-CLEF device control and operational support packages. The device control packages must integrate tightly with the state-machine driven software and controls reference architecture designed by the GMT Organization. A model-based systems engineering methodology is being used to develop a preliminary design that meets these requirements. Through this process we have identified some lessons that have general applicability to the development of software for ground-based instrumentation. For example, tasking an individual with overall responsibility for science/software/hardware integration is a key step to ensuring effective integration between these elements. An operational concept document that includes detailed routine and non- routine operational sequences should be prepared in parallel with the hardware design process to tie together these elements and identify any gaps. Appropriate time-phasing of the hardware and software design phases is important, but revisions to driving requirements that impact software requirements and preliminary design are inevitable. Such revisions must be carefully managed to ensure efficient use of resources.

  11. Computer software summaries. Numbers 325 through 423

    Energy Technology Data Exchange (ETDEWEB)

    1978-08-01

    The National Energy Software Center (NESC) serves as the software exchange and information center for the U.S. Department of Energy and the Nuclear Regulatory Commission. These summaries describe agency-sponsored software which is at the specification stage, under development, being checked out, in use, or available at agency offices, laboratories, and contractor installations. They describe software which is not included in the NESC library due to its preliminary status or because it is believed to be of limited interest. Codes dealing with the following subjects are included: cross section and resonance integral calculations; spectrum calculations, generation of group constants, lattice and cell problems; static design studies; depletion, fuel management, cost analysis, and power plant economics; space-independent kinetics; space--time kinetics, coupled neutronics--hydrodynamics--thermodynamics; and excursion simulations; radiological safety, hazard and accident analysis; heat transfer and fluid flow; deformation and stress distribution computations, structural analysis, and engineering design studies; gamma heating and shield design; reactor systems analysis; data preparation; data management; subsidiary calculations; experimental data processing; general mathematical and computing system routines; materials; environmental and earth sciences; space sciences; electronics and engineering equipment; chemistry; particle accelerators and high-voltage machines; physics; magnetic fusion research; biology and medicine; and data. (RWR)

  12. Improving Software Citation and Credit

    CERN Document Server

    Allen, Alice; DuPrie, Kimberly; Mink, Jessica; Nemiroff, Robert; Robitaille, Thomas; Shamir, Lior; Shortridge, Keith; Taylor, Mark; Teuben, Peter; Wallin, John

    2015-01-01

    The past year has seen movement on several fronts for improving software citation, including the Center for Open Science's Transparency and Openness Promotion (TOP) Guidelines, the Software Publishing Special Interest Group that was started at January's AAS meeting in Seattle at the request of that organization's Working Group on Astronomical Software, a Sloan-sponsored meeting at GitHub in San Francisco to begin work on a cohesive research software citation-enabling platform, the work of Force11 to "transform and improve" research communication, and WSSSPE's ongoing efforts that include software publication, citation, credit, and sustainability. Brief reports on these efforts were shared at the BoF, after which participants discussed ideas for improving software citation, generating a list of recommendations to the community of software authors, journal publishers, ADS, and research authors. The discussion, recommendations, and feedback will help form recommendations for software citation to those publishers...

  13. Software Engineering for Human Spaceflight

    Science.gov (United States)

    Fredrickson, Steven E.

    2014-01-01

    The Spacecraft Software Engineering Branch of NASA Johnson Space Center (JSC) provides world-class products, leadership, and technical expertise in software engineering, processes, technology, and systems management for human spaceflight. The branch contributes to major NASA programs (e.g. ISS, MPCV/Orion) with in-house software development and prime contractor oversight, and maintains the JSC Engineering Directorate CMMI rating for flight software development. Software engineering teams work with hardware developers, mission planners, and system operators to integrate flight vehicles, habitats, robotics, and other spacecraft elements. They seek to infuse automation and autonomy into missions, and apply new technologies to flight processor and computational architectures. This presentation will provide an overview of key software-related projects, software methodologies and tools, and technology pursuits of interest to the JSC Spacecraft Software Engineering Branch.

  14. Clustering Methodologies for Software Engineering

    Directory of Open Access Journals (Sweden)

    Mark Shtern

    2012-01-01

    Full Text Available The size and complexity of industrial strength software systems are constantly increasing. This means that the task of managing a large software project is becoming even more challenging, especially in light of high turnover of experienced personnel. Software clustering approaches can help with the task of understanding large, complex software systems by automatically decomposing them into smaller, easier-to-manage subsystems. The main objective of this paper is to identify important research directions in the area of software clustering that require further attention in order to develop more effective and efficient clustering methodologies for software engineering. To that end, we first present the state of the art in software clustering research. We discuss the clustering methods that have received the most attention from the research community and outline their strengths and weaknesses. Our paper describes each phase of a clustering algorithm separately. We also present the most important approaches for evaluating the effectiveness of software clustering.

  15. Capturing the impact of software

    Science.gov (United States)

    Piwowar, Heather

    2017-01-01

    Research software is undervalued in funding and tenure decisions because its impact is poorly evaluated within the traditional paper-based ecosystem. The talk presents the NSF-funded Depsy project (http://depsy.org) -- a proof-of-concept system designed to address this problem by tracking the impact of software in software-native ways. Depsy finds mentions of software itself in the literature, rather than just counting citations to a wrapper paper about the software. It discovers how software gets reused by other software, even when it's not cited at all. And finally Depsy attempts to represent the full complexity of software authorship, where one project can involve hundreds of contributors in multiple roles that don't map to traditional paper authorship.

  16. Patterns, principles, and practices of domain-driven design

    CERN Document Server

    Millett, Scott

    2015-01-01

    Methods for managing complex software construction following the practices, principles and patterns of Domain-Driven Design with code examples in C# This book presents the philosophy of Domain-Driven Design (DDD) in a down-to-earth and practical manner for experienced developers building applications for complex domains. A focus is placed on the principles and practices of decomposing a complex problem space as well as the implementation patterns and best practices for shaping a maintainable solution space. You will learn how to build effective domain models through the use of tactical pat

  17. Electrically driven optical antennas

    Science.gov (United States)

    Kern, Johannes; Kullock, René; Prangsma, Jord; Emmerling, Monika; Kamp, Martin; Hecht, Bert

    2015-09-01

    Unlike radiowave antennas, so far optical nanoantennas cannot be fed by electrical generators. Instead, they are driven by light or indirectly via excited discrete states in active materials in their vicinity. Here we demonstrate the direct electrical driving of an in-plane optical antenna by the broadband quantum-shot noise of electrons tunnelling across its feed gap. The spectrum of the emitted photons is determined by the antenna geometry and can be tuned via the applied voltage. Moreover, the direction and polarization of the light emission are controlled by the antenna resonance, which also improves the external quantum efficiency by up to two orders of magnitude. The one-material planar design offers facile integration of electrical and optical circuits and thus represents a new paradigm for interfacing electrons and photons at the nanometre scale, for example for on-chip wireless communication and highly configurable electrically driven subwavelength photon sources.

  18. The Software Management Environment (SME)

    Science.gov (United States)

    Valett, Jon D.; Decker, William; Buell, John

    1988-01-01

    The Software Management Environment (SME) is a research effort designed to utilize the past experiences and results of the Software Engineering Laboratory (SEL) and to incorporate this knowledge into a tool for managing projects. SME provides the software development manager with the ability to observe, compare, predict, analyze, and control key software development parameters such as effort, reliability, and resource utilization. The major components of the SME, the architecture of the system, and examples of the functionality of the tool are discussed.

  19. Software Validation using Power Profiles

    OpenAIRE

    Lencevicius, Raimondas; Metz, Edu; Ran, Alexander

    2002-01-01

    The validation of modern software systems incorporates both functional and quality requirements. This paper proposes a validation approach for software quality requirement - its power consumption. This approach validates whether the software produces the desired results with a minimum expenditure of energy. We present energy requirements and an approach for their validation using a power consumption model, test-case specification, software traces, and power measurements. Three different appro...

  20. Formal aspects of component software

    OpenAIRE

    Sun, Meng; Schatz, B.

    2014-01-01

    This issue includes extended versions of selected best papers from the 7th International Workshop on Formal Aspects of Component Software (FACS 2010) held in Guimarães, Portugal on October 14–16, 2010. The component-based software development approach has emerged as a promising paradigm to cope with an ever increasing complexity of present-day software solutions by bringing sound production and engineering principles into software engineering. However, many conceptual and technological iss...

  1. Design Principles for Interactive Software

    DEFF Research Database (Denmark)

    The book addresses the crucial intersection of human-computer interaction (HCI) and software engineering by asking both what users require from interactive systems and what developers need to produce well-engineered software. Needs are expressed as......The book addresses the crucial intersection of human-computer interaction (HCI) and software engineering by asking both what users require from interactive systems and what developers need to produce well-engineered software. Needs are expressed as...

  2. Software Security Requirements Gathering Instrument

    OpenAIRE

    2011-01-01

    Security breaches are largely caused by the vulnerable software. Since individuals and organizations mostly depend on softwares, it is important to produce in secured manner. The first step towards producing secured software is through gathering security requirements. This paper describes Software Security Requirements Gathering Instrument (SSRGI) that helps gather security requirements from the various stakeholders. This will guide the developers to gather security requirements along with th...

  3. Software engineering a practitioner's approach

    CERN Document Server

    Pressman, Roger S

    1997-01-01

    This indispensable guide to software engineering exploration enables practitioners to navigate the ins and outs of this rapidly changing field. Pressman's fully revised and updated Fourth Edition provides in-depth coverage of every important management and technical topic in software engineering. Moreover, readers will find the inclusion of the hottest developments in the field such as: formal methods and cleanroom software engineering, business process reengineering, and software reengineering.

  4. GNSS Software Receiver for UAVs

    DEFF Research Database (Denmark)

    Olesen, Daniel Madelung; Jakobsen, Jakob; von Benzon, Hans-Henrik

    2016-01-01

    This paper describes the current activities of GPS/GNSS Software receiver development at DTU Space. GNSS Software receivers have received a great deal of attention in the last two decades and numerous implementations have already been presented. DTU Space has just recently started development of ...... of our own GNSS software-receiver targeted for mini UAV applications, and we will in in this paper present our current progress and briefly discuss the benefits of Software Receivers in relation to our research interests....

  5. Noise-driven phenomena in hysteretic systems

    CERN Document Server

    Dimian, Mihai

    2014-01-01

    Noise-Driven Phenomena in Hysteretic Systems provides a general approach to nonlinear systems with hysteresis driven by noisy inputs, which leads to a unitary framework for the analysis of various stochastic aspects of hysteresis. This book includes integral, differential and algebraic models that are used to describe scalar and vector hysteretic nonlinearities originating from various areas of science and engineering. The universality of the authors approach is also reflected by the diversity of the models used to portray the input noise, from the classical Gaussian white noise to its impulsive forms, often encountered in economics and biological systems, and pink noise, ubiquitous in multi-stable electronic systems. The book is accompanied by HysterSoft© - a robust simulation environment designed to perform complex hysteresis modeling – that can be used by the reader to reproduce many of the results presented in the book as well as to research both disruptive and constructive effects of noise in hysteret...

  6. Surface chemistry driven actuation in nanoporous gold

    Energy Technology Data Exchange (ETDEWEB)

    Biener, J; Wittstock, A; Zepeda-Ruiz, L; Biener, M M; Zielasek, V; Kramer, D; Viswanath, R N; Weissmuller, J; Baumer, M; Hamza, A V

    2008-04-14

    Although actuation in biological systems is exclusively powered by chemical energy, this concept has not been realized in man-made actuator technologies, as these rely on generating heat or electricity first. Here, we demonstrate that surface-chemistry driven actuation can be realized in high surface area materials such as nanoporous gold. For example, we achieve reversible strain amplitudes in the order of a few tenths of a percent by alternating exposure of nanoporous Au to ozone and carbon monoxide. The effect can be explained by adsorbate-induced changes of the surface stress, and can be used to convert chemical energy directly into a mechanical response thus opening the door to surface-chemistry driven actuator and sensor technologies.

  7. Research on Software-Cell-Based Software System

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The aim of research on software architecture is to improve the quality attributes of software sys tems, such as security, reliability, maintainability, testability , reassembility , evolvability. However, a sin gle running system is hard to achieve all these goals. In this paper, software-cell is introduced as the basic u nit throughout developing process. Then it is further advanced that a robust, safe and high-quality software system is composed of a running system and four supportive systems. This paper especially discusses the structure of software-cell, the construction of the five systems, and the relations between them.

  8. The Gaggle: An open-source software system for integrating bioinformatics software and data sources

    Directory of Open Access Journals (Sweden)

    Bonneau Richard

    2006-03-01

    Full Text Available Abstract Background Systems biologists work with many kinds of data, from many different sources, using a variety of software tools. Each of these tools typically excels at one type of analysis, such as of microarrays, of metabolic networks and of predicted protein structure. A crucial challenge is to combine the capabilities of these (and other forthcoming data resources and tools to create a data exploration and analysis environment that does justice to the variety and complexity of systems biology data sets. A solution to this problem should recognize that data types, formats and software in this high throughput age of biology are constantly changing. Results In this paper we describe the Gaggle -a simple, open-source Java software environment that helps to solve the problem of software and database integration. Guided by the classic software engineering strategy of separation of concerns and a policy of semantic flexibility, it integrates existing popular programs and web resources into a user-friendly, easily-extended environment. We demonstrate that four simple data types (names, matrices, networks, and associative arrays are sufficient to bring together diverse databases and software. We highlight some capabilities of the Gaggle with an exploration of Helicobacter pylori pathogenesis genes, in which we identify a putative ricin-like protein -a discovery made possible by simultaneous data exploration using a wide range of publicly available data and a variety of popular bioinformatics software tools. Conclusion We have integrated diverse databases (for example, KEGG, BioCyc, String and software (Cytoscape, DataMatrixViewer, R statistical environment, and TIGR Microarray Expression Viewer. Through this loose coupling of diverse software and databases the Gaggle enables simultaneous exploration of experimental data (mRNA and protein abundance, protein-protein and protein-DNA interactions, functional associations (operon, chromosomal

  9. Affinity driven social networks

    Science.gov (United States)

    Ruyú, B.; Kuperman, M. N.

    2007-04-01

    In this work we present a model for evolving networks, where the driven force is related to the social affinity between individuals of a population. In the model, a set of individuals initially arranged on a regular ordered network and thus linked with their closest neighbors are allowed to rearrange their connections according to a dynamics closely related to that of the stable marriage problem. We show that the behavior of some topological properties of the resulting networks follows a non trivial pattern.

  10. Free Software and Free Textbooks

    Science.gov (United States)

    Takhteyev, Yuri

    2012-01-01

    Some of the world's best and most sophisticated software is distributed today under "free" or "open source" licenses, which allow the recipients of such software to use, modify, and share it without paying royalties or asking for permissions. If this works for software, could it also work for educational resources, such as books? The economics of…

  11. Software Startups - A Research Agenda

    Directory of Open Access Journals (Sweden)

    Michael Unterkalmsteiner

    2016-10-01

    Full Text Available Software startup companies develop innovative, software-intensive products within limited time frames and with few resources, searching for sustainable and scalable business models. Software startups are quite distinct from traditional mature software companies, but also from micro-, small-, and medium-sized enterprises, introducing new challenges relevant for software engineering research. This paper's research agenda focuses on software engineering in startups, identifying, in particular, 70+ research questions in the areas of supporting startup engineering activities, startup evolution models and patterns, ecosystems and innovation hubs, human aspects in software startups, applying startup concepts in non-startup environments, and methodologies and theories for startup research. We connect and motivate this research agenda with past studies in software startup research, while pointing out possible future directions. While all authors of this research agenda have their main background in Software Engineering or Computer Science, their interest in software startups broadens the perspective to the challenges, but also to the opportunities that emerge from multi-disciplinary research. Our audience is therefore primarily software engineering researchers, even though we aim at stimulating collaborations and research that crosses disciplinary boundaries. We believe that with this research agenda we cover a wide spectrum of the software startup industry current needs.

  12. Software product lines : Organizational alternatives

    NARCIS (Netherlands)

    Bosch, J

    2001-01-01

    Software product lines enjoy increasingly wide adoption in the software industry. Most authors focus on the technical and process aspects and assume an organizational model consisting of a domain engineering unit and several application engineering units. In our cooperation with several software dev

  13. Model-based Software Engineering

    DEFF Research Database (Denmark)

    2010-01-01

    The vision of model-based software engineering is to make models the main focus of software development and to automatically generate software from these models. Part of that idea works already today. But, there are still difficulties when it comes to behaviour. Actually, there is no lack in models...

  14. NASA's Approach to Software Assurance

    Science.gov (United States)

    Wetherholt, Martha

    2015-01-01

    NASA defines software assurance as: the planned and systematic set of activities that ensure conformance of software life cycle processes and products to requirements, standards, and procedures via quality, safety, reliability, and independent verification and validation. NASA's implementation of this approach to the quality, safety, reliability, security and verification and validation of software is brought together in one discipline, software assurance. Organizationally, NASA has software assurance at each NASA center, a Software Assurance Manager at NASA Headquarters, a Software Assurance Technical Fellow (currently the same person as the SA Manager), and an Independent Verification and Validation Organization with its own facility. An umbrella risk mitigation strategy for safety and mission success assurance of NASA's software, software assurance covers a wide area and is better structured to address the dynamic changes in how software is developed, used, and managed, as well as it's increasingly complex functionality. Being flexible, risk based, and prepared for challenges in software at NASA is essential, especially as much of our software is unique for each mission.

  15. Archiving a Software Development Project

    Science.gov (United States)

    2013-04-01

    24 H.4.3 Info on National Archives digital preservation software...a copy of a disposal authority? • Can I have more information on the National Archives digital preservation software? • Can I use the training...General Disposal Authority or under Normal Administrative Practice. H.4.3 Info on National Archives digital preservation software Information on National

  16. Visual assessment of software evolution

    NARCIS (Netherlands)

    Voinea, Lucian; Lukkien, Johan; Telea, Alexandru

    2007-01-01

    Configuration management tools have become well and widely accepted by the software industry. Software Configuration Management (SCM) systems hold minute information about the entire evolution of complex software systems and thus represent a good source for process accounting and auditing. However,

  17. The software factory: A fourth generation software engineering environment

    Energy Technology Data Exchange (ETDEWEB)

    Evans, M.W.

    1989-01-01

    The software-development process and its management are examined in a text intended for engineering managers and students of computer science. A unified concept based on the principle that software design is an engineering science rather than an art is applied, and a software engineering environment (SEE) analogous to an industrial plant is proposed. Chapters are devoted to the classical software environment, the history of software engineering, the evolution of the SEE, the fourth-generation SEE, the engineering process, software-data relationships, the SEE data base, data control in the SEE, software life cycles, information-system product assurance, business management and control, and automating and adapting the SEE. 143 refs.

  18. Software is a directed multigraph (and so is software process)

    CERN Document Server

    Dabrowski, Robert; Timoszuk, Grzegorz

    2011-01-01

    For a software system, its architecture is typically defined as the fundamental organization of the system incorporated by its components, their relationships to one another and their environment, and the principles governing their design. If contributed to by the artifacts coresponding to engineering processes that govern the system's evolution, the definition gets natually extended into the architecture of software and software process. Obviously, as long as there were no software systems, managing their architecture was no problem at all; when there were only small systems, managing their architecture became a mild problem; and now we have gigantic software systems, and managing their architecture has become an equally gigantic problem (to paraphrase Edsger Dijkstra). In this paper we propose a simple, yet we believe effective, model for organizing architecture of software systems. First of all we postulate that only a hollistic approach that supports continuous integration and verification for all softwar...

  19. Software Vulnerability Taxonomy Consolidation

    Energy Technology Data Exchange (ETDEWEB)

    Polepeddi, Sriram S. [Carnegie Mellon Univ., Pittsburgh, PA (United States)

    2004-12-07

    In today's environment, computers and networks are increasing exposed to a number of software vulnerabilities. Information about these vulnerabilities is collected and disseminated via various large publicly available databases such as BugTraq, OSVDB and ICAT. Each of these databases, individually, do not cover all aspects of a vulnerability and lack a standard format among them, making it difficult for end-users to easily compare various vulnerabilities. A central database of vulnerabilities has not been available until today for a number of reasons, such as the non-uniform methods by which current vulnerability database providers receive information, disagreement over which features of a particular vulnerability are important and how best to present them, and the non-utility of the information presented in many databases. The goal of this software vulnerability taxonomy consolidation project is to address the need for a universally accepted vulnerability taxonomy that classifies vulnerabilities in an unambiguous manner. A consolidated vulnerability database (CVDB) was implemented that coalesces and organizes vulnerability data from disparate data sources. Based on the work done in this paper, there is strong evidence that a consolidated taxonomy encompassing and organizing all relevant data can be achieved. However, three primary obstacles remain: lack of referencing a common ''primary key'', un-structured and free-form descriptions of necessary vulnerability data, and lack of data on all aspects of a vulnerability. This work has only considered data that can be unambiguously extracted from various data sources by straightforward parsers. It is felt that even with the use of more advanced, information mining tools, which can wade through the sea of unstructured vulnerability data, this current integration methodology would still provide repeatable, unambiguous, and exhaustive results. Though the goal of coalescing all available data

  20. Model-Driven Engineering Support for Building C# Applications

    Science.gov (United States)

    Derezińska, Anna; Ołtarzewski, Przemysław

    Realization of Model-Driven Engineering (MDE) vision of software development requires a comprehensive and user-friendly tool support. This paper presents a UML-based approach for building trustful C# applications. UML models are refined using profiles for assigning class model elements to C# concepts and to elements of implementation project. Stereotyped elements are verified on life and during model to code transformation in order to prevent creation of an incorrect code. The Transform OCL Fragments into C# system (T.O.F.I.C.) was created as a feature of the Eclipse environment. The system extends the IBM Rational Software Architect tool.

  1. Software Process Improvement

    DEFF Research Database (Denmark)

    Kuhrmann, Marco; Konopka, Claudia; Nellemann, Peter

    2016-01-01

    Software process improvement (SPI) is around for decades: frameworks are proposed, success factors are studied, and experiences have been reported. However, the sheer mass of concepts, approaches, and standards published over the years overwhelms practitioners as well as researchers. What is out...... directions. An analysis of 635 publications draws a big picture of SPI-related research of the past 25 years. Our study shows a high number of solution proposals, experience reports, and secondary studies, but only few theories. In particular, standard SPI models are analyzed and evaluated for applicability...

  2. Self-organising software

    CERN Document Server

    Serugendo, Giovanna Di Marzo; Karageorgos, Anthony

    2011-01-01

    Self-organisation, self-regulation, self-repair and self-maintenance are promising conceptual approaches for dealing with complex distributed interactive software and information-handling systems. Self-organising applications dynamically change their functionality and structure without direct user intervention, responding to changes in requirements and the environment. This is the first book to offer an integrated view of self-organisation technologies applied to distributed systems, particularly focusing on multiagent systems. The editors developed this integrated book with three aims: to exp

  3. Office software Individual coaching

    CERN Multimedia

    HR Department

    2010-01-01

    If one or several particular topics cause you sleepless nights, you can get help from our trainer who will come to your workplace for a multiple of 1-hour slots . All fields in which our trainer can help are detailed in the course description in our training catalogue (Microsoft Office software, Adobe applications, i-applications etc.) Discover these new courses in our catalogue! http://cta.cern.ch/cta2/f?p=110:9 Technical Training Service Technical.Training@cern.ch Tel 74924

  4. Software Replica of Minimal Living Processes

    Science.gov (United States)

    Bersini, Hugues

    2010-04-01

    There is a long tradition of software simulations in theoretical biology to complement pure analytical mathematics which are often limited to reproduce and understand the self-organization phenomena resulting from the non-linear and spatially grounded interactions of the huge number of diverse biological objects. Since John Von Neumann and Alan Turing pioneering works on self-replication and morphogenesis, proponents of artificial life have chosen to resolutely neglecting a lot of materialistic and quantitative information deemed not indispensable and have focused on the rule-based mechanisms making life possible, supposedly neutral with respect to their underlying material embodiment. Minimal life begins at the intersection of a series of processes which need to be isolated, differentiated and duplicated as such in computers. Only software developments and running make possible to understand the way these processes are intimately interconnected in order for life to appear at the crossroad. In this paper, I will attempt to set out the history of life as the disciples of artificial life understand it, by placing these different lessons on a temporal and causal axis, showing which one is indispensable to the appearance of the next and how does it connect to the next. I will discuss the task of artificial life as setting up experimental software platforms where these different lessons, whether taken in isolation or together, are tested, simulated, and, more systematically, analyzed. I will sketch some of these existing software platforms: chemical reaction networks, Varela’s autopoietic cellular automata, Ganti’s chemoton model, whose running delivers interesting take home messages to open-minded biologists.

  5. Knowledge-making distinctions in synthetic biology.

    Science.gov (United States)

    O'Malley, Maureen A; Powell, Alexander; Davies, Jonathan F; Calvert, Jane

    2008-01-01

    Synthetic biology is an increasingly high-profile area of research that can be understood as encompassing three broad approaches towards the synthesis of living systems: DNA-based device construction, genome-driven cell engineering and protocell creation. Each approach is characterized by different aims, methods and constructs, in addition to a range of positions on intellectual property and regulatory regimes. We identify subtle but important differences between the schools in relation to their treatments of genetic determinism, cellular context and complexity. These distinctions tie into two broader issues that define synthetic biology: the relationships between biology and engineering, and between synthesis and analysis. These themes also illuminate synthetic biology's connections to genetic and other forms of biological engineering, as well as to systems biology. We suggest that all these knowledge-making distinctions in synthetic biology raise fundamental questions about the nature of biological investigation and its relationship to the construction of biological components and systems.

  6. Entretian Model for Software Maintenance

    Directory of Open Access Journals (Sweden)

    Priya K Betala

    2013-10-01

    Full Text Available Maintenance refers to the act of modifying the software after putting in use in order to maintain its usability.[1]. In other words, Software maintenance can be defined as; it is the process of providing services to the customers after the delivery of the software. Despite the fact that maintaining software is very challenging, it is the most important routine that must be carried out in the development cycle. If the software is not maintained efficiently it may lead to the death of the software. Maintenance of software may be carried out in two ways. The first one is called „In-house maintenance‟ and the second one is called „Transition maintenance‟. The latter faces the drastic challenges when compared to former, as one team may not provide complete source code to the other, leading to unstructured code, lack of appropriate technique and knowledge about the functioning of the current software. There are a few aspects of software maintenance that set it apart from the other phases. Software maintenance cost comprises more than half of the total software development cost. Also, without software maintenance, it is impossible to change the problems within the product after its release, and many disasters can happen because of immature software. Recognising the importance of software maintenance, this paper proposes a model called “ENTRETIAN MODEL” (Entretian, a French word meaning Maintenance which consists of six basic steps to follow while maintaining software system. This model overcomes certain misconceptions about maintenance phase and it is highly beneficial to the Maintenance Support Team (MST to handle their maintenance activities systematically and efficiently. By employing the proposed model, the MST is able to overcome the technical and managerial issues that are faced earlier in the maintenance phase. The advantage of using “Entretian Model” is best illustrated in this paper with the help of the ERP package.

  7. Characteristics for Software Optimization Projects

    Directory of Open Access Journals (Sweden)

    Iulian NITESCU

    2008-01-01

    Full Text Available The increasing of the software systems complexity imposes the identification and implementation of some methods and techniques in order to manage it. The software optimization project is a way in which the software complexity is controlled. The software optimization project must face to the organization need to earn profit. The software optimization project is an integrated part of the application cycle because share same resources, depends on other stages and influences next phases. The optimization project has some particularities because it works on an finished product around its quality. The process is quality and performance oriented and it assumes that the product life cycle is almost finished.

  8. The Ragnarok Software Development Environment

    DEFF Research Database (Denmark)

    Christensen, Henrik Bærbak

    1999-01-01

    Ragnarok is an experimental software development environment that focuses on enhanced support for managerial activities in large scale software development taking the daily work of the software developer as its point of departure. The main emphasis is support in three areas: management, navigation......, and collaboration. The leitmotif is the software architecture, which is extended to handle managerial data in addition to source code; this extended software architecture is put under tight version- and configuration management control and furthermore used as basis for visualisation. Preliminary results of using...

  9. [Biological weapons].

    Science.gov (United States)

    Kerwat, K; Becker, S; Wulf, H; Densow, D

    2010-08-01

    Biological weapons are weapons of mass destruction that use pathogens (bacteria, viruses) or the toxins produced by them to target living organisms or to contaminate non-living substances. In the past, biological warfare has been repeatedly used. Anthrax, plague and smallpox are regarded as the most dangerous biological weapons by various institutions. Nowadays it seems quite unlikely that biological warfare will be employed in any military campaigns. However, the possibility remains that biological weapons may be used in acts of bioterrorism. In addition all diseases caused by biological weapons may also occur naturally or as a result of a laboratory accident. Risk assessment with regard to biological danger often proves to be difficult. In this context, an early identification of a potentially dangerous situation through experts is essential to limit the degree of damage.

  10. Software and Computing News

    CERN Multimedia

    Barberis, D

    The last several months have been very busy ones for the ATLAS software developers. They've been trying to cope with the competing demands of multiple software stress tests and testbeds. These include Data Challenge Two (DC2), the Combined Testbeam (CTB), preparations for the Physics Workshop to be held in Rome in June 2005, and other testbeds, primarily one for the High-Level Trigger. Data Challenge 2 (DC2) The primary goal of this was to validate the computing model and to provide a test of simulating a day's worth of ATLAS data (10 million events) and of fully processing it and making it available to the physicists within 10 days (i.e. a 10% scale test). DC2 consists of three parts - the generation, simulation, and mixing of a representative sample of physics events with background events; the reconstruction of the mixed samples with initial classification into the different physics signatures; and the distribution of the data to multiple remote sites (Tier-1 centers) for analysis by physicists. Figu...

  11. CSAM Metrology Software Tool

    Science.gov (United States)

    Vu, Duc; Sandor, Michael; Agarwal, Shri

    2005-01-01

    CSAM Metrology Software Tool (CMeST) is a computer program for analysis of false-color CSAM images of plastic-encapsulated microcircuits. (CSAM signifies C-mode scanning acoustic microscopy.) The colors in the images indicate areas of delamination within the plastic packages. Heretofore, the images have been interpreted by human examiners. Hence, interpretations have not been entirely consistent and objective. CMeST processes the color information in image-data files to detect areas of delamination without incurring inconsistencies of subjective judgement. CMeST can be used to create a database of baseline images of packages acquired at given times for comparison with images of the same packages acquired at later times. Any area within an image can be selected for analysis, which can include examination of different delamination types by location. CMeST can also be used to perform statistical analyses of image data. Results of analyses are available in a spreadsheet format for further processing. The results can be exported to any data-base-processing software.

  12. Software-Defined Cluster

    Institute of Scientific and Technical Information of China (English)

    聂华; 杨晓君; 刘淘英

    2015-01-01

    The cluster architecture has played an important role in high-end computing for the past 20 years. With the advent of Internet services, big data, and cloud computing, traditional clusters face three challenges: 1) providing flexible system balance among computing, memory, and I/O capabilities;2) reducing resource pooling overheads;and 3) addressing low performance-power efficiency. This position paper proposes a software-defined cluster (SDC) architecture to deal with these challenges. The SDC architecture inherits two features of traditional cluster: its architecture is multicomputer and it has loosely-coupled interconnect. SDC provides two new mechanisms: global I/O space (GIO) and hardware-supported native access (HNA) to remote devices. Application software can define a virtual cluster best suited to its needs from resources pools provided by a physical cluster, and traditional cluster ecosystems need no modification. We also discuss a prototype design and implementation of a 32-processor cloud server utilizing the SDC architecture.

  13. Numerical Optimization Algorithms and Software for Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Saunders, Michael

    2013-02-02

    The basic aims of this work are: to develop reliable algorithms for solving optimization problems involving large stoi- chiometric matrices; to investigate cyclic dependency between metabolic and macromolecular biosynthetic networks; and to quantify the significance of thermodynamic constraints on prokaryotic metabolism.

  14. 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

    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....

  15. New ATLAS Software & Computing Organization

    CERN Multimedia

    Barberis, D

    Following the election by the ATLAS Collaboration Board of Dario Barberis (Genoa University/INFN) as Computing Coordinator and David Quarrie (LBNL) as Software Project Leader, it was considered necessary to modify the organization of the ATLAS Software & Computing ("S&C") project. The new organization is based upon the following principles: separation of the responsibilities for computing management from those of software development, with the appointment of a Computing Coordinator and a Software Project Leader who are both members of the Executive Board; hierarchical structure of responsibilities and reporting lines; coordination at all levels between TDAQ, S&C and Physics working groups; integration of the subdetector software development groups with the central S&C organization. A schematic diagram of the new organization can be seen in Fig.1. Figure 1: new ATLAS Software & Computing organization. Two Management Boards will help the Computing Coordinator and the Software Project...

  16. Software Security Requirements Gathering Instrument

    Directory of Open Access Journals (Sweden)

    Smriti Jain

    2011-08-01

    Full Text Available Security breaches are largely caused by the vulnerable software. Since individuals and organizations mostly depend on softwares, it is important to produce in secured manner. The first step towards producing secured software is through gathering security requirements. This paper describes Software Security Requirements Gathering Instrument (SSRGI that helps gather security requirements from the various stakeholders. This will guide the developers to gather security requirements along with the functional requirements and further incorporate security during other phases of software development. We subsequently present case studies that describe the integration of the SSRGI instrument with Software Requirements Specification (SRS document as specified in standard IEEE 830-1998. Proposed SSRGI will support the software developers in gathering security requirements in detail during requirements gathering phase.

  17. Software libre vs. software propietario: programando nuestro futuro

    Directory of Open Access Journals (Sweden)

    Rafael Gómez Sánchez

    2008-12-01

    Full Text Available Este trabajo estudia la evolución de dos modelos contrapuestos: el software propietario y el software libre. Mientras el primero está plenamente establecido, y apoyado por la industria tradicional de los programas de ordenador, el software libre se presenta como una atractiva alternativa que promete corregir muchas de las deficiencias de aquel modelo. Basado en la filosofía de respetar las libertades del usuario -libertad de compartir, mejorar y utilizar los programas-, son cada vez más las administraciones, empresas y demás usuarios que optan por el software libre. La interacción entre ambos modelos y sus consecuencias, así como los intentos de las multinacionales del software por no perder mercado, serán asimismo objeto de estudio.________________________ABSTRACT:This work studies the evolution of two opposed models: propietary software and free software. Meanwhile the first one is fully established, and supported by the traditional computing industry, free software appears like an attractive alternative which promises to correct many deficiencies of that model. Based on the philosophy of respecting user’s liberties -freedom of sharing, improving and using the software-, an increasing number of administrations, companies and other users are moving to the model of free software. Interactions between both models and its consequences, as well as the attempts from the software’s multinational corporations of not to lose market, will also be objects to be studied.

  18. Optically trapped and driven paddle-wheel

    Science.gov (United States)

    Asavei, Theodor; Nieminen, Timo A.; Loke, Vincent L. Y.; Stilgoe, Alexander B.; Bowman, Richard; Preece, Daryl; Padgett, Miles J.; Heckenberg, Norman R.; Rubinsztein-Dunlop, Halina

    2013-06-01

    We demonstrate the control and rotation of an optically trapped object, an optical paddle-wheel, with the rotation direction normal to the beam axis. This is in contrast to the usual situation where the rotation is about the beam axis. The paddle-wheel can be optically driven and moved to any position in the field of view of the microscope, which can be of interest for various biological applications where controlled application of a fluid flow is needed in a particular location and in a specific direction. This is of particular interest in signal transduction studies in cells, especially when a cell is flat and spread out on a surface.

  19. Model-based software engineering for an imaging CubeSat and its extrapolation to other missions

    Science.gov (United States)

    Mohammad, Atif; Straub, Jeremy; Korvald, Christoffer; Grant, Emanuel

    Small satellites with their limited computational capabilities require that software engineering techniques promote efficient use of spacecraft resources. A model-driven approach to software engineering is an excellent solution to this resource maximization challenge as it facilitates visualization of the key solution processes and data elements.

  20. Experimental evaluation of a tool for the verification and transformation of source code in event-driven systems

    NARCIS (Netherlands)

    Gülesir, Gürcan; Berg, van den Klaas; Bergmans, Lodewijk; Aksit, Mehmet

    2009-01-01

    In event-driven systems, separating the reactive part of software (i.e., event-driven control) from the non-reactive part is a common design practice. The reactive part is typically structured according to the states and transitions of a system, whereas the non-reactive part is typically structured