Bioconductor: open software development for computational biology and bioinformatics

DEFF Research Database (Denmark)

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

2004-01-01

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

Model-driven design of simulation support for the TERRA robot software tool suite

NARCIS (Netherlands)

Lu, Zhou; Bezemer, M.M.; Broenink, Johannes F.

2015-01-01

Model-Driven Development (MDD) – based on the concepts of model, meta-model and model transformation – is an approach to develop predictable and re- liable software for Cyber-Physical Systems (CPS). The work presented here concerns a methodology to design simulation software based on MDD techniques,

Unit testing, model validation, and biological simulation.

Science.gov (United States)

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

2016-01-01

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

Constraint-Driven Software Design: An Escape from the Waterfall Model.

Science.gov (United States)

de Hoog, Robert; And Others

1994-01-01

Presents the principles of a development methodology for software design based on a nonlinear, product-driven approach that integrates quality aspects. Two examples are given to show that the flexibility needed for building high quality systems leads to integrated development environments in which methodology, product, and tools are closely…

The Systems Biology Research Tool: evolvable open-source software

OpenAIRE

Wright, J; Wagner, A

2008-01-01

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

BioContainers: an open-source and community-driven framework for software standardization

Science.gov (United States)

da Veiga Leprevost, Felipe; Grüning, Björn A.; Alves Aflitos, Saulo; Röst, Hannes L.; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; Bai, Mingze; Jimenez, Rafael C.; Sachsenberg, Timo; Pfeuffer, Julianus; Vera Alvarez, Roberto; Griss, Johannes; Nesvizhskii, Alexey I.; Perez-Riverol, Yasset

2017-01-01

Abstract Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). Availability and Implementation The software is freely available at github.com/BioContainers/. Contact yperez@ebi.ac.uk PMID:28379341

BioContainers: an open-source and community-driven framework for software standardization.

Science.gov (United States)

da Veiga Leprevost, Felipe; Grüning, Björn A; Alves Aflitos, Saulo; Röst, Hannes L; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; Bai, Mingze; Jimenez, Rafael C; Sachsenberg, Timo; Pfeuffer, Julianus; Vera Alvarez, Roberto; Griss, Johannes; Nesvizhskii, Alexey I; Perez-Riverol, Yasset

2017-08-15

BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). The software is freely available at github.com/BioContainers/. yperez@ebi.ac.uk. © The Author(s) 2017. Published by Oxford University Press.

Isobio software: biological dose distribution and biological dose volume histogram from physical dose conversion using linear-quadratic-linear model.

Science.gov (United States)

Jaikuna, Tanwiwat; Khadsiri, Phatchareewan; Chawapun, Nisa; Saekho, Suwit; Tharavichitkul, Ekkasit

2017-02-01

To develop an in-house software program that is able to calculate and generate the biological dose distribution and biological dose volume histogram by physical dose conversion using the linear-quadratic-linear (LQL) model. The Isobio software was developed using MATLAB version 2014b to calculate and generate the biological dose distribution and biological dose volume histograms. The physical dose from each voxel in treatment planning was extracted through Computational Environment for Radiotherapy Research (CERR), and the accuracy was verified by the differentiation between the dose volume histogram from CERR and the treatment planning system. An equivalent dose in 2 Gy fraction (EQD 2 ) was calculated using biological effective dose (BED) based on the LQL model. The software calculation and the manual calculation were compared for EQD 2 verification with pair t -test statistical analysis using IBM SPSS Statistics version 22 (64-bit). Two and three-dimensional biological dose distribution and biological dose volume histogram were displayed correctly by the Isobio software. Different physical doses were found between CERR and treatment planning system (TPS) in Oncentra, with 3.33% in high-risk clinical target volume (HR-CTV) determined by D 90% , 0.56% in the bladder, 1.74% in the rectum when determined by D 2cc , and less than 1% in Pinnacle. The difference in the EQD 2 between the software calculation and the manual calculation was not significantly different with 0.00% at p -values 0.820, 0.095, and 0.593 for external beam radiation therapy (EBRT) and 0.240, 0.320, and 0.849 for brachytherapy (BT) in HR-CTV, bladder, and rectum, respectively. The Isobio software is a feasible tool to generate the biological dose distribution and biological dose volume histogram for treatment plan evaluation in both EBRT and BT.

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

Science.gov (United States)

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

2008-08-12

New systems biology studies require researchers to understand how interplay among myriads of biomolecular entities is orchestrated in order to achieve high-level cellular and physiological functions. Many software tools have been developed in the past decade to help researchers visually navigate large networks of biomolecular interactions with built-in template-based query capabilities. To further advance researchers' ability to interrogate global physiological states of cells through multi-scale visual network explorations, new visualization software tools still need to be developed to empower the analysis. A robust visual data analysis platform driven by database management systems to perform bi-directional data processing-to-visualizations with declarative querying capabilities is needed. We developed ProteoLens as a JAVA-based visual analytic software tool for creating, annotating and exploring multi-scale biological networks. It supports direct database connectivity to either Oracle or PostgreSQL database tables/views, on which SQL statements using both Data Definition Languages (DDL) and Data Manipulation languages (DML) may be specified. The robust query languages embedded directly within the visualization software help users to bring their network data into a visualization context for annotation and exploration. ProteoLens supports graph/network represented data in standard Graph Modeling Language (GML) formats, and this enables interoperation with a wide range of other visual layout tools. The architectural design of ProteoLens enables the de-coupling of complex network data visualization tasks into two distinct phases: 1) creating network data association rules, which are mapping rules between network node IDs or edge IDs and data attributes such as functional annotations, expression levels, scores, synonyms, descriptions etc; 2) applying network data association rules to build the network and perform the visual annotation of graph nodes and edges

Biology Needs Evolutionary Software Tools: Let’s Build Them Right

Science.gov (United States)

Team, Galaxy; Goecks, Jeremy; Taylor, James

2018-01-01

Abstract Research in population genetics and evolutionary biology has always provided a computational backbone for life sciences as a whole. Today evolutionary and population biology reasoning are essential for interpretation of large complex datasets that are characteristic of all domains of today’s life sciences ranging from cancer biology to microbial ecology. This situation makes algorithms and software tools developed by our community more important than ever before. This means that we, developers of software tool for molecular evolutionary analyses, now have a shared responsibility to make these tools accessible using modern technological developments as well as provide adequate documentation and training. PMID:29688462

Constraint driven software design: an escape from the waterfall model

OpenAIRE

de Hoog, Robert; de Jong, Anthonius J.M.; de Vries, 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 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...

Agile Acceptance Test-Driven Development of Clinical Decision Support Advisories: Feasibility of Using Open Source Software.

Science.gov (United States)

Basit, Mujeeb A; Baldwin, Krystal L; Kannan, Vaishnavi; Flahaven, Emily L; Parks, Cassandra J; Ott, Jason M; Willett, Duwayne L

2018-04-13

Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test-driven development and automated regression testing promotes reliability. Test-driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a "safety net" for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and "living" design documentation. Rapid-cycle development or "agile" methods are being successfully applied to CDS development. The agile practice of automated test-driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as "executable requirements." We aimed to establish feasibility of acceptance test-driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse). Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory's expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with tests becoming part of the production regression test

Community-driven computational biology with Debian Linux.

Science.gov (United States)

Möller, Steffen; Krabbenhöft, Hajo Nils; Tille, Andreas; Paleino, David; Williams, Alan; Wolstencroft, Katy; Goble, Carole; Holland, Richard; Belhachemi, Dominique; Plessy, Charles

2010-12-21

The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments. The Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software. Debian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers.

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

Science.gov (United States)

King, Ellis; Hart, Jeremy; Odegard, Ryan

2010-01-01

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

UltraPse: A Universal and Extensible Software Platform for Representing Biological Sequences.

Science.gov (United States)

Du, Pu-Feng; Zhao, Wei; Miao, Yang-Yang; Wei, Le-Yi; Wang, Likun

2017-11-14

With the avalanche of biological sequences in public databases, one of the most challenging problems in computational biology is to predict their biological functions and cellular attributes. Most of the existing prediction algorithms can only handle fixed-length numerical vectors. Therefore, it is important to be able to represent biological sequences with various lengths using fixed-length numerical vectors. Although several algorithms, as well as software implementations, have been developed to address this problem, these existing programs can only provide a fixed number of representation modes. Every time a new sequence representation mode is developed, a new program will be needed. In this paper, we propose the UltraPse as a universal software platform for this problem. The function of the UltraPse is not only to generate various existing sequence representation modes, but also to simplify all future programming works in developing novel representation modes. The extensibility of UltraPse is particularly enhanced. It allows the users to define their own representation mode, their own physicochemical properties, or even their own types of biological sequences. Moreover, UltraPse is also the fastest software of its kind. The source code package, as well as the executables for both Linux and Windows platforms, can be downloaded from the GitHub repository.

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.

The Virtual Cell: a software environment for computational cell biology.

Science.gov (United States)

Loew, L M; Schaff, J C

2001-10-01

The newly emerging field of computational cell biology requires software tools that address the needs of a broad community of scientists. Cell biological processes are controlled by an interacting set of biochemical and electrophysiological events that are distributed within complex cellular structures. Computational modeling is familiar to researchers in fields such as molecular structure, neurobiology and metabolic pathway engineering, and is rapidly emerging in the area of gene expression. Although some of these established modeling approaches can be adapted to address problems of interest to cell biologists, relatively few software development efforts have been directed at the field as a whole. The Virtual Cell is a computational environment designed for cell biologists as well as for mathematical biologists and bioengineers. It serves to aid the construction of cell biological models and the generation of simulations from them. The system enables the formulation of both compartmental and spatial models, the latter with either idealized or experimentally derived geometries of one, two or three dimensions.

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.

SOA-Driven Business-Software Alignment

NARCIS (Netherlands)

Shishkov, Boris; van Sinderen, Marten J.; Quartel, Dick; Tsai, W.; Chung, J.; Younas, M.

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

Model Driven Engineering

Science.gov (United States)

Gaševic, Dragan; Djuric, Dragan; Devedžic, Vladan

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

Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

Science.gov (United States)

Hucka, M; Finney, A; Bornstein, B J; Keating, S M; Shapiro, B E; Matthews, J; Kovitz, B L; Schilstra, M J; Funahashi, A; Doyle, J C; Kitano, H

2004-06-01

Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The systems biology field needs agreed-upon information standards if models are to be shared, evaluated and developed cooperatively. Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. SBML has become a de facto standard format for representing formal, quantitative and qualitative models at the level of biochemical reactions and regulatory networks. In this article, we summarise the current and upcoming versions of SBML and our efforts at developing software infrastructure for supporting and broadening its use. We also provide a brief overview of the many SBML-compatible software tools available today.

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.

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

Directory of Open Access Journals (Sweden)

Rosalba Giugno

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

DAISY: a new software tool to test global identifiability of biological and physiological systems.

Science.gov (United States)

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

2007-10-01

A priori global identifiability is a structural property of biological and physiological models. It is considered a prerequisite for well-posed estimation, since it concerns the possibility of recovering uniquely the unknown model parameters from measured input-output data, under ideal conditions (noise-free observations and error-free model structure). Of course, determining if the parameters can be uniquely recovered from observed data is essential before investing resources, time and effort in performing actual biomedical experiments. Many interesting biological models are nonlinear but identifiability analysis for nonlinear system turns out to be a difficult mathematical problem. Different methods have been proposed in the literature to test identifiability of nonlinear models but, to the best of our knowledge, so far no software tools have been proposed for automatically checking identifiability of nonlinear models. In this paper, we describe a software tool implementing a differential algebra algorithm to perform parameter identifiability analysis for (linear and) nonlinear dynamic models described by polynomial or rational equations. Our goal is to provide the biological investigator a completely automatized software, requiring minimum prior knowledge of mathematical modelling and no in-depth understanding of the mathematical tools. The DAISY (Differential Algebra for Identifiability of SYstems) software will potentially be useful in biological modelling studies, especially in physiology and clinical medicine, where research experiments are particularly expensive and/or difficult to perform. Practical examples of use of the software tool DAISY are presented. DAISY is available at the web site http://www.dei.unipd.it/~pia/.

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 ...

Mechanically driven interface propagation in biological tissues

International Nuclear Information System (INIS)

Ranft, Jonas; Joanny, Jean-François; Aliee, Maryam; Jülicher, Frank; Prost, Jacques

2014-01-01

Many biological tissues consist of more than one cell type. We study the dynamics of an interface between two different cell populations as it occurs during the growth of a tumor in a healthy host tissue. Recent work suggests that the rates of cell division and cell death are under mechanical control, characterized by a homeostatic pressure. The difference in the homeostatic pressures of two cell types drives the propagation of the interface, corresponding to the invasion of one cell type into the other. We derive a front propagation equation that takes into account the coupling between cell number balance and tissue mechanics. We show that in addition to pulled fronts, pushed-front solutions occur as a result of convection driven by mechanics. (paper)

JColorGrid: software for the visualization of biological measurements.

OpenAIRE

Joachimiak, Marcin P; Weisman, Jennifer L; May, Barnaby Ch

2006-01-01

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 graphi...

DATABASES DEVELOPED IN INDIA FOR BIOLOGICAL SCIENCES

Directory of Open Access Journals (Sweden)

Gitanjali Yadav

2017-09-01

Full Text Available The complexity of biological systems requires use of a variety of experimental methods with ever increasing sophistication to probe various cellular processes at molecular and atomic resolution. The availability of technologies for determining nucleic acid sequences of genes and atomic resolution structures of biomolecules prompted development of major biological databases like GenBank and PDB almost four decades ago. India was one of the few countries to realize early, the utility of such databases for progress in modern biology/biotechnology. Department of Biotechnology (DBT, India established Biotechnology Information System (BTIS network in late eighties. Starting with the genome sequencing revolution at the turn of the century, application of high-throughput sequencing technologies in biology and medicine for analysis of genomes, transcriptomes, epigenomes and microbiomes have generated massive volumes of sequence data. BTIS network has not only provided state of the art computational infrastructure to research institutes and universities for utilizing various biological databases developed abroad in their research, it has also actively promoted research and development (R&D projects in Bioinformatics to develop a variety of biological databases in diverse areas. It is encouraging to note that, a large number of biological databases or data driven software tools developed in India, have been published in leading peer reviewed international journals like Nucleic Acids Research, Bioinformatics, Database, BMC, PLoS and NPG series publication. Some of these databases are not only unique, they are also highly accessed as reflected in number of citations. Apart from databases developed by individual research groups, BTIS has initiated consortium projects to develop major India centric databases on Mycobacterium tuberculosis, Rice and Mango, which can potentially have practical applications in health and agriculture. Many of these biological

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.

Biological impact of music and software-based auditory training

Science.gov (United States)

Kraus, Nina

2012-01-01

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

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.

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

SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology.

Science.gov (United States)

Adams, Richard; Clark, Allan; Yamaguchi, Azusa; Hanlon, Neil; Tsorman, Nikos; Ali, Shakir; Lebedeva, Galina; Goltsov, Alexey; Sorokin, Anatoly; Akman, Ozgur E; Troein, Carl; Millar, Andrew J; Goryanin, Igor; Gilmore, Stephen

2013-03-01

Complex computational experiments in Systems Biology, such as fitting model parameters to experimental data, can be challenging to perform. Not only do they frequently require a high level of computational power, but the software needed to run the experiment needs to be usable by scientists with varying levels of computational expertise, and modellers need to be able to obtain up-to-date experimental data resources easily. We have developed a software suite, the Systems Biology Software Infrastructure (SBSI), to facilitate the parameter-fitting process. SBSI is a modular software suite composed of three major components: SBSINumerics, a high-performance library containing parallelized algorithms for performing parameter fitting; SBSIDispatcher, a middleware application to track experiments and submit jobs to back-end servers; and SBSIVisual, an extensible client application used to configure optimization experiments and view results. Furthermore, we have created a plugin infrastructure to enable project-specific modules to be easily installed. Plugin developers can take advantage of the existing user-interface and application framework to customize SBSI for their own uses, facilitated by SBSI's use of standard data formats. All SBSI binaries and source-code are freely available from http://sourceforge.net/projects/sbsi under an Apache 2 open-source license. The server-side SBSINumerics runs on any Unix-based operating system; both SBSIVisual and SBSIDispatcher are written in Java and are platform independent, allowing use on Windows, Linux and Mac OS X. The SBSI project website at http://www.sbsi.ed.ac.uk provides documentation and tutorials.

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

International Nuclear Information System (INIS)

Arista Romeu, Eduardo J.; La Rosa Vazquez, Jose Manuel de; Valor, Alma; Stolik, Suren

2016-01-01

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

BicPAMS: software for biological data analysis with pattern-based biclustering.

Science.gov (United States)

Henriques, Rui; Ferreira, Francisco L; Madeira, Sara C

2017-02-02

Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlated in subsets of conditions) and network data (groups of coherently interconnected biological entities). However, given its computational complexity, only recent breakthroughs on pattern-based biclustering enabled efficient searches without the restrictions that state-of-the-art biclustering algorithms place on the structure and homogeneity of biclusters. As a result, pattern-based biclustering provides the unprecedented opportunity to discover non-trivial yet meaningful biological modules with putative functions, whose coherency and tolerance to noise can be tuned and made problem-specific. To enable the effective use of pattern-based biclustering by the scientific community, we developed BicPAMS (Biclustering based on PAttern Mining Software), a software that: 1) makes available state-of-the-art pattern-based biclustering algorithms (BicPAM (Henriques and Madeira, Alg Mol Biol 9:27, 2014), BicNET (Henriques and Madeira, Alg Mol Biol 11:23, 2016), BicSPAM (Henriques and Madeira, BMC Bioinforma 15:130, 2014), BiC2PAM (Henriques and Madeira, Alg Mol Biol 11:1-30, 2016), BiP (Henriques and Madeira, IEEE/ACM Trans Comput Biol Bioinforma, 2015), DeBi (Serin and Vingron, AMB 6:1-12, 2011) and BiModule (Okada et al., IPSJ Trans Bioinf 48(SIG5):39-48, 2007)); 2) consistently integrates their dispersed contributions; 3) further explores additional accuracy and efficiency gains; and 4) makes available graphical and application programming interfaces. Results on both synthetic and real data confirm the relevance of BicPAMS for biological data analysis, highlighting its essential role for the discovery of putative modules with non-trivial yet biologically significant functions from expression and network data. BicPAMS is the first biclustering tool offering the

Observation-Driven Configuration of Complex Software Systems

Science.gov (United States)

Sage, Aled

2010-06-01

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 the system's behaviour. The design and use of ACT (Automated Configuration Tool) for running such experiments is described, in combination a number of search strategies for deciding on the configurations to measure. Design Of Experiments (DOE) is discussed, with emphasis on Taguchi Methods. These statistical methods have been used extensively in manufacturing, but have not previously been used for configuring software systems. The novel contribution here is an industrial case study, applying the combination of ACT and Taguchi Methods to DC-Directory, a product from Data Connection Ltd (DCL). The case study investigated the applicability of Taguchi Methods for configuring complex software systems. Taguchi Methods were found to be useful for modelling and configuring DC- Directory, making them a valuable addition to the techniques available to system administrators and developers.

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......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...

Epithelioid Sarcoma: Opportunities for Biology-Driven Targeted Therapy.

Science.gov (United States)

Noujaim, Jonathan; Thway, Khin; Bajwa, Zia; Bajwa, Ayeza; Maki, Robert G; Jones, Robin L; Keller, Charles

2015-01-01

Epithelioid sarcoma (ES) is a soft tissue sarcoma of children and young adults for which the preferred treatment for localized 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. Toward building a consortium of pharmaceutical, academic, and non-profit collaborators, we will discuss the state of resources for investigating ES with respect to cell line resources, tissue banks, and registries so that a roadmap can be developed toward effective biology-driven therapies.

Temporal code-driven stimulation: definition and application to electric fish signaling

Directory of Open Access Journals (Sweden)

Angel Lareo

2016-10-01

Full Text Available 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.

JColorGrid: software for the visualization of biological measurements.

Science.gov (United States)

Joachimiak, Marcin P; Weisman, Jennifer L; May, Barnaby Ch

2006-04-27

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. 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. 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.

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

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

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…

Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

Science.gov (United States)

Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

2018-01-01

Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

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.

qPortal: A platform for data-driven biomedical research.

Science.gov (United States)

Mohr, Christopher; Friedrich, Andreas; Wojnar, David; Kenar, Erhan; Polatkan, Aydin Can; Codrea, Marius Cosmin; Czemmel, Stefan; Kohlbacher, Oliver; Nahnsen, Sven

2018-01-01

Modern biomedical research aims at drawing biological conclusions from large, highly complex biological datasets. It has become common practice to make extensive use of high-throughput technologies that produce big amounts of heterogeneous data. In addition to the ever-improving accuracy, methods are getting faster and cheaper, resulting in a steadily increasing need for scalable data management and easily accessible means of analysis. We present qPortal, a platform providing users with an intuitive way to manage and analyze quantitative biological data. The backend leverages a variety of concepts and technologies, such as relational databases, data stores, data models and means of data transfer, as well as front-end solutions to give users access to data management and easy-to-use analysis options. Users are empowered to conduct their experiments from the experimental design to the visualization of their results through the platform. Here, we illustrate the feature-rich portal by simulating a biomedical study based on publically available data. We demonstrate the software's strength in supporting the entire project life cycle. The software supports the project design and registration, empowers users to do all-digital project management and finally provides means to perform analysis. We compare our approach to Galaxy, one of the most widely used scientific workflow and analysis platforms in computational biology. Application of both systems to a small case study shows the differences between a data-driven approach (qPortal) and a workflow-driven approach (Galaxy). qPortal, a one-stop-shop solution for biomedical projects offers up-to-date analysis pipelines, quality control workflows, and visualization tools. Through intensive user interactions, appropriate data models have been developed. These models build the foundation of our biological data management system and provide possibilities to annotate data, query metadata for statistics and future re-analysis on

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

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.

A Software Development Platform for Mechatronic Systems

DEFF Research Database (Denmark)

Guan, Wei

Software has become increasingly determinative for development of mechatronic systems, which underscores the importance of demands for shortened time-to-market, increased productivity, higher quality, and improved dependability. As the complexity of systems is dramatically increasing, these demands...... 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...

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

Science.gov (United States)

Garcia-Garcia, Javier; Guney, Emre; Aragues, Ramon; Planas-Iglesias, Joan; Oliva, Baldo

2010-01-27

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. 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. 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.

Evaluation of Model Driven Development of Safety Critical Software in the Nuclear Power Plant I and C system

International Nuclear Information System (INIS)

Jung, Jae Cheon; Chang, Hoon Seon; Chang, Young Woo; Kim, Jae Hack; Sohn, Se Do

2005-01-01

The major issues of the safety critical software are formalism and V and V. Implementing these two characteristics in the safety critical software will greatly enhance the quality of software product. The structure based development requires lots of output documents from the requirements phase to the testing phase. The requirements analysis phase is open omitted. According to the Standish group report in 2001, 49% of software project is cancelled before completion or never implemented. In addition, 23% is completed and become operational, but over-budget, over the time estimation, and with fewer features and functions than initially specified. They identified ten success factors. Among them, firm basic requirements and formal methods are technically achievable factors while the remaining eight are management related. Misunderstanding of requirements due to lack of communication between the design engineer and verification engineer causes unexpected result such as functionality error of system. Safety critical software shall comply with such characteristics as; modularity, simplicity, minimizing the sub-routine, and excluding the interrupt routine. In addition, the crosslink fault and erroneous function shall be eliminated. The easiness of repairing work after the installation shall be achieved as well. In consideration of the above issues, we evaluate the model driven development (MDD) methods for nuclear I and C systems software. For qualitative analysis, the unified modeling language (UML), functional block language (FBL) and the safety critical application environment (SCADE) are tested for the above characteristics

Software development processes and analysis software: a mismatch and a novel framework

International Nuclear Information System (INIS)

Kelly, D.; Harauz, J.

2011-01-01

This paper discusses the salient characteristics of analysis software and the impact of those characteristics on its development. From this discussion, it can be seen that mainstream software development processes, usually characterized as Plan Driven or Agile, are built upon assumptions that are mismatched to the development and maintenance of analysis software. We propose a novel software development framework that would match the process normally observed in the development of analysis software. In the discussion of this framework, we suggest areas of research and directions for future work. (author)

Consistent Evolution of Software Artifacts and Non-Functional Models

Science.gov (United States)

2014-11-14

induce bad software performance)? 15. SUBJECT TERMS EOARD, Nano particles, Photo-Acoustic Sensors, Model-Driven Engineering ( MDE ), Software Performance...Università degli Studi dell’Aquila, Via Vetoio, 67100 L’Aquila, Italy Email: vittorio.cortellessa@univaq.it Web : http: // www. di. univaq. it/ cortelle/ Phone...Model-Driven Engineering ( MDE ), Software Performance Engineering (SPE), Change Propagation, Performance Antipatterns. For sake of readability of the

Towards a New Paradigm of Software Development: an Ambassador Driven Process in Distributed Software Companies

Science.gov (United States)

Kumlander, Deniss

The globalization of companies operations and competitor between software vendors demand improving quality of delivered software and decreasing the overall cost. The same in fact introduce a lot of problem into software development process as produce distributed organization breaking the co-location rule of modern software development methodologies. Here we propose a reformulation of the ambassador position increasing its productivity in order to bridge communication and workflow gap by managing the entire communication process rather than concentrating purely on the communication result.

Open-source, community-driven microfluidics with Metafluidics.

Science.gov (United States)

Kong, David S; Thorsen, Todd A; Babb, Jonathan; Wick, Scott T; Gam, Jeremy J; Weiss, Ron; Carr, Peter A

2017-06-07

Microfluidic devices have the potential to automate and miniaturize biological experiments, but open-source sharing of device designs has lagged behind sharing of other resources such as software. Synthetic biologists have used microfluidics for DNA assembly, cell-free expression, and cell culture, but a combination of expense, device complexity, and reliance on custom set-ups hampers their widespread adoption. We present Metafluidics, an open-source, community-driven repository that hosts digital design files, assembly specifications, and open-source software to enable users to build, configure, and operate a microfluidic device. We use Metafluidics to share designs and fabrication instructions for both a microfluidic ring-mixer device and a 32-channel tabletop microfluidic controller. This device and controller are applied to build genetic circuits using standard DNA assembly methods including ligation, Gateway, Gibson, and Golden Gate. Metafluidics is intended to enable a broad community of engineers, DIY enthusiasts, and other nontraditional participants with limited fabrication skills to contribute to microfluidic research.

New Algorithm and Software (BNOmics) for Inferring and Visualizing Bayesian Networks from Heterogeneous Big Biological and Genetic Data.

Science.gov (United States)

Gogoshin, Grigoriy; Boerwinkle, Eric; Rodin, Andrei S

2017-04-01

Bayesian network (BN) reconstruction is a prototypical systems biology data analysis approach that has been successfully used to reverse engineer and model networks reflecting different layers of biological organization (ranging from genetic to epigenetic to cellular pathway to metabolomic). It is especially relevant in the context of modern (ongoing and prospective) studies that generate heterogeneous high-throughput omics datasets. However, there are both theoretical and practical obstacles to the seamless application of BN modeling to such big data, including computational inefficiency of optimal BN structure search algorithms, ambiguity in data discretization, mixing data types, imputation and validation, and, in general, limited scalability in both reconstruction and visualization of BNs. To overcome these and other obstacles, we present BNOmics, an improved algorithm and software toolkit for inferring and analyzing BNs from omics datasets. BNOmics aims at comprehensive systems biology-type data exploration, including both generating new biological hypothesis and testing and validating the existing ones. Novel aspects of the algorithm center around increasing scalability and applicability to varying data types (with different explicit and implicit distributional assumptions) within the same analysis framework. An output and visualization interface to widely available graph-rendering software is also included. Three diverse applications are detailed. BNOmics was originally developed in the context of genetic epidemiology data and is being continuously optimized to keep pace with the ever-increasing inflow of available large-scale omics datasets. As such, the software scalability and usability on the less than exotic computer hardware are a priority, as well as the applicability of the algorithm and software to the heterogeneous datasets containing many data types-single-nucleotide polymorphisms and other genetic/epigenetic/transcriptome variables, metabolite

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/.

Intelligent Data-Driven Reverse Engineering of Software Design Patterns

OpenAIRE

Alhusain, Sultan

2016-01-01

Recognising implemented instances of Design Patterns (DPs) in software design discloses and recovers a wealth of information about the intention of the original designers and the rationale for their design decisions. Because it is often the case that the documentation available for software systems, if any, is poor and/or obsolete, recovering such information can be of great help and importance for maintenance tasks. However, since DPs are abstractly and vaguely defined, a set of software cla...

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

A stress driven growth model for soft tissue considering biological availability

International Nuclear Information System (INIS)

Oller, S; Bellomo, F J; Nallim, L G; Armero, F

2010-01-01

Some of the key factors that regulate growth and remodeling of tissues are fundamentally mechanical. However, it is important to take into account the role of bioavailability together with the stresses and strains in the processes of normal or pathological growth. In this sense, the model presented in this work is oriented to describe the growth of soft biological tissue under 'stress driven growth' and depending on the biological availability of the organism. The general theoretical framework is given by a kinematic formulation in large strain combined with the thermodynamic basis of open systems. The formulation uses a multiplicative decomposition of deformation gradient, splitting it in a growth part and visco-elastic part. The strains due to growth are incompatible and are controlled by an unbalanced stresses related to a homeostatic state. Growth implies a volume change with an increase of mass maintaining constant the density. One of the most interesting features of the proposed model is the generation of new tissue taking into account the contribution of mass to the system controlled through biological availability. Because soft biological tissues in general have a hierarchical structure with several components (usually a soft matrix reinforced with collagen fibers), the developed growth model is suitable for the characterization of the growth of each component. This allows considering a different behavior for each of them in the context of a generalized theory of mixtures. Finally, we illustrate the response of the model in case of growth and atrophy with an application example.

Software process improvement in the NASA software engineering laboratory

Science.gov (United States)

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

1994-01-01

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

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…

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 ...

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; Chaudhuri, 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.

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.

Modelling and Simulating Complex Systems in Biology: introducing NetBioDyn : A Pedagogical and Intuitive Agent-Based Software

OpenAIRE

Ballet, Pascal; Rivière, Jérémy; Pothet, Alain; Théron, Michaël; Pichavant, Karine; Abautret, Frank; Fronville, Alexandra; Rodin, Vincent

2017-01-01

International audience; Modelling and teaching complex biological systems is a difficult process. Multi-Agent Based Simulations (MABS) have proved to be an appropriate approach both in research and education when dealing with such systems including emergent, self-organizing phenomena. This chapter presents NetBioDyn, an original software aimed at biologists (students, teachers, researchers) to easily build and simulate complex biological mechanisms observed in multicellular and molecular syst...

Water-driven micromotors for rapid photocatalytic degradation of biological and chemical warfare agents.

Science.gov (United States)

Li, Jinxing; Singh, Virendra V; Sattayasamitsathit, Sirilak; Orozco, Jahir; Kaufmann, Kevin; Dong, Renfeng; Gao, Wei; Jurado-Sanchez, Beatriz; Fedorak, Yuri; Wang, Joseph

2014-11-25

Threats of chemical and biological warfare agents (CBWA) represent a serious global concern and require rapid and efficient neutralization methods. We present a highly effective micromotor strategy for photocatalytic degradation of CBWA based on light-activated TiO2/Au/Mg microspheres that propel autonomously in natural water and obviate the need for external fuel, decontaminating reagent, or mechanical agitation. The activated TiO2/Au/Mg micromotors generate highly reactive oxygen species responsible for the efficient destruction of the cell membranes of the anthrax simulant Bacillus globigii spore, as well as rapid and complete in situ mineralization of the highly persistent organophosphate nerve agents into nonharmful products. The water-driven propulsion of the TiO2/Au/Mg micromotors facilitates efficient fluid transport and dispersion of the photogenerated reactive oxidative species and their interaction with the CBWA. Coupling of the photocatalytic surface of the micromotors and their autonomous water-driven propulsion thus leads to a reagent-free operation which holds a considerable promise for diverse "green" defense and environmental applications.

Functional Domain Driven Design

OpenAIRE

Herrera Guzmán, Sergio

2016-01-01

Las tecnologías están en constante expansión y evolución, diseñando nuevas técnicas para cumplir con su fin. En el desarrollo de software, las herramientas y pautas para la elaboración de productos software constituyen una pieza en constante evolución, necesarias para la toma de decisiones sobre los proyectos a realizar. Uno de los arquetipos para el desarrollo de software es el denominado Domain Driven Design, donde es importante conocer ampliamente el negocio que se desea modelar en form...

The Event-Driven Software Library for YARP—With Algorithms and iCub Applications

Directory of Open Access Journals (Sweden)

Arren Glover

2018-01-01

Full Text Available Event-driven (ED cameras are an emerging technology that sample the visual signal based on changes in the signal magnitude, rather than at a fixed-rate over time. The change in paradigm results in a camera with a lower latency, that uses less power, has reduced bandwidth, and higher dynamic range. Such cameras offer many potential advantages for on-line, autonomous, robots; however, the sensor data do not directly integrate with current “image-based” frameworks and software libraries. The iCub robot uses Yet Another Robot Platform (YARP as middleware to provide modular processing and connectivity to sensors and actuators. This paper introduces a library that incorporates an event-based framework into the YARP architecture, allowing event cameras to be used with the iCub (and other YARP-based robots. We describe the philosophy and methods for structuring events to facilitate processing, while maintaining low-latency and real-time operation. We also describe several processing modules made available open-source, and three example demonstrations that can be run on the neuromorphic iCub.

VANESA - A Software Application for the Visualization and Analysis of Networks in Systems Biology Applications

Directory of Open Access Journals (Sweden)

Brinkrolf Christoph

2014-06-01

Full Text Available VANESA is a modeling software for the automatic reconstruction and analysis of biological networks based on life-science database information. Using VANESA, scientists are able to model any kind of biological processes and systems as biological networks. It is now possible for scientists to automatically reconstruct important molecular systems with information from the databases KEGG, MINT, IntAct, HPRD, and BRENDA. Additionally, experimental results can be expanded with database information to better analyze the investigated elements and processes in an overall context. Users also have the possibility to use graph theoretical approaches in VANESA to identify regulatory structures and significant actors within the modeled systems. These structures can then be further investigated in the Petri net environment of VANESA. It is platform-independent, free-of-charge, and available at http://vanesa.sf.net.

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.

Design of SGLT2 Inhibitors for the Treatment of Type 2 Diabetes: A History Driven by Biology to Chemistry.

Science.gov (United States)

Cai, Wenqing; Jiang, Linlin; Xie, Yafei; Liu, Yuqiang; Liu, Wei; Zhao, Guilong

2015-01-01

A brief history of the design of sodium-dependent glucose cotransporter 2 (SGLT2) inhibitors is reviewed. The design of O-glucoside SGLT2 inhibitors by structural modification of phlorizin, a naturally occurring O-glucoside, in the early stage was a process mainly driven by biology with anticipation of improving SGLT2/SGLT1 selectivity and increasing metabolic stability. Discovery of dapagliflozin, a pioneering C-glucoside SGLT2 inhibitor developed by Bristol-Myers Squibb, represents an important milestone in this history. In the second stage, the design of C-glycoside SGLT2 inhibitors by modifications of the aglycone and glucose moiety of dapagliflozin, an original structural template for almost all C-glycoside SGLT2 inhibitors, was mainly driven by synthetic organic chemistry due to the challenge of designing dapagliflozin derivatives that are patentable, biologically active and synthetically accessible. Structure-activity relationships (SAR) of the SGLT2 inhibitors are also discussed.

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.

From napkin sketches to reliable software

NARCIS (Netherlands)

Engelen, L.J.P.

2012-01-01

In the past few years, model-driven software engineering (MDSE) and domain-specific modeling languages (DSMLs) have received a lot of attention from both research and industry. The main goal of MDSE is generating software from models that describe systems on a high level of abstraction. DSMLs are

Software quality assurance and software safety in the Biomed Control System

International Nuclear Information System (INIS)

Singh, R.P.; Chu, W.T.; Ludewigt, B.A.; Marks, K.M.; Nyman, M.A.; Renner, T.R.; Stradtner, R.

1989-01-01

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

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.

Statistical Data Processing with R – Metadata Driven Approach

Directory of Open Access Journals (Sweden)

Rudi SELJAK

2016-06-01

Full Text Available In recent years the Statistical Office of the Republic of Slovenia has put a lot of effort into re-designing its statistical process. We replaced the classical stove-pipe oriented production system with general software solutions, based on the metadata driven approach. This means that one general program code, which is parametrized with process metadata, is used for data processing for a particular survey. Currently, the general program code is entirely based on SAS macros, but in the future we would like to explore how successfully statistical software R can be used for this approach. Paper describes the metadata driven principle for data validation, generic software solution and main issues connected with the use of statistical software R for this approach.

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...

CLAIRE, an event-driven simulation tool for testing software

International Nuclear Information System (INIS)

Raguideau, J.; Schoen, D.; Henry, J.Y.; Boulc'h, J.

1994-06-01

CLAIRE is a software tool created to perform validations on executable codes or on specifications of distributed real-time applications for nuclear safety. CLAIRE can be used both to verify the safety properties by modelling the specifications, and also to validate the final code by simulating the behaviour of its equipment and software interfaces. It can be used to observe and provide dynamic control of the simulation process, and also to record changes to the simulated data for off-line analysis. (R.P.)

User-driven integrated software lives: ``Paleomag'' paleomagnetics analysis on the Macintosh

Science.gov (United States)

Jones, Craig H.

2002-12-01

"PaleoMag," a paleomagnetics analysis package originally developed for the Macintosh operating system in 1988, allows examination of demagnetization of individual samples and analysis of directional data from collections of samples. Prior to recent reinvigorated development of the software for both Macintosh and Windows, it was widely used despite not running properly on machines and operating systems sold after 1995. This somewhat surprising situation demonstrates that there is a continued need for integrated analysis software within the earth sciences, in addition to well-developed scripting and batch-mode software. One distinct advantage of software like PaleoMag is in the ability to combine quality control with analysis within a unique graphical environment. Because such demands are frequent within the earth sciences, means of nurturing the development of similar software should be found.

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 ...

Test Driven Development of Scientific Models

Science.gov (United States)

Clune, Thomas L.

2012-01-01

Test-Driven Development (TDD) is a software development process that promises many advantages for developer productivity and has become widely accepted among professional software engineers. As the name suggests, TDD practitioners alternate between writing short automated tests and producing code that passes those tests. Although this overly simplified description will undoubtedly sound prohibitively burdensome to many uninitiated developers, the advent of powerful unit-testing frameworks greatly reduces the effort required to produce and routinely execute suites of tests. By testimony, many developers find TDD to be addicting after only a few days of exposure, and find it unthinkable to return to previous practices. Of course, scientific/technical software differs from other software categories in a number of important respects, but I nonetheless believe that TDD is quite applicable to the development of such software and has the potential to significantly improve programmer productivity and code quality within the scientific community. After a detailed introduction to TDD, I will present the experience within the Software Systems Support Office (SSSO) in applying the technique to various scientific applications. This discussion will emphasize the various direct and indirect benefits as well as some of the difficulties and limitations of the methodology. I will conclude with a brief description of pFUnit, a unit testing framework I co-developed to support test-driven development of parallel Fortran applications.

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

LHCb software strategy

CERN Document Server

Van Herwijnen, Eric

1998-01-01

This document describes the software strategy of the LHCb experiment. The main objective is to reuse designs and code wherever possible; We will implement an architecturally driven design process; This architectural process will be implemented using Object Technology; We aim for platform indepence; try to take advantage of distributed computing and will use industry standards, commercial software and profit from HEP developments; We will implement a common software process and development environment. One of the major problems that we are immediately faced with is the conversion of our current code from Fortran into an Object Oriented language and the conversion of our current developers to Object technology. Some technical terms related to OO programming are defined in Annex A.1

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...

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

Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks.

Science.gov (United States)

Tian, Ye; Zhang, Bai; Hoffman, Eric P; Clarke, Robert; Zhang, Zhen; Shih, Ie-Ming; Xuan, Jianhua; Herrington, David M; Wang, Yue

2014-07-24

Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context-specific and dynamic in nature. To systematically characterize the selectively activated regulatory components and mechanisms, modeling tools must be able to effectively distinguish significant rewiring from random background fluctuations. While differential networks cannot be constructed by existing knowledge alone, novel incorporation of prior knowledge into data-driven approaches can improve the robustness and biological relevance of network inference. However, the major unresolved roadblocks include: big solution space but a small sample size; highly complex networks; imperfect prior knowledge; missing significance assessment; and heuristic structural parameter learning. To address these challenges, we formulated the inference of differential dependency networks that incorporate both conditional data and prior knowledge as a convex optimization problem, and developed an efficient learning algorithm to jointly infer the conserved biological network and the significant rewiring across different conditions. We used a novel sampling scheme to estimate the expected error rate due to "random" knowledge. Based on that scheme, we developed a strategy that fully exploits the benefit of this data-knowledge integrated approach. We demonstrated and validated the principle and performance of our method using synthetic datasets. We then applied our method to yeast cell line and breast cancer microarray data and obtained biologically plausible results. The open-source R software package and the experimental data are freely available at http://www.cbil.ece.vt.edu/software.htm. Experiments on both synthetic and real data demonstrate the effectiveness of the knowledge-fused differential dependency network in revealing the statistically significant rewiring in biological

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/. 2010 Elsevier Ltd. All rights reserved.

A menu-driven software package of Bayesian nonparametric (and parametric) mixed models for regression analysis and density estimation.

Science.gov (United States)

Karabatsos, George

2017-02-01

Most of applied statistics involves regression analysis of data. In practice, it is important to specify a regression model that has minimal assumptions which are not violated by data, to ensure that statistical inferences from the model are informative and not misleading. This paper presents a stand-alone and menu-driven software package, Bayesian Regression: Nonparametric and Parametric Models, constructed from MATLAB Compiler. Currently, this package gives the user a choice from 83 Bayesian models for data analysis. They include 47 Bayesian nonparametric (BNP) infinite-mixture regression models; 5 BNP infinite-mixture models for density estimation; and 31 normal random effects models (HLMs), including normal linear models. Each of the 78 regression models handles either a continuous, binary, or ordinal dependent variable, and can handle multi-level (grouped) data. All 83 Bayesian models can handle the analysis of weighted observations (e.g., for meta-analysis), and the analysis of left-censored, right-censored, and/or interval-censored data. Each BNP infinite-mixture model has a mixture distribution assigned one of various BNP prior distributions, including priors defined by either the Dirichlet process, Pitman-Yor process (including the normalized stable process), beta (two-parameter) process, normalized inverse-Gaussian process, geometric weights prior, dependent Dirichlet process, or the dependent infinite-probits prior. The software user can mouse-click to select a Bayesian model and perform data analysis via Markov chain Monte Carlo (MCMC) sampling. After the sampling completes, the software automatically opens text output that reports MCMC-based estimates of the model's posterior distribution and model predictive fit to the data. Additional text and/or graphical output can be generated by mouse-clicking other menu options. This includes output of MCMC convergence analyses, and estimates of the model's posterior predictive distribution, for selected

REVEAL - A tool for rule driven analysis of safety critical software

International Nuclear Information System (INIS)

Miedl, H.; Kersken, M.

1998-01-01

As the determination of ultrahigh reliability figures for safety critical software is hardly possible, national and international guidelines and standards give mainly requirements for the qualitative evaluation of software. An analysis whether all these requirements are fulfilled is time and effort consuming and prone to errors, if performed manually by analysts, and should instead be dedicated to tools as far as possible. There are many ''general-purpose'' software analysis tools, both static and dynamic, which help analyzing the source code. However, they are not designed to assess the adherence to specific requirements of guidelines and standards in the nuclear field. Against the background of the development of I and C systems in the nuclear field which are based on digital techniques and implemented in high level language, it is essential that the assessor or licenser has a tool with which he can automatically and uniformly qualify as many aspects as possible of the high level language software. For this purpose the software analysis tool REVEAL has been developed at ISTec and the Halden Reactor Project. (author)

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

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

2013-06-01

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.

Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology.

Science.gov (United States)

Pazos, Florencio; Chagoyen, Monica

2018-01-16

Daily work in molecular biology presently depends on a large number of computational tools. An in-depth, large-scale study of that 'ecosystem' of Web tools, its characteristics, interconnectivity, patterns of usage/citation, temporal evolution and rate of decay is crucial for understanding the forces that shape it and for informing initiatives aimed at its funding, long-term maintenance and improvement. In particular, the long-term maintenance of these tools is compromised because of their specific development model. Hundreds of published studies become irreproducible de facto, as the software tools used to conduct them become unavailable. In this study, we present a large-scale survey of >5400 publications describing Web servers within the two main bibliographic resources for disseminating new software developments in molecular biology. For all these servers, we studied their citation patterns, the subjects they address, their citation networks and the temporal evolution of these factors. We also analysed how these factors affect the availability of these servers (whether they are alive). Our results show that this ecosystem of tools is highly interconnected and adapts to the 'trendy' subjects in every moment. The servers present characteristic temporal patterns of citation/usage, and there is a worrying rate of server 'death', which is influenced by factors such as the server popularity and the institutions that hosts it. These results can inform initiatives aimed at the long-term maintenance of these resources. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Toward a User Driven Innovation for Distributed Software Teams

Science.gov (United States)

Hossain, Liaquat; Zhou, David

The software industry has emerged to include some of the most revolutionized distributed work groups; however, not all such groups achieve their set goals and some even fail miserably. The distributed nature of open source software project teams provides an intriguing context for the study of distributed coordination. OSS team structures have traditionally been geographically dispersed and, therefore, the coordination of post-release activities such as testing are made difficult due to the fact that the only means of communication is via electronic forms, such as e-mail or message boards and forums. Nevertheless, large scale, complex, and innovative software packages have been the fruits of labor for some OSS teams set in such coordination-unfriendly environments, while others end in flames. Why are some distributed work groups more effective than others? In our current communication-enriched environment, best practices for coordination are adopted by all software projects yet some still fall by the wayside. Does the team structure have bearing on the success of the project? How does the communication between the team and external parties affect the project's ultimate success or failure? In this study, we seek to answer these questions by applying existing theories from social networks and their analytical methods in the coordination of defect management activities found in OSS projects. We propose the social network based theoretical model for exploring distributed coordination structures and apply that for the case of the OSS defect management process for exploring the structural properties, which induce the greatest coordination performance. The outcome suggests that there is correlation between certain network measures such as density, centrality, and betweenness and coordination performance measures of defect management systems such as quality and timeliness.

Modeling Student Software Testing Processes: Attitudes, Behaviors, Interventions, and Their Effects

Science.gov (United States)

Buffardi, Kevin John

2014-01-01

Effective software testing identifies potential bugs and helps correct them, producing more reliable and maintainable software. As software development processes have evolved, incremental testing techniques have grown in popularity, particularly with introduction of test-driven development (TDD). However, many programmers struggle to adopt TDD's…

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…

Molecular Cloning Designer Simulator (MCDS: All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects

Directory of Open Access Journals (Sweden)

Zhenyu Shi

2016-12-01

Full Text Available Molecular Cloning Designer Simulator (MCDS is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1 it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2 it can perform a user-defined workflow of cloning steps in a single execution of the software; (3 it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4 it includes experimental information to conveniently guide wet lab work; and (5 it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com. Keywords: BioCAD, Genetic engineering software, Molecular cloning software, Synthetic biology, Workflow simulation and management

Diffusion-advection within dynamic biological gaps driven by structural motion

Science.gov (United States)

Asaro, Robert J.; Zhu, Qiang; Lin, Kuanpo

2018-04-01

To study the significance of advection in the transport of solutes, or particles, within thin biological gaps (channels), we examine theoretically the process driven by stochastic fluid flow caused by random thermal structural motion, and we compare it with transport via diffusion. The model geometry chosen resembles the synaptic cleft; this choice is motivated by the cleft's readily modeled structure, which allows for well-defined mechanical and physical features that control the advection process. Our analysis defines a Péclet-like number, AD, that quantifies the ratio of time scales of advection versus diffusion. Another parameter, AM, is also defined by the analysis that quantifies the full potential extent of advection in the absence of diffusion. These parameters provide a clear and compact description of the interplay among the well-defined structural, geometric, and physical properties vis-a ̀-vis the advection versus diffusion process. For example, it is found that AD˜1 /R2 , where R is the cleft diameter and hence diffusion distance. This curious, and perhaps unexpected, result follows from the dependence of structural motion that drives fluid flow on R . AM, on the other hand, is directly related (essentially proportional to) the energetic input into structural motion, and thereby to fluid flow, as well as to the mechanical stiffness of the cleftlike structure. Our model analysis thus provides unambiguous insight into the prospect of competition of advection versus diffusion within biological gaplike structures. The importance of the random, versus a regular, nature of structural motion and of the resulting transient nature of advection under random motion is made clear in our analysis. Further, by quantifying the effects of geometric and physical properties on the competition between advection and diffusion, our results clearly demonstrate the important role that metabolic energy (ATP) plays in this competitive process.

P-MartCancer–Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets

Energy Technology Data Exchange (ETDEWEB)

Webb-Robertson, Bobbie-Jo M.; Bramer, Lisa M.; Jensen, Jeffrey L.; Kobold, Markus A.; Stratton, Kelly G.; White, Amanda M.; Rodland, Karin D.

2017-10-31

P-MartCancer is a new interactive web-based software environment that enables biomedical and biological scientists to perform in-depth analyses of global proteomics data without requiring direct interaction with the data or with statistical software. P-MartCancer offers a series of statistical modules associated with quality assessment, peptide and protein statistics, protein quantification and exploratory data analyses driven by the user via customized workflows and interactive visualization. Currently, P-MartCancer offers access to multiple cancer proteomic datasets generated through the Clinical Proteomics Tumor Analysis Consortium (CPTAC) at the peptide, gene and protein levels. P-MartCancer is deployed using Azure technologies (http://pmart.labworks.org/cptac.html), the web-service is alternatively available via Docker Hub (https://hub.docker.com/r/pnnl/pmart-web/) and many statistical functions can be utilized directly from an R package available on GitHub (https://github.com/pmartR).

Active resources concept of computation for enterprise software

Directory of Open Access Journals (Sweden)

Koryl Maciej

2017-06-01

Full Text Available Traditional computational models for enterprise software are still to a great extent centralized. However, rapid growing of modern computation techniques and frameworks causes that contemporary software becomes more and more distributed. Towards development of new complete and coherent solution for distributed enterprise software construction, synthesis of three well-grounded concepts is proposed: Domain-Driven Design technique of software engineering, REST architectural style and actor model of computation. As a result new resources-based framework arises, which after first cases of use seems to be useful and worthy of further research.

Test-driven modeling of embedded systems

DEFF Research Database (Denmark)

Munck, Allan; Madsen, Jan

2015-01-01

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

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.

A Comparison and Evaluation of Real-Time Software Systems Modeling Languages

Science.gov (United States)

Evensen, Kenneth D.; Weiss, Kathryn Anne

2010-01-01

A model-driven approach to real-time software systems development enables the conceptualization of software, fostering a more thorough understanding of its often complex architecture and behavior while promoting the documentation and analysis of concerns common to real-time embedded systems such as scheduling, resource allocation, and performance. Several modeling languages have been developed to assist in the model-driven software engineering effort for real-time systems, and these languages are beginning to gain traction with practitioners throughout the aerospace industry. This paper presents a survey of several real-time software system modeling languages, namely the Architectural Analysis and Design Language (AADL), the Unified Modeling Language (UML), Systems Modeling Language (SysML), the Modeling and Analysis of Real-Time Embedded Systems (MARTE) UML profile, and the AADL for UML profile. Each language has its advantages and disadvantages, and in order to adequately describe a real-time software system's architecture, a complementary use of multiple languages is almost certainly necessary. This paper aims to explore these languages in the context of understanding the value each brings to the model-driven software engineering effort and to determine if it is feasible and practical to combine aspects of the various modeling languages to achieve more complete coverage in architectural descriptions. To this end, each language is evaluated with respect to a set of criteria such as scope, formalisms, and architectural coverage. An example is used to help illustrate the capabilities of the various languages.

Bioboxes: standardised containers for interchangeable bioinformatics software.

Science.gov (United States)

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

2015-01-01

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

Documentation Driven Development for Complex Real-Time Systems

Science.gov (United States)

2004-12-01

This paper presents a novel approach for development of complex real - time systems , called the documentation-driven development (DDD) approach. This... time systems . DDD will also support automated software generation based on a computational model and some relevant techniques. DDD includes two main...stakeholders to be easily involved in development processes and, therefore, significantly improve the agility of software development for complex real

Scenario driven data modelling: a method for integrating diverse sources of data and data streams

Science.gov (United States)

2011-01-01

Background Biology is rapidly becoming a data intensive, data-driven science. It is essential that data is represented and connected in ways that best represent its full conceptual content and allows both automated integration and data driven decision-making. Recent advancements in distributed multi-relational directed graphs, implemented in the form of the Semantic Web make it possible to deal with complicated heterogeneous data in new and interesting ways. Results This paper presents a new approach, scenario driven data modelling (SDDM), that integrates multi-relational directed graphs with data streams. SDDM can be applied to virtually any data integration challenge with widely divergent types of data and data streams. In this work, we explored integrating genetics data with reports from traditional media. SDDM was applied to the New Delhi metallo-beta-lactamase gene (NDM-1), an emerging global health threat. The SDDM process constructed a scenario, created a RDF multi-relational directed graph that linked diverse types of data to the Semantic Web, implemented RDF conversion tools (RDFizers) to bring content into the Sematic Web, identified data streams and analytical routines to analyse those streams, and identified user requirements and graph traversals to meet end-user requirements. Conclusions We provided an example where SDDM was applied to a complex data integration challenge. The process created a model of the emerging NDM-1 health threat, identified and filled gaps in that model, and constructed reliable software that monitored data streams based on the scenario derived multi-relational directed graph. The SDDM process significantly reduced the software requirements phase by letting the scenario and resulting multi-relational directed graph define what is possible and then set the scope of the user requirements. Approaches like SDDM will be critical to the future of data intensive, data-driven science because they automate the process of converting

Model-Driven Development for PDS4 Software and Services

Science.gov (United States)

Hughes, J. S.; Crichton, D. J.; Algermissen, S. S.; Cayanan, M. D.; Joyner, R. S.; Hardman, S. H.; Padams, J. H.

2018-04-01

PDS4 data product labels provide the information necessary for processing the referenced digital object. However, significantly more information is available in the PDS4 Information Model. This additional information is made available for use, by both software and services, to configure, promote resiliency, and improve interoperability.

Good Practices for Software Configuration Management with MDA Metodology

OpenAIRE

Manuel Morejón Espinosa

2012-01-01

Software Configuration Management (SCM) forms part of the software development process. Its principal goal is to coordinate this development and minimize all possible errors. In order to meet its goal various activities are carried out, of which can be identified: items identification, change control, version control, audit and status reporting. Inside enterprise applications the software development can be guided from system model as methodology. The name of this methodology is Model Driven ...

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…

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.

Concurrent Design of Embedded Control Software

NARCIS (Netherlands)

Groothuis, M.A.; Frijns, Raymond; Voeten, Jeroen; Broenink, Johannes F.; Margaria, T.; Padberg, J.; Taentzer, G.; Levendovszky, T.; Lengyel, L.; Karsai, G.; Hardebolle, C.

2009-01-01

Embedded software design for mechatronic systems is becoming an increasingly time-consuming and error-prone task. In order to cope with the heterogeneity and complexity, a systematic model-driven design approach is needed, where several parts of the system can be designed concurrently. There is

ONTOLOGY-DRIVEN TOOL FOR UTILIZING PROGRAMMING STYLES

Directory of Open Access Journals (Sweden)

Nikolay Sidorov

2017-07-01

Full Text Available Activities of a programmer will be more effective and the software will be more understandable when within the process of software development, programming styles (standards are used, providing clarity of software texts. Purpose: In this research, we present the tool for the realization of new ontology-based methodology automated reasoning techniques for utilizing programming styles. In particular, we focus on representing programming styles in the form of formal ontologies, and study how description logic reasoner can assist programmers in utilizing programming standards. Our research hypothesis is as follows: ontological representation of programming styles can provide additional benefits over existing approaches in utilizing programmer of programming standards. Our research goal is to develop a tool to support the ontology-based utilizing programming styles. Methods: ontological representation of programming styles; object-oriented programming; ontology-driven utilizing of programming styles. Results: the architecture was obtained and the tool was developed in the Java language, which provide tool support of ontology-driven programming styles application method. On the example of naming of the Java programming language standard, features of implementation and application of the tool are provided. Discussion: application of programming styles in coding of program; lack of automated tools for the processes of programming standards application; tool based on new method of ontology-driven application of programming styles; an example of the implementation of tool architecture for naming rules of the Java language standard.

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.

Molecular dynamics for irradiation driven chemistry

DEFF Research Database (Denmark)

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

2016-01-01

A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes...... 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...... involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields...

Just-in-time Database-Driven Web Applications

Science.gov (United States)

2003-01-01

"Just-in-time" database-driven Web applications are inexpensive, quickly-developed software that can be put to many uses within a health care organization. Database-driven Web applications garnered 73873 hits on our system-wide intranet in 2002. They enabled collaboration and communication via user-friendly Web browser-based interfaces for both mission-critical and patient-care-critical functions. Nineteen database-driven Web applications were developed. The application categories that comprised 80% of the hits were results reporting (27%), graduate medical education (26%), research (20%), and bed availability (8%). The mean number of hits per application was 3888 (SD = 5598; range, 14-19879). A model is described for just-in-time database-driven Web application development and an example given with a popular HTML editor and database program. PMID:14517109

Quality management using model-driven engineering: an overview

OpenAIRE

Ruiz-Rube, Iván; Escalona, María José

2014-01-01

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

ORNL's DCAL software package

International Nuclear Information System (INIS)

Eckerman, K.F.

2007-01-01

Oak Ridge National Laboratory has released its Dose and Risk Calculation software, DCAL. DCAL, developed with the support of the U.S. Environmental Protection Agency, consists of a series of computational modules, driven in either an interactive or a batch mode for computation of dose and risk coefficients from intakes of radionuclides or exposure to radionuclides in environmental media. The software package includes extensive libraries of biokinetic and dosimetric data that represent the current state of the art. The software has unique capability for addressing intakes of radionuclides by non-adults. DCAL runs as 32-bit extended DOS and console applications under Windows 98/NT/2000/XP. It is intended for users familiar with the basic elements of computational radiation dosimetry. Components of DCAL have been used to prepare U.S. Environmental Protection Agency's Federal Guidance Reports 12 and 13 and several publications of the International Commission on Radiological Protection. (author)

SPADE - software package to aid diffraction experiments

International Nuclear Information System (INIS)

Farren, J.; Giltrap, J.W.

1978-10-01

A software package is described which enables the DEC PDP-11/03 microcomputer to execute several different X-ray diffraction experiments and other similar experiments where stepper motors are driven and data is gathered and processed in real time. (author)

A refinement driven component-based design

DEFF Research Database (Denmark)

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

2007-01-01

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...

Model Driven Architecture: Foundations and Applications

NARCIS (Netherlands)

Rensink, Arend

The OMG's Model Driven Architecture (MDA) initiative has been the focus of much attention in both academia and industry, due to its promise of more rapid and consistent software development through the increased use of models. In order for MDA to reach its full potential, the ability to manipulate

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

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.

Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.

Science.gov (United States)

Roehner, Nicholas; Zhang, Zhen; Nguyen, Tramy; Myers, Chris J

2015-08-21

In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and introduces the foundational concepts of standards and model annotation that make this process useful. Finally, this paper presents an implementation of model generation in the GDA software tool iBioSim and provides an example of generating a Systems Biology Markup Language (SBML) model from a design of a 4-input AND sensor written in the Synthetic Biology Open Language (SBOL).

COSINE software development based on code generation technology

International Nuclear Information System (INIS)

Ren Hao; Mo Wentao; Liu Shuo; Zhao Guang

2013-01-01

The code generation technology can significantly improve the quality and productivity of software development and reduce software development risk. At present, the code generator is usually based on UML model-driven technology, which can not satisfy the development demand of nuclear power calculation software. The feature of scientific computing program was analyzed and the FORTRAN code generator (FCG) based on C# was developed in this paper. FCG can generate module variable definition FORTRAN code automatically according to input metadata. FCG also can generate memory allocation interface for dynamic variables as well as data access interface. FCG was applied to the core and system integrated engine for design and analysis (COSINE) software development. The result shows that FCG can greatly improve the development efficiency of nuclear power calculation software, and reduce the defect rate of software development. (authors)

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.

The MDE Diploma: First International Postgraduate Specialization in Model-Driven Engineering

Science.gov (United States)

Cabot, Jordi; Tisi, Massimo

2011-01-01

Model-Driven Engineering (MDE) is changing the way we build, operate, and maintain our software-intensive systems. Several projects using MDE practices are reporting significant improvements in quality and performance but, to be able to handle these projects, software engineers need a set of technical and interpersonal skills that are currently…

Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.

Science.gov (United States)

Ham, Timothy S; Dmytriv, Zinovii; Plahar, Hector; Chen, Joanna; Hillson, Nathan J; Keasling, Jay D

2012-10-01

The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about 'legacy' parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.

System on chip module configured for event-driven architecture

Science.gov (United States)

Robbins, Kevin; Brady, Charles E.; Ashlock, Tad A.

2017-10-17

A system on chip (SoC) module is described herein, wherein the SoC modules comprise a processor subsystem and a hardware logic subsystem. The processor subsystem and hardware logic subsystem are in communication with one another, and transmit event messages between one another. The processor subsystem executes software actors, while the hardware logic subsystem includes hardware actors, the software actors and hardware actors conform to an event-driven architecture, such that the software actors receive and generate event messages and the hardware actors receive and generate event messages.

A flexible modelling software for data acquisition

International Nuclear Information System (INIS)

Shu Yantai; Chen Yanhui; Yang Songqi; Liu Genchen

1992-03-01

A flexible modelling software for data acquisition is based on an event-driven simulator. It can be used to simulate a wide variety of systems which can be modelled as open queuing networks. The main feature of the software is its flexibility to evaluate the performance of various data acquisition system, whether pulsed or not. The flexible features of this software as follow: The user can choose the number of processors in the model and the route which every job takes to move the model. the service rate of a processor is automatically adapted. The simulator has a pipe-line mechanism. A job can be divided into several segments and a processor may be used as a compression component etc. Some modelling techniques and applications of this software in plasma physics laboratories are also presented

Usability and user driven innovation - unity or clash?

DEFF Research Database (Denmark)

Fronczek-Munter, Aneta

2011-01-01

Aim: To present different understandings of the concepts ‗usability‘ and ‗user driven innovation‘ and discuss if and how the built environment can benefit from these concepts and the unity of them. Approach and methodology: The paper is based on literature reviews of scientific journals and other...... influential publications within the academic fields of Facilities Management, Architecture and Engineering, Participatory Design and Software design. Outline: The paper will discuss different understandings of the concept ‗usability‘ and its relation to ‗user driven innovation‘, which depends on the academic...... field and area of professional application. The concept of usability has its roots in evaluations of consumer products and user interfaces of computer software. During the last 5-10 years there has been a new development of research in usability of buildings and workplaces. Recently researchers have...

Model Driven Development of Web Application with SPACE Method and Tool-suit

OpenAIRE

Rehana, Jinat

2010-01-01

Enterprise level software development using traditional software engineeringapproaches with third-generation programming languages is becoming morechallenging and cumbersome task with the increased complexity of products,shortened development cycles and heightened expectations of quality. MDD(Model Driven Development) has been counting as an exciting and magicaldevelopment approach in the software industry from several years. The ideabehind MDD is the separation of business logic of a system ...

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

Science.gov (United States)

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

2016-01-01

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

Software Assurance Curriculum Project Volume 3: Master of Software Assurance Course Syllabi

Science.gov (United States)

2011-07-01

thods and process of model-driven development. • Pressman , Roger S., Software Engineering: A Practitioner’s Approach, 6th ed. McGraw Hill, 2009...audience • [Bishop 2002] Chapter 18 • [Allen 2008] Chapters 1, 2 • [ Pressman 2009] Chapter 1 • [Merkow 2010] Chapter 3 • [Mouratidis 2007...Allen 2008] Chapters 3,4 • [ Pressman 2009] Chapters 3,4 • [Merkow 2010] Chapter 5 • [DHS 2008-2009a] • [Mellado 2010] • [CERT 2009] 3

Designing an optimal software intensive system acquisition: A game theoretic approach

Science.gov (United States)

Buettner, Douglas John

The development of schedule-constrained software-intensive space systems is challenging. Case study data from national security space programs developed at the U.S. Air Force Space and Missile Systems Center (USAF SMC) provide evidence of the strong desire by contractors to skip or severely reduce software development design and early defect detection methods in these schedule-constrained environments. The research findings suggest recommendations to fully address these issues at numerous levels. However, the observations lead us to investigate modeling and theoretical methods to fundamentally understand what motivated this behavior in the first place. As a result, Madachy's inspection-based system dynamics model is modified to include unit testing and an integration test feedback loop. This Modified Madachy Model (MMM) is used as a tool to investigate the consequences of this behavior on the observed defect dynamics for two remarkably different case study software projects. Latin Hypercube sampling of the MMM with sample distributions for quality, schedule and cost-driven strategies demonstrate that the higher cost and effort quality-driven strategies provide consistently better schedule performance than the schedule-driven up-front effort-reduction strategies. Game theory reasoning for schedule-driven engineers cutting corners on inspections and unit testing is based on the case study evidence and Austin's agency model to describe the observed phenomena. Game theory concepts are then used to argue that the source of the problem and hence the solution to developers cutting corners on quality for schedule-driven system acquisitions ultimately lies with the government. The game theory arguments also lead to the suggestion that the use of a multi-player dynamic Nash bargaining game provides a solution for our observed lack of quality game between the government (the acquirer) and "large-corporation" software developers. A note is provided that argues this multi

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. Copyright (c) 2010 Elsevier B.V. All rights reserved.

User driven innovation in mobile technologies?

DEFF Research Database (Denmark)

Larsen, Casper Schultz; Koch, Christian

2007-01-01

by systems already in function. Stories of prior business successes can be an important tool to ensure further innovative investments since lack of enterprise strategies is often an obstacle for innovation, especially user driven. Both small and large software houses develops dedicated software for coupling...... technology systems relying on the concept of affordance. This paper examines how innovation processes mediate between user orientations and technology offers. There is a great potential for mobile handheld ICT-systems to support numerous work processes in the AEC-industry and this can be substantiated...... site practises, and headquarters - inspired by specific user needs for optimizing work processes. The most important mechanisms evoked for creating the mediating found in the paper are ‘hybrids’ where professionals from AEC establishes a software house, developing ICT-products for specific on...

Community-driven development for computational biology at Sprints, Hackathons and Codefests.

Science.gov (United States)

Möller, Steffen; Afgan, Enis; Banck, Michael; Bonnal, Raoul J P; Booth, Timothy; Chilton, John; Cock, Peter J A; Gumbel, Markus; Harris, Nomi; Holland, Richard; Kalaš, Matúš; Kaján, László; Kibukawa, Eri; Powel, David R; Prins, Pjotr; Quinn, Jacqueline; Sallou, Olivier; Strozzi, Francesco; Seemann, Torsten; Sloggett, Clare; Soiland-Reyes, Stian; Spooner, William; Steinbiss, Sascha; Tille, Andreas; Travis, Anthony J; Guimera, Roman; Katayama, Toshiaki; Chapman, Brad A

2014-01-01

Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches. Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by informal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large. Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together. This report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled "unconferences" (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how

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)

Test Driven Development of Scientific Models

Science.gov (United States)

Clune, Thomas L.

2014-01-01

Test-Driven Development (TDD), a software development process that promises many advantages for developer productivity and software reliability, has become widely accepted among professional software engineers. As the name suggests, TDD practitioners alternate between writing short automated tests and producing code that passes those tests. Although this overly simplified description will undoubtedly sound prohibitively burdensome to many uninitiated developers, the advent of powerful unit-testing frameworks greatly reduces the effort required to produce and routinely execute suites of tests. By testimony, many developers find TDD to be addicting after only a few days of exposure, and find it unthinkable to return to previous practices.After a brief overview of the TDD process and my experience in applying the methodology for development activities at Goddard, I will delve more deeply into some of the challenges that are posed by numerical and scientific software as well as tools and implementation approaches that should address those challenges.

EMMA: a new paradigm in configurable software

International Nuclear Information System (INIS)

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

2017-01-01

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. As a result, 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.

EMMA: a new paradigm in configurable software

Science.gov (United States)

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

2017-10-01

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.

A Systematic Review of Published Respondent-Driven Sampling Surveys Collecting Behavioral and Biologic Data.

Science.gov (United States)

Johnston, Lisa G; Hakim, Avi J; Dittrich, Samantha; Burnett, Janet; Kim, Evelyn; White, Richard G

2016-08-01

Reporting key details of respondent-driven sampling (RDS) survey implementation and analysis is essential for assessing the quality of RDS surveys. RDS is both a recruitment and analytic method and, as such, it is important to adequately describe both aspects in publications. We extracted data from peer-reviewed literature published through September, 2013 that reported collected biological specimens using RDS. We identified 151 eligible peer-reviewed articles describing 222 surveys conducted in seven regions throughout the world. Most published surveys reported basic implementation information such as survey city, country, year, population sampled, interview method, and final sample size. However, many surveys did not report essential methodological and analytical information for assessing RDS survey quality, including number of recruitment sites, seeds at start and end, maximum number of waves, and whether data were adjusted for network size. Understanding the quality of data collection and analysis in RDS is useful for effectively planning public health service delivery and funding priorities.

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.

"A mission-driven discipline": the growth of conservation biology.

Science.gov (United States)

Meine, Curt; Soulé, Michael; Noss, Reed E

2006-06-01

Conservation biology emerged in the mid-1980s, drawing on established disciplines and integrating them in pursuit of a coherent goal: the protection and perpetuation of the Earth's biological diversity. Opportunistic in its borrowing and application of knowledge, conservation biology had its roots within the established biological sciences and resource management disciplines but has continually incorporated insights from the empirical experience of resource managers, from the social sciences and humanities, and from diverse cultural sources. The Society for Conservation Biology (SCB) has represented the field's core constituency, while expanding that constituency in keeping with the field's integrative spirit. Conservation Biology has served as SCB's flagship publication, promoting research, dialog, debate, and application of the field's essential concepts. Over the last 20 years the field, SCB, and the journal have evolved to meet changing conservation needs, to explore gaps in our knowledge base, to incorporate new information from related fields, to build professional capacity, and to provide expanded opportunities for international participation. In turn, the field, SCB, and journal have prompted change in related fields, organizations, and publications. In its dedication to advancing the scientific foundations of biodiversity conservation and placing that science at the service of society in a world whose variety, wildness, and beauty we care for conservation biology represents both a continuation and radical reconfiguration of the traditional relationship between science and conservation.

Toward computational cumulative biology by combining models of biological datasets.

Science.gov (United States)

Faisal, Ali; Peltonen, Jaakko; Georgii, Elisabeth; Rung, Johan; Kaski, Samuel

2014-01-01

A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to include both biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or automatically by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition, we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer, and the model-based search was more accurate than the keyword search; moreover, it recovered biologically meaningful relationships that are not straightforwardly visible from annotations-for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database.

Top 10 metrics for life science software good practices.

Science.gov (United States)

Artaza, Haydee; Chue Hong, Neil; Corpas, Manuel; Corpuz, Angel; Hooft, Rob; Jimenez, Rafael C; Leskošek, Brane; Olivier, Brett G; Stourac, Jan; Svobodová Vařeková, Radka; Van Parys, Thomas; Vaughan, Daniel

2016-01-01

Metrics for assessing adoption of good development practices are a useful way to ensure that software is sustainable, reusable and functional. Sustainability means that the software used today will be available - and continue to be improved and supported - in the future. We report here an initial set of metrics that measure good practices in software development. This initiative differs from previously developed efforts in being a community-driven grassroots approach where experts from different organisations propose good software practices that have reasonable potential to be adopted by the communities they represent. We not only focus our efforts on understanding and prioritising good practices, we assess their feasibility for implementation and publish them here.

"SABER": A new software tool for radiotherapy treatment plan evaluation.

Science.gov (United States)

Zhao, Bo; Joiner, Michael C; Orton, Colin G; Burmeister, Jay

2010-11-01

Both spatial and biological information are necessary in order to perform true optimization of a treatment plan and for predicting clinical outcome. The goal of this work is to develop an enhanced treatment plan evaluation tool which incorporates biological parameters and retains spatial dose information. A software system is developed which provides biological plan evaluation with a novel combination of features. It incorporates hyper-radiosensitivity using the induced-repair model and applies the new concept of dose convolution filter (DCF) to simulate dose wash-out effects due to cell migration, bystander effect, and/or tissue motion during treatment. Further, the concept of spatial DVH (sDVH) is introduced to evaluate and potentially optimize the spatial dose distribution in the target volume. Finally, generalized equivalent uniform dose is derived from both the physical dose distribution (gEUD) and the distribution of equivalent dose in 2 Gy fractions (gEUD2) and the software provides three separate models for calculation of tumor control probability (TCP), normal tissue complication probability (NTCP), and probability of uncomplicated tumor control (P+). TCP, NTCP, and P+ are provided as a function of prescribed dose and multivariable TCP, NTCP, and P+ plots are provided to illustrate the dependence on individual parameters used to calculate these quantities. Ten plans from two clinical treatment sites are selected to test the three calculation models provided by this software. By retaining both spatial and biological information about the dose distribution, the software is able to distinguish features of radiotherapy treatment plans not discernible using commercial systems. Plans that have similar DVHs may have different spatial and biological characteristics and the application of novel tools such as sDVH and DCF within the software may substantially change the apparent plan quality or predicted plan metrics such as TCP and NTCP. For the cases examined

Test and Behaviour Driven Development with Python

CERN Multimedia

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.

EDS operator and control software

International Nuclear Information System (INIS)

Ott, L.L.

1985-04-01

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

Laser-driven particle acceleration towards radiobiology and medicine

CERN Document Server

2016-01-01

This book deals with the new method of laser-driven acceleration for application to radiation biophysics and medicine. It provides multidisciplinary contributions from world leading scientist in order to assess the state of the art of innovative tools for radiation biology research and medical applications of ionizing radiation. The book contains insightful contributions on highly topical aspects of spatio-temporal radiation biophysics, evolving over several orders of magnitude, typically from femtosecond and sub-micrometer scales. Particular attention is devoted to the emerging technology of laser-driven particle accelerators and their applicatio to spatio-temporal radiation biology and medical physics, customization of non-conventional and selective radiotherapy and optimized radioprotection protocols.

Multibiodose radiation emergency triage categorization software.

Science.gov (United States)

Ainsbury, Elizabeth A; Barnard, Stephen; Barrios, Lleonard; Fattibene, Paola; de Gelder, Virginie; Gregoire, Eric; Lindholm, Carita; Lloyd, David; Nergaard, Inger; Rothkamm, Kai; Romm, Horst; Scherthan, Harry; Thierens, Hubert; Vandevoorde, Charlot; Woda, Clemens; Wojcik, Andrzej

2014-07-01

In this note, the authors describe the MULTIBIODOSE software, which has been created as part of the MULTIBIODOSE project. The software enables doses estimated by networks of laboratories, using up to five retrospective (biological and physical) assays, to be combined to give a single estimate of triage category for each individual potentially exposed to ionizing radiation in a large scale radiation accident or incident. The MULTIBIODOSE software has been created in Java. The usage of the software is based on the MULTIBIODOSE Guidance: the program creates a link to a single SQLite database for each incident, and the database is administered by the lead laboratory. The software has been tested with Java runtime environment 6 and 7 on a number of different Windows, Mac, and Linux systems, using data from a recent intercomparison exercise. The Java program MULTIBIODOSE_1.0.jar is freely available to download from http://www.multibiodose.eu/software or by contacting the software administrator: MULTIBIODOSE-software@gmx.com.

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

Seismology software: state of the practice

Science.gov (United States)

Smith, W. Spencer; Zeng, Zheng; Carette, Jacques

2018-05-01

We analyzed the state of practice for software development in the seismology domain by comparing 30 software packages on four aspects: product, implementation, design, and process. We found room for improvement in most seismology software packages. The principal areas of concern include a lack of adequate requirements and design specification documents, a lack of test data to assess reliability, a lack of examples to get new users started, and a lack of technological tools to assist with managing the development process. To assist going forward, we provide recommendations for a document-driven development process that includes a problem statement, development plan, requirement specification, verification and validation (V&V) plan, design specification, code, V&V report, and a user manual. We also provide advice on tool use, including issue tracking, version control, code documentation, and testing tools.

Seismology software: state of the practice

Science.gov (United States)

Smith, W. Spencer; Zeng, Zheng; Carette, Jacques

2018-02-01

We analyzed the state of practice for software development in the seismology domain by comparing 30 software packages on four aspects: product, implementation, design, and process. We found room for improvement in most seismology software packages. The principal areas of concern include a lack of adequate requirements and design specification documents, a lack of test data to assess reliability, a lack of examples to get new users started, and a lack of technological tools to assist with managing the development process. To assist going forward, we provide recommendations for a document-driven development process that includes a problem statement, development plan, requirement specification, verification and validation (V&V) plan, design specification, code, V&V report, and a user manual. We also provide advice on tool use, including issue tracking, version control, code documentation, and testing tools.

Ontology Driven Meta-Modeling of Service Oriented Architecture

African Journals Online (AJOL)

pc

2018-03-05

Mar 5, 2018 ... #Department of Computer Applications, National Institute of ... *5Department of Computer Science, Winona State University, MN, USA ..... Further, it has aided in service .... Software: A Research Roadmap”, Workshop on the Future of ... and A. Solberg, “Model-driven service engineering with SoaML”, in.

Editorial - Special Issue on Model-driven Service-oriented architectures

NARCIS (Netherlands)

Andrade Almeida, João; Ferreira Pires, Luis; van Sinderen, Marten J.; Steen, M.W.A.

2009-01-01

Model-driven approaches to software development have proliferated in recent years owing to the availability of techniques based on metamodelling and model transformations, such as the meta-object facility (MOF) and the query view transformation (QVT) standards. During the same period,

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

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

STSE: Spatio-Temporal Simulation Environment Dedicated to Biology.

Science.gov (United States)

Stoma, Szymon; Fröhlich, Martina; Gerber, Susanne; Klipp, Edda

2011-04-28

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. 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 of the STSE design and workflow. We

Improving the quality of numerical software through user-centered design

Energy Technology Data Exchange (ETDEWEB)

Pancake, C. M., Oregon State University

1998-06-01

The software interface - whether graphical, command-oriented, menu-driven, or in the form of subroutine calls - shapes the user`s perception of what software can do. It also establishes upper bounds on software usability. Numerical software interfaces typically are based on the designer`s understanding of how the software should be used. That is a poor foundation for usability, since the features that are ``instinctively right`` from the developer`s perspective are often the very ones that technical programmers find most objectionable or most difficult to learn. This paper discusses how numerical software interfaces can be improved by involving users more actively in design, a process known as user-centered design (UCD). While UCD requires extra organization and effort, it results in much higher levels of usability and can actually reduce software costs. This is true not just for graphical user interfaces, but for all software interfaces. Examples show how UCD improved the usability of a subroutine library, a command language, and an invocation interface.

Water-driven micromotors.

Science.gov (United States)

Gao, Wei; Pei, Allen; Wang, Joseph

2012-09-25

We demonstrate the first example of a water-driven bubble-propelled micromotor that eliminates the requirement for the common hydrogen peroxide fuel. The new water-driven Janus micromotor is composed of a partially coated Al-Ga binary alloy microsphere prepared via microcontact mixing of aluminum microparticles and liquid gallium. The ejection of hydrogen bubbles from the exposed Al-Ga alloy hemisphere side, upon its contact with water, provides a powerful directional propulsion thrust. Such spontaneous generation of hydrogen bubbles reflects the rapid reaction between the aluminum alloy and water. The resulting water-driven spherical motors can move at remarkable speeds of 3 mm s(-1) (i.e., 150 body length s(-1)), while exerting large forces exceeding 500 pN. Factors influencing the efficiency of the aluminum-water reaction and the resulting propulsion behavior and motor lifetime, including the ionic strength and environmental pH, are investigated. The resulting water-propelled Al-Ga/Ti motors move efficiently in different biological media (e.g., human serum) and hold considerable promise for diverse biomedical or industrial applications.

Implementing Genome-Driven Oncology

Science.gov (United States)

Hyman, David M.; Taylor, Barry S.; Baselga, José

2017-01-01

Early successes in identifying and targeting individual oncogenic drivers, together with the increasing feasibility of sequencing tumor genomes, have brought forth the promise of genome-driven oncology care. As we expand the breadth and depth of genomic analyses, the biological and clinical complexity of its implementation will be unparalleled. Challenges include target credentialing and validation, implementing drug combinations, clinical trial designs, targeting tumor heterogeneity, and deploying technologies beyond DNA sequencing, among others. We review how contemporary approaches are tackling these challenges and will ultimately serve as an engine for biological discovery and increase our insight into cancer and its treatment. PMID:28187282

An ontology-driven semantic mashup of gene and biological pathway information: application to the domain of nicotine dependence.

Science.gov (United States)

Sahoo, Satya S; Bodenreider, Olivier; Rutter, Joni L; Skinner, Karen J; Sheth, Amit P

2008-10-01

This paper illustrates how Semantic Web technologies (especially RDF, OWL, and SPARQL) can support information integration and make it easy to create semantic mashups (semantically integrated resources). In the context of understanding the genetic basis of nicotine dependence, we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base. We use an ontology-driven approach to integrate two gene resources (Entrez Gene and HomoloGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans. We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources. The integrated schema is populated with data from the pathway resources, publicly available in BioPAX-compatible format, and gene resources for which a population procedure was created. The SPARQL query language is used to formulate queries over the integrated knowledge base to answer the three biological queries. Simple SPARQL queries could easily identify hub genes, i.e., those genes whose gene products participate in many pathways or interact with many other gene products. The identification of the genes expressed in the brain turned out to be more difficult, due to the lack of a common identification scheme for proteins. Semantic Web technologies provide a valid framework for information integration in the life sciences. Ontology-driven integration represents a flexible, sustainable and extensible solution to the integration of large volumes of information. Additional resources, which enable the creation of mappings between information sources, are required to compensate for heterogeneity across namespaces. RESOURCE PAGE: http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/

User-Driven Quality Certification of Workplace Software, the UsersAward Experience

Science.gov (United States)

2004-06-01

the set of criteria and the chosen level of approval was sufficiently balanced . Furthermore, the fact that both software providers experienced... Worklife - Building Social Capacity - European Approaches, Edition sigma Berlin. Lind, T. (2002). IT-kartan, användare och IT-system i svenskt

Graphics processing units in bioinformatics, computational biology and systems biology.

Science.gov (United States)

Nobile, Marco S; Cazzaniga, Paolo; Tangherloni, Andrea; Besozzi, Daniela

2017-09-01

Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools. © The Author 2016. Published by Oxford University Press.

Dependability modeling and assessment in UML-based software development.

Science.gov (United States)

Bernardi, Simona; Merseguer, José; Petriu, Dorina C

2012-01-01

Assessment of software nonfunctional properties (NFP) is an important problem in software development. In the context of model-driven development, an emerging approach for the analysis of different NFPs consists of the following steps: (a) to extend the software models with annotations describing the NFP of interest; (b) to transform automatically the annotated software model to the formalism chosen for NFP analysis; (c) to analyze the formal model using existing solvers; (d) to assess the software based on the results and give feedback to designers. Such a modeling→analysis→assessment approach can be applied to any software modeling language, be it general purpose or domain specific. In this paper, we focus on UML-based development and on the dependability NFP, which encompasses reliability, availability, safety, integrity, and maintainability. The paper presents the profile used to extend UML with dependability information, the model transformation to generate a DSPN formal model, and the assessment of the system properties based on the DSPN results.

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

General Purpose Data-Driven Monitoring for Space Operations

Science.gov (United States)

Iverson, David L.; Martin, Rodney A.; Schwabacher, Mark A.; Spirkovska, Liljana; Taylor, William McCaa; Castle, Joseph P.; Mackey, Ryan M.

2009-01-01

As modern space propulsion and exploration systems improve in capability and efficiency, their designs are becoming increasingly sophisticated and complex. Determining the health state of these systems, using traditional parameter limit checking, model-based, or rule-based methods, is becoming more difficult as the number of sensors and component interactions grow. Data-driven monitoring techniques have been developed to address these issues by analyzing system operations data to automatically characterize normal system behavior. System health can be monitored by comparing real-time operating data with these nominal characterizations, providing detection of anomalous data signatures indicative of system faults or failures. The Inductive Monitoring System (IMS) is a data-driven system health monitoring software tool that has been successfully applied to several aerospace applications. IMS uses a data mining technique called clustering to analyze archived system data and characterize normal interactions between parameters. The scope of IMS based data-driven monitoring applications continues to expand with current development activities. Successful IMS deployment in the International Space Station (ISS) flight control room to monitor ISS attitude control systems has led to applications in other ISS flight control disciplines, such as thermal control. It has also generated interest in data-driven monitoring capability for Constellation, NASA's program to replace the Space Shuttle with new launch vehicles and spacecraft capable of returning astronauts to the moon, and then on to Mars. Several projects are currently underway to evaluate and mature the IMS technology and complementary tools for use in the Constellation program. These include an experiment on board the Air Force TacSat-3 satellite, and ground systems monitoring for NASA's Ares I-X and Ares I launch vehicles. The TacSat-3 Vehicle System Management (TVSM) project is a software experiment to integrate fault

PATTERN-BASED AND REUSE-DRIVEN ARCHITECTING OF MOBILE CLOUD SOFTWARE

OpenAIRE

Aakash Ahmad1 , Ahmed B. Altamimi1 , Abdulrahman Alreshidi1 , Mohammad T. Alshammari1 , Numra Saeed2 , Jamal M. Aqib1

2018-01-01

Context: Mobile Cloud Computing (MCC) represents the state-of-the-art technology that unifies mobile computing and cloud computing to develop systems that are portable yet resource sufficient. Mobile computing allows portable communication and context-aware computation, however, due to the energy and resource constraints mobile computing lacks performance for computationally intensive tasks. Cloud computing model uses the ‘as a service’ model - providing hardware and software services - to of...

PATTERN-BASED AND REUSE-DRIVEN ARCHITECTING OF MOBILE CLOUD SOFTWARE

OpenAIRE

Aakash Ahmad

2017-01-01

Context: Mobile Cloud Computing (MCC) represents the state-of-the-art technology that unifies mobile computing and cloud computing to develop systems that are portable yet resource sufficient. Mobile computing allows portable communication and context-aware computation, however, due to the energy and resource constraints mobile computing lacks performance for computationally intensive tasks. Cloud computing model uses the ‘as a service’ model - providing hardware and software services - to of...

Built To Last: Using Iterative Development Models for Sustainable Scientific Software Development

Science.gov (United States)

Jasiak, M. E.; Truslove, I.; Savoie, M.

2013-12-01

In scientific research, software development exists fundamentally for the results they create. The core research must take focus. It seems natural to researchers, driven by grant deadlines, that every dollar invested in software development should be used to push the boundaries of problem solving. This system of values is frequently misaligned with those of the software being created in a sustainable fashion; short-term optimizations create longer-term sustainability issues. The National Snow and Ice Data Center (NSIDC) has taken bold cultural steps in using agile and lean development and management methodologies to help its researchers meet critical deadlines, while building in the necessary support structure for the code to live far beyond its original milestones. Agile and lean software development and methodologies including Scrum, Kanban, Continuous Delivery and Test-Driven Development have seen widespread adoption within NSIDC. This focus on development methods is combined with an emphasis on explaining to researchers why these methods produce more desirable results for everyone, as well as promoting developers interacting with researchers. This presentation will describe NSIDC's current scientific software development model, how this addresses the short-term versus sustainability dichotomy, the lessons learned and successes realized by transitioning to this agile and lean-influenced model, and the current challenges faced by the organization.

Designing an economic-driven evaluation framework for process-oriented software technologies.

NARCIS (Netherlands)

Mutschler, B.B.; Bumiller, J.; Reichert, M.U.

2006-01-01

During the last decade there has been a dramatic increase in the number of paradigms, standards and tools that can be used to realize process-oriented information systems. A major problem neglected in software engineering research so far has been the systematic determination of costs, benefits, and

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....

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.

Configuring the Orion Guidance, Navigation, and Control Flight Software for Automated Sequencing

Science.gov (United States)

Odegard, Ryan G.; Siliwinski, Tomasz K.; King, Ellis T.; Hart, Jeremy J.

2010-01-01

The Orion Crew Exploration Vehicle is being designed with greater automation capabilities than any other crewed spacecraft in NASA s history. The Guidance, Navigation, and Control (GN&C) flight software architecture is designed to provide a flexible and evolvable framework that accommodates increasing levels of automation over time. Within the GN&C flight software, a data-driven approach is used to configure software. This approach allows data reconfiguration and updates to automated sequences without requiring recompilation of the software. Because of the great dependency of the automation and the flight software on the configuration data, the data management is a vital component of the processes for software certification, mission design, and flight operations. To enable the automated sequencing and data configuration of the GN&C subsystem on Orion, a desktop database configuration tool has been developed. The database tool allows the specification of the GN&C activity sequences, the automated transitions in the software, and the corresponding parameter reconfigurations. These aspects of the GN&C automation on Orion are all coordinated via data management, and the database tool provides the ability to test the automation capabilities during the development of the GN&C software. In addition to providing the infrastructure to manage the GN&C automation, the database tool has been designed with capabilities to import and export artifacts for simulation analysis and documentation purposes. Furthermore, the database configuration tool, currently used to manage simulation data, is envisioned to evolve into a mission planning tool for generating and testing GN&C software sequences and configurations. A key enabler of the GN&C automation design, the database tool allows both the creation and maintenance of the data artifacts, as well as serving the critical role of helping to manage, visualize, and understand the data-driven parameters both during software development

Cross-instrument Analysis Correlation Software

Energy Technology Data Exchange (ETDEWEB)

2017-06-28

This program has been designed to assist with the tracking of a sample from one analytical instrument to another such as SEM, microscopes, micro x-ray diffraction and other instruments where particular positions/locations on the sample are examined, photographed, etc. The software is designed to easily enter the position of fiducials and locations of interest such that in a future session in the same of different instrument the positions of interest can be re-found through using the known location fiducials in the current and reference session to transform the point into the current sessions coordinate system. The software is dialog box driven guiding the user through the necessary data entry and program choices. Information is stored in a series of text based extensible markup language (XML) files.

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

International Nuclear Information System (INIS)

Smith, W. Spencer; Koothoor, Mimitha

2016-01-01

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

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.

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…

OEDIPE, a software for personalized Monte Carlo dosimetry and treatment planning optimization in nuclear medicine: absorbed dose and biologically effective dose considerations

International Nuclear Information System (INIS)

Petitguillaume, A.; Broggio, D.; Franck, D.; Desbree, A.; Bernardini, M.; Labriolle Vaylet, C. de

2014-01-01

For targeted radionuclide therapies, treatment planning usually consists of the administration of standard activities without accounting for the patient-specific activity distribution, pharmacokinetics and dosimetry to organs at risk. The OEDIPE software is a user-friendly interface which has an automation level suitable for performing personalized Monte Carlo 3D dosimetry for diagnostic and therapeutic radionuclide administrations. Mean absorbed doses to regions of interest (ROIs), isodose curves superimposed on a personalized anatomical model of the patient and dose-volume histograms can be extracted from the absorbed dose 3D distribution. Moreover, to account for the differences in radiosensitivity between tumoral and healthy tissues, additional functionalities have been implemented to calculate the 3D distribution of the biologically effective dose (BED), mean BEDs to ROIs, isoBED curves and BED-volume histograms along with the Equivalent Uniform Biologically Effective Dose (EUD) to ROIs. Finally, optimization tools are available for treatment planning optimization using either the absorbed dose or BED distributions. These tools enable one to calculate the maximal injectable activity which meets tolerance criteria to organs at risk for a chosen fractionation protocol. This paper describes the functionalities available in the latest version of the OEDIPE software to perform personalized Monte Carlo dosimetry and treatment planning optimization in targeted radionuclide therapies. (authors)

Test-Driven Development as an Innovation Value Chain

Directory of Open Access Journals (Sweden)

Ana Paula Ress

2013-04-01

Full Text Available For all companies that consider their Information Technology Department to be of strategic value, it is important to incorporate an innovation value chain into their software development lifecycles to enhance their teams' performance. One model is TDD (Test-Driven Development, which is a process that detects failures and improves the productivity and quality of the team’s work. Data were collected from a Financial Company with 3,500 employees to demonstrate that software projects that require more than 4,000 hours of development benefit from TDD if a clear knowledge conversion step occurs between the client and the developers.

The iCub Software Architecture: evolution and lessons learned

Directory of Open Access Journals (Sweden)

Lorenzo eNatale

2016-04-01

Full Text Available The complexity of humanoid robots is increasing with the availability of new sensors, embedded CPUs and actuators. This wealth of technologies allows researchers to investigate new problems like whole-body force control, multi-modal human-robot interaction and sensory fusion. Under the hood of these robots, the software architecture has an important role: it allows researchers to get access to the robot functionalities focusing primarily on their research problems, it supports code reuse to minimize development and debugging, especially when new hardware becomes available. But more importantly it allows increasing the complexity of the experiments that can be implemented before system integration becomes unmanageable and debugging draws more resources than research itself.In this paper we illustrate the software architecture of the iCub humanoid robot and the software engineering best practices that have emerged driven by the needs of our research community. We describe the latest developments at the level of the middleware supporting interface definition and automatic code generation, logging, ROS compatibility and channel prioritization. We show the robot abstraction layer and how it has been modified to better address the requirements of the users and to support new hardware as it became available. We also describe the testing framework we have recently adopted for developing code using a test driven methodology. We conclude the paper discussing the lessons we have learned during the past eleven years of software development on the iCub humanoid robot.

Arena3D: visualizing time-driven phenotypic differences in biological systems

Directory of Open Access Journals (Sweden)

Secrier Maria

2012-03-01

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

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....

Software configuration management plan for the Hanford site technical database

International Nuclear Information System (INIS)

GRAVES, N.J.

1999-01-01

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

An ontology-driven semantic mash-up of gene and biological pathway information: Application to the domain of nicotine dependence

Science.gov (United States)

Sahoo, Satya S.; Bodenreider, Olivier; Rutter, Joni L.; Skinner, Karen J.; Sheth, Amit P.

2008-01-01

Objectives This paper illustrates how Semantic Web technologies (especially RDF, OWL, and SPARQL) can support information integration and make it easy to create semantic mashups (semantically integrated resources). In the context of understanding the genetic basis of nicotine dependence, we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base. Methods We use an ontology-driven approach to integrate two gene resources (Entrez Gene and HomoloGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans. We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources. The integrated schema is populated with data from the pathway resources, publicly available in BioPAX-compatible format, and gene resources for which a population procedure was created. The SPARQL query language is used to formulate queries over the integrated knowledge base to answer the three biological queries. Results Simple SPARQL queries could easily identify hub genes, i.e., those genes whose gene products participate in many pathways or interact with many other gene products. The identification of the genes expressed in the brain turned out to be more difficult, due to the lack of a common identification scheme for proteins. Conclusion Semantic Web technologies provide a valid framework for information integration in the life sciences. Ontology-driven integration represents a flexible, sustainable and extensible solution to the integration of large volumes of information. Additional resources, which enable the creation of mappings between information sources, are required to compensate for heterogeneity across namespaces. Resource page http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/ PMID:18395495

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.

A software communication tool for the tele-ICU.

Science.gov (United States)

Pimintel, Denise M; Wei, Shang Heng; Odor, Alberto

2013-01-01

The Tele Intensive Care Unit (tele-ICU) supports a high volume, high acuity population of patients. There is a high-volume of incoming and outgoing calls, especially during the evening and night hours, through the tele-ICU hubs. The tele-ICU clinicians must be able to communicate effectively to team members in order to support the care of complex and critically ill patients while supporting and maintaining a standard to improve time to intervention. This study describes a software communication tool that will improve the time to intervention, over the paper-driven communication format presently used in the tele-ICU. The software provides a multi-relational database of message instances to mine information for evaluation and quality improvement for all entities that touch the tele-ICU. The software design incorporates years of critical care and software design experience combined with new skills acquired in an applied Health Informatics program. This software tool will function in the tele-ICU environment and perform as a front-end application that gathers, routes, and displays internal communication messages for intervention by priority and provider.

Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping.

Science.gov (United States)

Busby, Ben; Lesko, Matthew; Federer, Lisa

2016-01-01

In genomics, bioinformatics and other areas of data science, gaps exist between extant public datasets and the open-source software tools built by the community to analyze similar data types.  The purpose of biological data science hackathons is to assemble groups of genomics or bioinformatics professionals and software developers to rapidly prototype software to address these gaps.  The only two rules for the NCBI-assisted hackathons run so far are that 1) data either must be housed in public data repositories or be deposited to such repositories shortly after the hackathon's conclusion, and 2) all software comprising the final pipeline must be open-source or open-use.  Proposed topics, as well as suggested tools and approaches, are distributed to participants at the beginning of each hackathon and refined during the event.  Software, scripts, and pipelines are developed and published on GitHub, a web service providing publicly available, free-usage tiers for collaborative software development. The code resulting from each hackathon is published at https://github.com/NCBI-Hackathons/ with separate directories or repositories for each team.

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

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

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...

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...

Executable Use Cases: a Supplement to Model-Driven Development?

DEFF Research Database (Denmark)

Jørgensen, Jens Bæk

2007-01-01

-level requirements and more technical software specifications. In MDD, userlevel requirements are not always explicitly described; it is sufficient for MDD that a specification, or platformindependent model, of the software that we are going to develop is provided. Therefore, a combination of EUCs and MDD may have......Executable Use Cases (EUCs) is a model-based approach to requirements engineering. In the introduction to this paper, we briefly discuss how EUCs may be used as a supplement to Model-Driven Development (MDD). Then we present the EUC approach in more detail. An EUC can describe and link user...... potential to cover the full software engineering path from user-level requirements via specifications to implementations of running computer systems....

Fiji: an open-source platform for biological-image analysis.

Science.gov (United States)

Schindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin; Kaynig, Verena; Longair, Mark; Pietzsch, Tobias; Preibisch, Stephan; Rueden, Curtis; Saalfeld, Stephan; Schmid, Benjamin; Tinevez, Jean-Yves; White, Daniel James; Hartenstein, Volker; Eliceiri, Kevin; Tomancak, Pavel; Cardona, Albert

2012-06-28

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

Virtual immunology: software for teaching basic immunology.

Science.gov (United States)

Berçot, Filipe Faria; Fidalgo-Neto, Antônio Augusto; Lopes, Renato Matos; Faggioni, Thais; Alves, Luiz Anastácio

2013-01-01

As immunology continues to evolve, many educational methods have found difficulty in conveying the degree of complexity inherent in its basic principles. Today, the teaching-learning process in such areas has been improved with tools such as educational software. This article introduces "Virtual Immunology," a software program available free of charge in Portuguese and English, which can be used by teachers and students in physiology, immunology, and cellular biology classes. We discuss the development of the initial two modules: "Organs and Lymphoid Tissues" and "Inflammation" and the use of interactive activities to provide microscopic and macroscopic understanding in immunology. Students, both graduate and undergraduate, were questioned along with university level professors about the quality of the software and intuitiveness of use, facility of navigation, and aesthetic organization using a Likert scale. An overwhelmingly satisfactory result was obtained with both students and immunology teachers. Programs such as "Virtual Immunology" are offering more interactive, multimedia approaches to complex scientific principles that increase student motivation, interest, and comprehension. © 2013 by The International Union of Biochemistry and Molecular Biology.

Test-driven verification/validation of model transformations

Institute of Scientific and Technical Information of China (English)

László LENGYEL; Hassan CHARAF

2015-01-01

Why is it important to verify/validate model transformations? The motivation is to improve the quality of the trans-formations, and therefore the quality of the generated software artifacts. Verified/validated model transformations make it possible to ensure certain properties of the generated software artifacts. In this way, verification/validation methods can guarantee different requirements stated by the actual domain against the generated/modified/optimized software products. For example, a verified/ validated model transformation can ensure the preservation of certain properties during the model-to-model transformation. This paper emphasizes the necessity of methods that make model transformation verified/validated, discusses the different scenarios of model transformation verification and validation, and introduces the principles of a novel test-driven method for verifying/ validating model transformations. We provide a solution that makes it possible to automatically generate test input models for model transformations. Furthermore, we collect and discuss the actual open issues in the field of verification/validation of model transformations.

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.

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

International Nuclear Information System (INIS)

Hsi, Wen C.; Zeidan, Omar A.; Law, Aaron; Schreuder, Andreas N.

2014-01-01

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

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

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

Science.gov (United States)

Hsi, Wen C; Law, Aaron; Schreuder, Andreas N; Zeidan, Omar A

2014-08-01

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. 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. 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 misalignments of GeoIso and RadIso in

CyberGIS software: a synthetic review and integration roadmap

Energy Technology Data Exchange (ETDEWEB)

Wang, Shaowen [University of Illinois, Urbana-Champaign; Anselin, Luc [Arizona State University; Bhaduri, Budhendra L [ORNL; Cosby, Christopher [University Navstar Consortium, Boulder, CO; Goodchild, Michael [University of California, Santa Barbara; Liu, Yan [University of Illinois, Urbana-Champaign; Nygers, Timothy L. [University of Washington, Seattle

2013-01-01

CyberGIS defined as cyberinfrastructure-based geographic information systems (GIS) has emerged as a new generation of GIS representing an important research direction for both cyberinfrastructure and geographic information science. This study introduces a 5-year effort funded by the US National Science Foundation to advance the science and applications of CyberGIS, particularly for enabling the analysis of big spatial data, computationally intensive spatial analysis and modeling (SAM), and collaborative geospatial problem-solving and decision-making, simultaneously conducted by a large number of users. Several fundamental research questions are raised and addressed while a set of CyberGIS challenges and opportunities are identified from scientific perspectives. The study reviews several key CyberGIS software tools that are used to elucidate a vision and roadmap for CyberGIS software research. The roadmap focuses on software integration and synthesis of cyberinfrastructure, GIS, and SAM by defining several key integration dimensions and strategies. CyberGIS, based on this holistic integration roadmap, exhibits the following key characteristics: high-performance and scalable, open and distributed, collaborative, service-oriented, user-centric, and community-driven. As a major result of the roadmap, two key CyberGIS modalities gateway and toolkit combined with a community-driven and participatory approach have laid a solid foundation to achieve scientific breakthroughs across many geospatial communities that would be otherwise impossible.

The ATLAS data management software engineering process

International Nuclear Information System (INIS)

Lassnig, M; Garonne, V; Stewart, G A; Barisits, M; Serfon, C; Goossens, L; Nairz, A; Beermann, T; Vigne, R; 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 highlight the social aspects of an environment where every action is subject to detailed scrutiny.

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.

Shaping Biological Knowledge: Applications in Proteomics

Directory of Open Access Journals (Sweden)

R. Appel

2006-04-01

Full Text Available The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since the laws governing protein folding and interactivity are not quite understood. In our effort to bring together independent pieces of information relative to proteins in a biologically meaningful way, we assess the bias of bioinformatics resources and consequent approximations in the framework of small-scale studies. We analyse proteomics data while following both a data-driven (focus on proteins smaller than 10 kDa and a hypothesis-driven (focus on whole bacterial proteomes approach. These applications are potentially the source of specialized complements to classical biological ontologies.

Shaping biological knowledge: applications in proteomics.

Science.gov (United States)

Lisacek, F; Chichester, C; Gonnet, P; Jaillet, O; Kappus, S; Nikitin, F; Roland, P; Rossier, G; Truong, L; Appel, R

2004-01-01

The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since the laws governing protein folding and interactivity are not quite understood. In our effort to bring together independent pieces of information relative to proteins in a biologically meaningful way, we assess the bias of bioinformatics resources and consequent approximations in the framework of small-scale studies. We analyse proteomics data while following both a data-driven (focus on proteins smaller than 10 kDa) and a hypothesis-driven (focus on whole bacterial proteomes) approach. These applications are potentially the source of specialized complements to classical biological ontologies.

Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite

Energy Technology Data Exchange (ETDEWEB)

Jurrus, Elizabeth [Pacific Northwest National Laboratory, Richland Washington; Engel, Dave [Pacific Northwest National Laboratory, Richland Washington; Star, Keith [Pacific Northwest National Laboratory, Richland Washington; Monson, Kyle [Pacific Northwest National Laboratory, Richland Washington; Brandi, Juan [Pacific Northwest National Laboratory, Richland Washington; Felberg, Lisa E. [University of California, Berkeley California; Brookes, David H. [University of California, Berkeley California; Wilson, Leighton [University of Michigan, Ann Arbor Michigan; Chen, Jiahui [Southern Methodist University, Dallas Texas; Liles, Karina [Pacific Northwest National Laboratory, Richland Washington; Chun, Minju [Pacific Northwest National Laboratory, Richland Washington; Li, Peter [Pacific Northwest National Laboratory, Richland Washington; Gohara, David W. [St. Louis University, St. Louis Missouri; Dolinsky, Todd [FoodLogiQ, Durham North Carolina; Konecny, Robert [University of California San Diego, San Diego California; Koes, David R. [University of Pittsburgh, Pittsburgh Pennsylvania; Nielsen, Jens Erik [Protein Engineering, Novozymes A/S, Copenhagen Denmark; Head-Gordon, Teresa [University of California, Berkeley California; Geng, Weihua [Southern Methodist University, Dallas Texas; Krasny, Robert [University of Michigan, Ann Arbor Michigan; Wei, Guo-Wei [Michigan State University, East Lansing Michigan; Holst, Michael J. [University of California San Diego, San Diego California; McCammon, J. Andrew [University of California San Diego, San Diego California; Baker, Nathan A. [Pacific Northwest National Laboratory, Richland Washington; Brown University, Providence Rhode Island

2017-10-24

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.

Towards an Experimental Framework for Measuring Usability of Model-Driven Tools

NARCIS (Netherlands)

Panach, Jose Ignacio; Condori-Fernandez, Nelly; Baar, Arthur; Vos, Tanja; Romeu, Ignacio; Pastor, Oscar; Campos, Pedro; Graham, Nicholas; Jorge, Joaquim; Nunes, Nuno; Palanque, Philippe; Winckler, Marco

2011-01-01

According to the Model-Driven Development (MDD) paradigm, analysts can substantially improve the software development process concentrating their efforts on a conceptual model, which can be transformed into code by means of transformation rules applied by a model compiler. However, MDD tools are not

Elsevier special issue on foundations and applications of model driven architecture

NARCIS (Netherlands)

Aksit, Mehmet; Ivanov, Ivan

2008-01-01

Model Driven Architecture (MDA) is an approach for software development proposed by Object Management Group (OMG). The basic principle of MDA is the separation of the specification of system functionality from the specification of the implementation of that functionality on a specific platform. The

The metal-driven biogeochemistry of gaseous compounds in the environment

CERN Document Server

Kroneck, Peter MH

2014-01-01

MILS-14 provides a most up-to-date view of the exciting biogeochemistry of gases in our environment as driven mostly by microorganisms. These employ a machinery of sophisticated metalloenzymes, where especially transition metals (such as Fe, Ni, Cu, Mo, W) play a fundamental role, that is, in the activation, transformation and syntheses of gases like dihydrogen, methane, carbon monoxide, acetylene and those of the biological nitrogen and sulfur cycles. The Metal-Driven Biogeochemistry of Gaseous Compounds in the Environment is a vibrant research area based mainly on structural and microbial biology, inorganic biological chemistry and environmental biochemistry. All this is covered in an authoritative manner in 11 stimulating chapters, written by 26 internationally recognized experts and supported by nearly 1200 references, informative tables and about 100 illustrations (two thirds in color). MILS-14 also provides excellent information for teaching. Peter M. H. Kroneck is a bioinorganic chemist who is explorin...

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...

EELS data acquisition, processing and display for the Zeiss CEM 902 based on LOTUS 1-2-3: application examples from a biological system and inorganic transition metal compounds.

Science.gov (United States)

Drechsler, M; Cantow, H J

1991-04-01

A personal computer combined with LOTUS 1-2-3 software, including the RS232 module of LOTUS MEASURE and a 12-bit ADC, has been used for data acquisition of electron energy-loss spectroscopy (EELS) spectra with the Zeiss CEM 902. The internal macro language of LOTUS 1-2-3 allows a menu-driven procedure. Macro-programs partly combined with external FORTRAN programs can be chosen from the menu for background subtraction, removal of multiple scattering effects by deconvolution, elemental quantification and several utilities. For special applications or conditions the macro programs can easily be modified. Spectra from crystals of two inorganic transition metal compounds, ruthenium trichloride and vanadium disulphide, and from a biological sample are presented as examples of the application of this software.

78 FR 75362 - Notice of Issuance of Final Determination Concerning Docave Computer Software

Science.gov (United States)

2013-12-11

... designed by a U.S. project engineer with many years of experience in ``designing and building hardware... design concept and user- driven features of the software are the result of work performed in the U.S...

The ATLAS software installation system for LCG/EGEE

Energy Technology Data Exchange (ETDEWEB)

Salvo, A D [Istituto Nazionale di Fisica Nucleare, sez. Roma 1 (Italy); Barchiesi, A [Universita di Roma I ' La Sapienza' (Italy); Gnanvo, K [Queen Mary and Westfield College (United Kingdom); Gwilliam, C [University of Liverpool (United Kingdom); Kennedy, J; Krobath, G [Ludwig-Maximilians-Universitaet Muenchen (Germany); Olszewski, A [Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences (Poland); Rybkine, G [Royal Holloway College (United Kingdom)

2008-07-15

The huge amount of resources available in the Grids, and the necessity to have the most up-to-date experimental software deployed in all the sites within a few hours, have driven the need for an automatic installation system for the LHC experiments. In this work we describe the ATLAS system for the experiment software installation in LCG/EGEE, based on the Light Job Submission Framework for Installation (LJSFi), an independent job submission framework for generic submission and job tracking in EGEE. LJSFi is able to automatically discover, check, install, test and tag the full set of resources made available in LCG/EGEE to the ATLAS Virtual Organization in a few hours, depending on the site availability.

DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts.

Science.gov (United States)

Czerwinska, Urszula; Calzone, Laurence; Barillot, Emmanuel; Zinovyev, Andrei

2015-08-14

Visualization and analysis of molecular profiling data together with biological networks are able to provide new mechanistic insights into biological functions. Currently, it is possible to visualize high-throughput data on top of pre-defined network layouts, but they are not always adapted to a given data analysis task. A network layout based simultaneously on the network structure and the associated multidimensional data might be advantageous for data visualization and analysis in some cases. We developed a Cytoscape app, which allows constructing biological network layouts based on the data from molecular profiles imported as values of node attributes. DeDaL is a Cytoscape 3 app, which uses linear and non-linear algorithms of dimension reduction to produce data-driven network layouts based on multidimensional data (typically gene expression). DeDaL implements several data pre-processing and layout post-processing steps such as continuous morphing between two arbitrary network layouts and aligning one network layout with respect to another one by rotating and mirroring. The combination of all these functionalities facilitates the creation of insightful network layouts representing both structural network features and correlation patterns in multivariate data. We demonstrate the added value of applying DeDaL in several practical applications, including an example of a large protein-protein interaction network. DeDaL is a convenient tool for applying data dimensionality reduction methods and for designing insightful data displays based on data-driven layouts of biological networks, built within Cytoscape environment. DeDaL is freely available for downloading at http://bioinfo-out.curie.fr/projects/dedal/.

Automated Creation of Datamarts from a Clinical Data Warehouse, Driven by an Active Metadata Repository

Science.gov (United States)

Rogerson, Charles L.; Kohlmiller, Paul H.; Stutman, Harris

1998-01-01

A methodology and toolkit are described which enable the automated metadata-driven creation of datamarts from clinical data warehouses. The software uses schema-to-schema transformation driven by an active metadata repository. Tools for assessing datamart data quality are described, as well as methods for assessing the feasibility of implementing specific datamarts. A methodology for data remediation and the re-engineering of operational data capture is described.

Migrating C/C++ Software to Mobile Platforms in the ADM Context

Directory of Open Access Journals (Sweden)

Liliana Martinez

2017-03-01

Full Text Available Software technology is constantly evolving and therefore the development of applications requires adapting software components and applications in order to be aligned to new paradigms such as Pervasive Computing, Cloud Computing and Internet of Things. In particular, many desktop software components need to be migrated to mobile technologies. This migration faces many challenges due to the proliferation of different mobile platforms. Developers usually make applications tailored for each type of device expending time and effort. As a result, new programming languages are emerging to integrate the native behaviors of the different platforms targeted in development projects. In this direction, the Haxe language allows writing mobile applications that target all major mobile platforms. Novel technical frameworks for information integration and tool interoperability such as Architecture-Driven Modernization (ADM proposed by the Object Management Group (OMG can help to manage a huge diversity of mobile technologies. The Architecture-Driven Modernization Task Force (ADMTF was formed to create specifications and promote industry consensus on the modernization of existing applications. In this work, we propose a migration process from C/C++ software to different mobile platforms that integrates ADM standards with Haxe. We exemplify the different steps of the process with a simple case study, the migration of “the Set of Mandelbrot” C++ application. The proposal was validated in Eclipse Modeling Framework considering that some of its tools and run-time environments are aligned with ADM standards.

Composable Framework Support for Software-FMEA Through Model Execution

Science.gov (United States)

Kocsis, Imre; Patricia, Andras; Brancati, Francesco; Rossi, Francesco

2016-08-01

Performing Failure Modes and Effect Analysis (FMEA) during software architecture design is becoming a basic requirement in an increasing number of domains; however, due to the lack of standardized early design phase model execution, classic SW-FMEA approaches carry significant risks and are human effort-intensive even in processes that use Model-Driven Engineering.Recently, modelling languages with standardized executable semantics have emerged. Building on earlier results, this paper describes framework support for generating executable error propagation models from such models during software architecture design. The approach carries the promise of increased precision, decreased risk and more automated execution for SW-FMEA during dependability- critical system development.

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).

Model-driven design, simulation and implementation of service compositions in COSMO

NARCIS (Netherlands)

Quartel, Dick; Dirgahayu, T.; van Sinderen, Marten J.

2009-01-01

The success of software development projects to a large extent depends on the quality of the models that are produced in the development process, which in turn depends on the conceptual and practical support that is available for modelling, design and analysis. This paper focuses on model-driven

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.

Molecular Cloning Designer Simulator (MCDS): All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects.

Science.gov (United States)

Shi, Zhenyu; Vickers, Claudia E

2016-12-01

Molecular Cloning Designer Simulator (MCDS) is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1) it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2) it can perform a user-defined workflow of cloning steps in a single execution of the software; (3) it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4) it includes experimental information to conveniently guide wet lab work; and (5) it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com.

The VAXONLINE software system at Fermilab

International Nuclear Information System (INIS)

White, V.; Heinicke, P.; Berman, E.

1987-06-01

The VAXONLINE software system, started in late 1984, is now in use at 12 experiments at Fermilab, with at least one VAX or MicroVax. Data acquisition features now provide for the collection and combination of data from one or more sources, via a list-driven Event Builder program. Supported sources include CAMAC, FASTBUS, Front-end PDP-11's, Disk, Tape, DECnet, and other processors running VAXONLINE. This paper describes the functionality provided by the VAXONLINE system, gives performance figures, and discusses the ongoing program of enhancements

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.

Automated analyses of model-driven artifacts : obtaining insights into industrial application of MDE

NARCIS (Netherlands)

Mengerink, J.G.M.; Serebrenik, A.; Schiffelers, R.R.H.; van den Brand, M.G.J.

2017-01-01

Over the past years, there has been an increase in the application of model driven engineering in industry. Similar to traditional software engineering, understanding how technologies are actually used in practice is essential for developing good tooling, and decision making processes.

Development of a methodology for assessing the safety of embedded software systems

Science.gov (United States)

Garrett, C. J.; Guarro, S. B.; Apostolakis, G. E.

1993-01-01

A Dynamic Flowgraph Methodology (DFM) based on an integrated approach to modeling and analyzing the behavior of software-driven embedded systems for assessing and verifying reliability and safety is discussed. DFM is based on an extension of the Logic Flowgraph Methodology to incorporate state transition models. System models which express the logic of the system in terms of causal relationships between physical variables and temporal characteristics of software modules are analyzed to determine how a certain state can be reached. This is done by developing timed fault trees which take the form of logical combinations of static trees relating the system parameters at different point in time. The resulting information concerning the hardware and software states can be used to eliminate unsafe execution paths and identify testing criteria for safety critical software functions.

Construction of UML class diagram with Model-Driven Development

Directory of Open Access Journals (Sweden)

Tomasz Górski

2016-03-01

Full Text Available Model transformations play a key role in software development projects based on Model--Driven Development (MDD principles. Transformations allow for automation of repetitive and well-defined steps, thus shortening design time and reducing a number of errors. In the object-oriented approach, the key elements are use cases. They are described, modelled and later designed until executable application code is obtained. The aim of the paper is to present transformation of a model-to-model type, Communication-2-Class, which automates construction of Unified Modelling Language (UML class diagram in the context of the analysis/design model. An UML class diagram is created based on UML communication diagram within use case realization. As a result, a class diagram shows all of the classes involved in the use case realization and the relationships among them. The plug-in which implements Communication-2-Class transformation was implemented in the IBM Rational Software Architect. The article presents the tests results of developed plug-in, which realizes Communication-2-Class transformation, showing capabilities of shortening use case realization’s design time.[b]Keywords[/b]: Model-Driven Development, transformations, Unified Modelling Language, analysis/design model, UML class diagram, UML communication diagram

Software Updating in Wireless Sensor Networks: A Survey and Lacunae

Directory of Open Access Journals (Sweden)

Cormac J. Sreenan

2013-11-01

Full Text Available Wireless Sensor Networks are moving out of the laboratory and into the field. For a number of reasons there is often a need to update sensor node software, or node configuration, after deployment. The need for over-the-air updates is driven both by the scale of deployments, and by the remoteness and inaccessibility of sensor nodes. This need has been recognized since the early days of sensor networks, and research results from the related areas of mobile networking and distributed systems have been applied to this area. In order to avoid any manual intervention, the update process needs to be autonomous. This paper presents a comprehensive survey of software updating in Wireless Sensor Networks, and analyses the features required to make these updates autonomous. A new taxonomy of software update features and a new model for fault detection and recovery are presented. The paper concludes by identifying the lacunae relating to autonomous software updates, providing direction for future research.

STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

KAUST Repository

Klingbeil, G.

2011-02-25

Motivation: The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. Results: The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user\\'s models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. © The Author 2011. Published by Oxford University Press. All rights reserved.

Top 10 metrics for life science software good practices [version 1; referees: 2 approved

Directory of Open Access Journals (Sweden)

Haydee Artaza

2016-08-01

Full Text Available Metrics for assessing adoption of good development practices are a useful way to ensure that software is sustainable, reusable and functional. Sustainability means that the software used today will be available - and continue to be improved and supported - in the future. We report here an initial set of metrics that measure good practices in software development. This initiative differs from previously developed efforts in being a community-driven grassroots approach where experts from different organisations propose good software practices that have reasonable potential to be adopted by the communities they represent. We not only focus our efforts on understanding and prioritising good practices, we assess their feasibility for implementation and publish them here.

Incubator Display Software Cost Reduction Toolset Software Requirements Specification

Science.gov (United States)

Moran, Susanne; Jeffords, Ralph

2005-01-01

The Incubator Display Software Requirements Specification was initially developed by Intrinsyx Technologies Corporation (Intrinsyx) under subcontract to Lockheed Martin, Contract Number NAS2-02090, for the National Aeronautics and Space Administration (NASA) Ames Research Center (ARC) Space Station Biological Research Project (SSBRP). The Incubator Display is a User Payload Application (UPA) used to control an Incubator subrack payload for the SSBRP. The Incubator Display functions on-orbit as part of the subrack payload laptop, on the ground as part of the Communication and Data System (CDS) ground control system, and also as part of the crew training environment.

A Pattern Language for the Evolution of Component-based Software Architectures

DEFF Research Database (Denmark)

Ahmad, Aakash; Jamshidi, Pooyan; Pahl, Claus

2013-01-01

Modern software systems are prone to a continuous evolution under frequently varying requirements. Architecture-centric software evolution enables change in system’s structure and behavior while maintaining a global view of the software to address evolution-centric tradeoffs. Lehman’s law...... evolution problems. We propose that architectural evolution process requires an explicit evolution-centric knowledge – that can be discovered, shared, and reused – to anticipate and guide change management. Therefore, we present a pattern language as a collection of interconnected change patterns......) as a complementary and integrated phase to facilitate reuse-driven architecture change execution (pattern language application). Reuse-knowledge in the proposed pattern language is expressed as a formalised collection of interconnected-patterns. Individual patterns in the language build on each other to facilitate...

A Model-driven and Service-oriented framework for the business process improvement

Directory of Open Access Journals (Sweden)

Andrea Delgado

2010-07-01

Full Text Available Business Process Management (BPM importance and benefits for organizations to focus on their business processes is nowadays broadly recognized, as business and technology areas are embracing and adopting the paradigm. The Service Oriented Computing (SOC paradigm bases software development on services to realize business processes. The implementation of business processes as services helps in reducing the gap between these two areas, easing the communication and understanding of business needs. The Model Driven Development (MDD paradigm bases software development in models, metamodels and languages that allow transformation between them. The automatic generation of service models from business process models is a key issue to support the separation of its definition from its technical implementation. In this article, we present MINERVA framework which applies Model Driven Development (MDD and Service Oriented Computing (SOC paradigms to business processes for the continuous business process improvement in organizations, giving support to the stages defined in the business process lifecycle from modeling to evaluation of its execution.

Formal Model-Driven Engineering: Generating Data and Behavioural Components

Directory of Open Access Journals (Sweden)

Chen-Wei Wang

2012-12-01

Full Text Available Model-driven engineering is the automatic production of software artefacts from abstract models of structure and functionality. By targeting a specific class of system, it is possible to automate aspects of the development process, using model transformations and code generators that encode domain knowledge and implementation strategies. Using this approach, questions of correctness for a complex, software system may be answered through analysis of abstract models of lower complexity, under the assumption that the transformations and generators employed are themselves correct. This paper shows how formal techniques can be used to establish the correctness of model transformations used in the generation of software components from precise object models. The source language is based upon existing, formal techniques; the target language is the widely-used SQL notation for database programming. Correctness is established by giving comparable, relational semantics to both languages, and checking that the transformations are semantics-preserving.

SpaceWire Driver Software for Special DSPs

Science.gov (United States)

Clark, Douglas; Lux, James; Nishimoto, Kouji; Lang, Minh

2003-01-01

A computer program provides a high-level C-language interface to electronics circuitry that controls a SpaceWire interface in a system based on a space qualified version of the ADSP-21020 digital signal processor (DSP). SpaceWire is a spacecraft-oriented standard for packet-switching data-communication networks that comprise nodes connected through bidirectional digital serial links that utilize low-voltage differential signaling (LVDS). The software is tailored to the SMCS-332 application-specific integrated circuit (ASIC) (also available as the TSS901E), which provides three highspeed (150 Mbps) serial point-to-point links compliant with the proposed Institute of Electrical and Electronics Engineers (IEEE) Standard 1355.2 and equivalent European Space Agency (ESA) Standard ECSS-E-50-12. In the specific application of this software, the SpaceWire ASIC was combined with the DSP processor, memory, and control logic in a Multi-Chip Module DSP (MCM-DSP). The software is a collection of low-level driver routines that provide a simple message-passing application programming interface (API) for software running on the DSP. Routines are provided for interrupt-driven access to the two styles of interface provided by the SMCS: (1) the "word at a time" conventional host interface (HOCI); and (2) a higher performance "dual port memory" style interface (COMI).

A Chado case study: an ontology-based modular schema for representing genome-associated biological information.

Science.gov (United States)

Mungall, Christopher J; Emmert, David B

2007-07-01

A few years ago, FlyBase undertook to design a new database schema to store Drosophila data. It would fully integrate genomic sequence and annotation data with bibliographic, genetic, phenotypic and molecular data from the literature representing a distillation of the first 100 years of research on this major animal model system. In developing this new integrated schema, FlyBase also made a commitment to ensure that its design was generic, extensible and available as open source, so that it could be employed as the core schema of any model organism data repository, thereby avoiding redundant software development and potentially increasing interoperability. Our question was whether we could create a relational database schema that would be successfully reused. Chado is a relational database schema now being used to manage biological knowledge for a wide variety of organisms, from human to pathogens, especially the classes of information that directly or indirectly can be associated with genome sequences or the primary RNA and protein products encoded by a genome. Biological databases that conform to this schema can interoperate with one another, and with application software from the Generic Model Organism Database (GMOD) toolkit. Chado is distinctive because its design is driven by ontologies. The use of ontologies (or controlled vocabularies) is ubiquitous across the schema, as they are used as a means of typing entities. The Chado schema is partitioned into integrated subschemas (modules), each encapsulating a different biological domain, and each described using representations in appropriate ontologies. To illustrate this methodology, we describe here the Chado modules used for describing genomic sequences. GMOD is a collaboration of several model organism database groups, including FlyBase, to develop a set of open-source software for managing model organism data. The Chado schema is freely distributed under the terms of the Artistic License (http

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

Swarming Robot Design, Construction and Software Implementation

Science.gov (United States)

Stolleis, Karl A.

2014-01-01

In this paper is presented an overview of the hardware design, construction overview, software design and software implementation for a small, low-cost robot to be used for swarming robot development. In addition to the work done on the robot, a full simulation of the robotic system was developed using Robot Operating System (ROS) and its associated simulation. The eventual use of the robots will be exploration of evolving behaviors via genetic algorithms and builds on the work done at the University of New Mexico Biological Computation Lab.

STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB.

Science.gov (United States)

Klingbeil, Guido; Erban, Radek; Giles, Mike; Maini, Philip K

2011-04-15

The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user's models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. The software is open source under the GPL v3 and available at http://www.maths.ox.ac.uk/cmb/STOCHSIMGPU. The web site also contains supplementary information. klingbeil@maths.ox.ac.uk Supplementary data are available at Bioinformatics online.

Global Software Development: A Review of the State-Of-The-Art (2007-2011)

DEFF Research Database (Denmark)

Ali Babar, Muhammad; Zahedi, Mansooreh

a state-of-the-art review of the GSD research literature published in the main venue of Global Software Engineering in order to identify the main research trends and gaps that needs to be filled by future research. We were also interested placing the findings of our review with respect to a practice......-driven GSD research agenda. Method: We used structured literature review methodology for which we decided to select and review the recently published research papers (i.e., 2007 - 2011) from the International Conference in Global Software Engineering (ICGSE). We used a framework for organizing GSD research...... challenges and threats and a practice-driven research agenda for extracting and organizing the data from the reviewed papers. We used theoretical reasoning for classifying the reviewed papers under different categories, which were mainly based on the framework, a decision that also enabled us to propose...

Radiobiological modelling with MarCell software

International Nuclear Information System (INIS)

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

1996-01-01

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

EPRI engineering workstation software - Discussion and demonstration

International Nuclear Information System (INIS)

Stewart, R.P.; Peterson, C.E.; Agee, L.J.

1992-01-01

Computing technology is undergoing significant changes with respect to engineering applications in the electric utility industry. These changes result mainly from the introduction of several UNIX workstations that provide mainframe calculational capability at much lower costs. The workstations are being coupled with microcomputers through local area networks to provide engineering groups with a powerful and versatile analysis capability. PEGASYS, the Professional Engineering Graphic Analysis System, is a software package for use with engineering analysis codes executing in a workstation environment. PEGASYS has a menu driven, user-friendly interface to provide pre-execution support for preparing unput and graphical packages for post-execution analysis and on-line monitoring capability for engineering codes. The initial application of this software is for use with RETRAN-02 operating on an IBM RS/6000 workstation using X-Windows/UNIX and a personal computer under DOS

Integrating systems biology models and biomedical ontologies.

Science.gov (United States)

Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

2011-08-11

Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

The NOvA software testing framework

International Nuclear Information System (INIS)

Tamsett, M; Group, C

2015-01-01

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. (paper)

An optimized workflow for the integration of biological information into radiotherapy planning: experiences with T1w DCE-MRI

International Nuclear Information System (INIS)

Neff, T; Kiessling, F; Brix, G; Baudendistel, K; Zechmann, C; Giesel, F L; Bendl, R

2005-01-01

Planning of radiotherapy is often difficult due to restrictions on morphological images. New imaging techniques enable the integration of biological information into treatment planning and help to improve the detection of vital and aggressive tumour areas. This might improve clinical outcome. However, nowadays morphological data sets are still the gold standard in the planning of radiotherapy. In this paper, we introduce an in-house software platform enabling us to combine images from different imaging modalities yielding biological and morphological information in a workflow driven approach. This is demonstrated for the combination of morphological CT, MRI, functional DCE-MRI and PET data. Data of patients with a tumour of the prostate and with a meningioma were examined with DCE-MRI by applying pharmacokinetic two-compartment models for post-processing. The results were compared with the clinical plans for radiation therapy. Generated parameter maps give additional information about tumour spread, which can be incorporated in the definition of safety margins

SOFTWARE OPEN SOURCE, SOFTWARE GRATIS?

Directory of Open Access Journals (Sweden)

Nur Aini Rakhmawati

2006-01-01

Full Text Available Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 Berlakunya Undang – undang Hak Atas Kekayaan Intelektual (HAKI, memunculkan suatu alternatif baru untuk menggunakan software open source. Penggunaan software open source menyebar seiring dengan isu global pada Information Communication Technology (ICT saat ini. Beberapa organisasi dan perusahaan mulai menjadikan software open source sebagai pertimbangan. Banyak konsep mengenai software open source ini. Mulai dari software yang gratis sampai software tidak berlisensi. Tidak sepenuhnya isu software open source benar, untuk itu perlu dikenalkan konsep software open source mulai dari sejarah, lisensi dan bagaimana cara memilih lisensi, serta pertimbangan dalam memilih software open source yang ada. Kata kunci :Lisensi, Open Source, HAKI

The D OE software trigger

International Nuclear Information System (INIS)

Linnemann, J.T.; Michigan State Univ., East Lansing, MI

1992-10-01

In the D OE experiment, the software filter operates in a processor farm with each node processing a single event. Processing is data-driven: the filter does local processing to verify the candidates from the hardware trigger. The filter code consists of independent pieces called ''tools''; processing for a given hardware bit is a ''script'' invoking one or more ''tools'' sequentially. An offline simulator drives the same code with the same configuration files, running on real or simulated data. Online tests use farm nodes parasiting on the data stream. We discuss the performance of the system and how we attempt to verify its correctness

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

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

Science.gov (United States)

2012-01-01

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<0.05) gene targets in BRM indicates that nicotine exposure disrupts genes involved in neurogenesis, possibly through misregulation of nicotine-sensitive miRNAs. 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

Pascal software structures achieve definite control of the 24 MFTF sustaining neutral-beam power supplies

International Nuclear Information System (INIS)

Anon.

1982-01-01

Precise control of large, complex systems is not assured unless there is known to be no unintended interactions in the control system. The software controlling the sustaining neutral-beam power supplies of the Mirror Fusion Test Facility accomplishes this feat. The software structures comprise some 16,000 lines of commented Pascal code, distributed amoung 10 different tasks. Each task may control any of the 24 power supplies. All the tasks are strictly event-driven, and are not subject to any system mode. Since there is no global information in the software, we know that all the power supplies are controlled independently

Implementation of 252Cf-source-driven power spectrum density measurement system

International Nuclear Information System (INIS)

Ren Yong; Wei Biao; Feng Peng; Li Jiansheng; Ye Cenming

2012-01-01

The principle of 252 Cf-source-driven power spectrum density measurement method is introduced. A measurement system and platform is realized accordingly, which is a combination of hardware and software, for measuring nuclear parameters. The detection method of neutron pulses based on an ultra-high-speed data acquisition card (three channels, 1 GHz sampling rate, 1 ns synchronization) is described, and the data processing process and the power spectrum density algorithm on PC are designed. This 252 Cf-source-driven power spectrum density measurement system can effectively obtain the nuclear tag parameters of nuclear random processes, such as correlation function and power spectrum density. (authors)

A program code generator for multiphysics biological simulation using markup languages.

Science.gov (United States)

Amano, Akira; Kawabata, Masanari; Yamashita, Yoshiharu; Rusty Punzalan, Florencio; Shimayoshi, Takao; Kuwabara, Hiroaki; Kunieda, Yoshitoshi

2012-01-01

To cope with the complexity of the biological function simulation models, model representation with description language is becoming popular. However, simulation software itself becomes complex in these environment, thus, it is difficult to modify the simulation conditions, target computation resources or calculation methods. In the complex biological function simulation software, there are 1) model equations, 2) boundary conditions and 3) calculation schemes. Use of description model file is useful for first point and partly second point, however, third point is difficult to handle for various calculation schemes which is required for simulation models constructed from two or more elementary models. We introduce a simulation software generation system which use description language based description of coupling calculation scheme together with cell model description file. By using this software, we can easily generate biological simulation code with variety of coupling calculation schemes. To show the efficiency of our system, example of coupling calculation scheme with three elementary models are shown.

Thermochemical performance analysis of solar driven CO_2 methane reforming

International Nuclear Information System (INIS)

Fuqiang, Wang; Jianyu, Tan; Huijian, Jin; Yu, Leng

2015-01-01

Increasing CO_2 emission problems create urgent challenges for alleviating global warming, and the capture of CO_2 has become an essential field of scientific research. In this study, a finite volume method (FVM) coupled with thermochemical kinetics was developed to analyze the solar driven CO_2 methane reforming process in a metallic foam reactor. The local thermal non-equilibrium (LTNE) model coupled with radiative heat transfer was developed to provide more temperature information. A joint inversion method based on chemical process software and the FVM coupled with thermochemical kinetics was developed to obtain the thermochemical reaction parameters and guarantee the calculation accuracy. The detailed thermal and thermochemical performance in the metal foam reactor was analyzed. In addition, the effects of heat flux distribution and porosity on the solar driven CO_2 methane reforming process were analyzed. The numerical results can serve as theoretical guidance for the solar driven CO_2 methane reforming application. - Highlights: • Solar driven CO_2 methane reforming process in metal foam reactor is analyzed. • FVM with chemical reactions was developed to analyze solar CO_2 methane reforming. • A joint inversion method was developed to obtain thermochemical reaction parameters. • Results can be a guidance for the solar driven CO_2 methane reforming application.

Software design space exploration for exascale combustion co-design

Energy Technology Data Exchange (ETDEWEB)

Chan, Cy [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Unat, Didem [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Lijewski, Michael [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Zhang, Weiqun [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Bell, John [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Shalf, John [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

2013-09-26

The design of hardware for next-generation exascale computing systems will require a deep understanding of how software optimizations impact hardware design trade-offs. In order to characterize how co-tuning hardware and software parameters affects the performance of combustion simulation codes, we created ExaSAT, a compiler-driven static analysis and performance modeling framework. Our framework can evaluate hundreds of hardware/software configurations in seconds, providing an essential speed advantage over simulators and dynamic analysis techniques during the co-design process. Our analytic performance model shows that advanced code transformations, such as cache blocking and loop fusion, can have a significant impact on choices for cache and memory architecture. Our modeling helped us identify tuned configurations that achieve a 90% reduction in memory traffic, which could significantly improve performance and reduce energy consumption. These techniques will also be useful for the development of advanced programming models and runtimes, which must reason about these optimizations to deliver better performance and energy efficiency.

Biosecurity and Open-Source Biology: The Promise and Peril of Distributed Synthetic Biological Technologies.

Science.gov (United States)

Evans, Nicholas G; Selgelid, Michael J

2015-08-01

In this article, we raise ethical concerns about the potential misuse of open-source biology (OSB): biological research and development that progresses through an organisational model of radical openness, deskilling, and innovation. We compare this organisational structure to that of the open-source software model, and detail salient ethical implications of this model. We demonstrate that OSB, in virtue of its commitment to openness, may be resistant to governance attempts.

Towards Analysis-Driven Scientific Software Architecture: The Case for Abstract Data Type Calculus

Directory of Open Access Journals (Sweden)

Damian W.I. Rouson

2008-01-01

Full Text Available This article approaches scientific software architecture from three analytical paths. Each path examines discrete time advancement of multiphysics phenomena governed by coupled differential equations. The new object-oriented Fortran 2003 constructs provide a formal syntax for an abstract data type (ADT calculus. The first analysis uses traditional object-oriented software design metrics to demonstrate the high cohesion and low coupling associated with the calculus. A second analysis from the viewpoint of computational complexity theory demonstrates that a more representative bug search strategy than that considered by Rouson et al. (ACM Trans. Math. Soft. 34(1 (2008 reduces the number of lines searched in a code with λ total lines from O(λ2 to O(λ log2 λ , which in turn becomes nearly independent of the overall code size in the context of ADT calculus. The third analysis derives from information theory an argument that ADT calculus simplifies developer communications in part by minimizing the growth in interface information content as developers add new physics to a multiphysics package.

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.

Science.gov (United States)

Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H L; Onami, Shuichi

2015-04-01

Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Combining Capability Assessment and Value Engineering: a New Two-dimensional Method for Software Process Improvement

Directory of Open Access Journals (Sweden)

Pasi Ojala

2008-02-01

Full Text Available During the last decades software process improvement (SPI has been recognized as a usable possibility to increase the quality of software development. Implemented SPI investments have often indicated increased process capabilities as well. Recently more attention has been focused on the costs of SPI as well as on the cost-effectiveness and productivity of software development, although the roots of economic-driven software engineering originate from the very early days of software engineering research. This research combines Value Engineering and capability assessment into usable new method in order to better respond to the challenges that cost-effectiveness and productivity has brought to software companies. This is done in part by defining the concepts of value, worth and cost and in part by defining the Value Engineering process and different enhancements it has seen to offer to software assessment. The practical industrial cases show that proposed two-dimensional method works in practise and is useful to assessed companies.

Symmetry breaking in clogging for oppositely driven particles

Science.gov (United States)

Glanz, Tobias; Wittkowski, Raphael; Löwen, Hartmut

2016-11-01

The clogging behavior of a symmetric binary mixture of colloidal particles that are driven in opposite directions through constrictions is explored by Brownian dynamics simulations and theory. A dynamical state with a spontaneously broken symmetry occurs where one species is flowing and the other is blocked for a long time, which can be tailored by the size of the constrictions. Moreover, we find self-organized oscillations in clogging and unclogging of the two species. Apart from statistical physics, our results are of relevance for fields like biology, chemistry, and crowd management, where ions, microparticles, pedestrians, or other particles are driven in opposite directions through constrictions.

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

Science.gov (United States)

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

2013-12-01

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

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

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.

D-VASim: A Software Tool to Simulate and Analyze Genetic Logic Circuits

DEFF Research Database (Denmark)

Baig, Hasan; Madsen, Jan

2016-01-01

-stage researchers with limited experience in the field of biology. The Solution: Using LabVIEW to develop a user-friendly simulation tool named Dynamic Virtual Analyzer and Simulator (D-VASim), which is the first software tool in the domain of synthetic biology that provides a virtual laboratory environment...

Physical mechanisms of biological molecular motors

International Nuclear Information System (INIS)

Miller, John H. Jr.; Vajrala, Vijayanand; Infante, Hans L.; Claycomb, James R.; Palanisami, Akilan; Fang Jie; Mercier, George T.

2009-01-01

Biological motors generally fall into two categories: (1) those that convert chemical into mechanical energy via hydrolysis of a nucleoside triphosphate, usually adenosine triphosphate, regarded as life's chemical currency of energy and (2) membrane bound motors driven directly by an ion gradient and/or membrane potential. Here we argue that electrostatic interactions play a vital role for both types of motors and, therefore, the tools of physics can greatly contribute to understanding biological motors

SLIMarray: Lightweight software for microarray facility management

Directory of Open Access Journals (Sweden)

Marzolf Bruz

2006-10-01

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

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…

Open cyberGIS software for geospatial research and education in the big data era

Science.gov (United States)

Wang, Shaowen; Liu, Yan; Padmanabhan, Anand

CyberGIS represents an interdisciplinary field combining advanced cyberinfrastructure, geographic information science and systems (GIS), spatial analysis and modeling, and a number of geospatial domains to improve research productivity and enable scientific breakthroughs. It has emerged as new-generation GIS that enable unprecedented advances in data-driven knowledge discovery, visualization and visual analytics, and collaborative problem solving and decision-making. This paper describes three open software strategies-open access, source, and integration-to serve various research and education purposes of diverse geospatial communities. These strategies have been implemented in a leading-edge cyberGIS software environment through three corresponding software modalities: CyberGIS Gateway, Toolkit, and Middleware, and achieved broad and significant impacts.

Open cyberGIS software for geospatial research and education in the big data era

Directory of Open Access Journals (Sweden)

Shaowen Wang

2016-01-01

Full Text Available CyberGIS represents an interdisciplinary field combining advanced cyberinfrastructure, geographic information science and systems (GIS, spatial analysis and modeling, and a number of geospatial domains to improve research productivity and enable scientific breakthroughs. It has emerged as new-generation GIS that enable unprecedented advances in data-driven knowledge discovery, visualization and visual analytics, and collaborative problem solving and decision-making. This paper describes three open software strategies–open access, source, and integration–to serve various research and education purposes of diverse geospatial communities. These strategies have been implemented in a leading-edge cyberGIS software environment through three corresponding software modalities: CyberGIS Gateway, Toolkit, and Middleware, and achieved broad and significant impacts.

Contemporary issues in HIM. Software engineering--what does it mean to you?

Science.gov (United States)

Wear, L L

1994-02-01

There have been significant advances in the way we develop software in the last two decades. Many companies are using the new process oriented approach to software development. Companies that use the new techniques and tools have reported improvements in both productivity and quality, but there are still companies developing software the way we did 30 years ago. If you saw the movie Jurassic Park, you saw the perfect way not to develop software. The programmer in the movie was the only person who knew the details of the system. No processes were followed, and there was no documentation. This was an absolutely perfect prescription for failure. Some of you are probably familiar with the term hacker which describes a person who spends hours sitting at a terminal hacking out code. Hackers have created some outstanding software products, but with today's complex systems, most companies are trying to get away from their dependence on hackers. They are instead turning to the process-oriented approach. When selecting software vendors, don't just look at the functionality of a product. Try to determine how the vendor develops software, and determine if you are dealing with hackers or a process-driven company. In the long run, you should get better, more reliable products from the latter.

Transportation dose analysis using an interactive menu-driven computer program

International Nuclear Information System (INIS)

Strenge, D.L.; Peloquin, R.A.

1984-10-01

An easy-to-use software package is described for performing radiological consequence analyses for transportation scenarios involving truck or rail transport of spent fuel, HLW and other radioactive waste forms. The consequence analysis is based on the unit radiological factors (person-rem/km) developed by the Transportation Technology Center (Sandia National Laboratories). These generic unit radiological factors are combined with user-supplied information describing transporation distances, routes and waste types to estimate total exposure of the population. The software was developed for use in preparing the Environmental Assessment for the Monitored Retrievable Storage Program and is suitable for such analyses as siting waste repositories. The key feature of the software is the user-oriented, menu-driven interactive input mode available as an alternative to formatted input. The interactive input option allows the user to supply all input data, edit the data and run the program. Output reports can be diverted to a high-speed printer

Software Development in the Water Sciences: a view from the divide (Invited)

Science.gov (United States)

Miles, B.; Band, L. E.

2013-12-01

While training in statistical methods is an important part of many earth scientists' training, these scientists often learn the bulk of their software development skills in an ad hoc, just-in-time manner. Yet to carry out contemporary research scientists are spending more and more time developing software. Here I present perspectives - as an earth sciences graduate student with professional software engineering experience - on the challenges scientists face adopting software engineering practices, with an emphasis on areas of the science software development lifecycle that could benefit most from improved engineering. This work builds on experience gained as part of the NSF-funded Water Science Software Institute (WSSI) conceptualization award (NSF Award # 1216817). Throughout 2013, the WSSI team held a series of software scoping and development sprints with the goals of: (1) adding features to better model green infrastructure within the Regional Hydro-Ecological Simulation System (RHESSys); and (2) infusing test-driven agile software development practices into the processes employed by the RHESSys team. The goal of efforts such as the WSSI is to ensure that investments by current and future scientists in software engineering training will enable transformative science by improving both scientific reproducibility and researcher productivity. Experience with the WSSI indicates: (1) the potential for achieving this goal; and (2) while scientists are willing to adopt some software engineering practices, transformative science will require continued collaboration between domain scientists and cyberinfrastructure experts for the foreseeable future.

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...

Models of the atomic nucleus. With interactive software

International Nuclear Information System (INIS)

Cook, N.D.

2006-01-01

This book-and-CD-software package supplies users with an interactive experience for nuclear visualization via a computer-graphical interface, similar in principle to the molecular visualizations already available in chemistry. Models of the Atomic Nucleus, a largely non-technical introduction to nuclear theory, explains the nucleus in a way that makes nuclear physics as comprehensible as chemistry or cell biology. The book/software supplements virtually any of the current textbooks in nuclear physics by providing a means for 3D visual display of the diverse models of nuclear structure. For the first time, an easy-to-master software for scientific visualization of the nucleus makes this notoriously ''non-visual'' field become immediately 'visible.' After a review of the basics, the book explores and compares the competing models, and addresses how the lattice model best resolves remaining controversies. The appendix explains how to obtain the most from the software provided on the accompanying CD. (orig.)

NOvA Event Building, Buffering and Data-Driven Triggering From Within the DAQ System

Energy Technology Data Exchange (ETDEWEB)

Fischler, M. [Fermilab; Green, C. [Fermilab; Kowalkowski, J. [Fermilab; Norman, A. [Fermilab; Paterno, M. [Fermilab; Rechenmacher, R. [Fermilab

2012-06-22

To make its core measurements, the NOvA experiment needs to make real-time data-driven decisions involving beam-spill time correlation and other triggering issues. NOvA-DDT is a prototype Data-Driven Triggering system, built using the Fermilab artdaq generic DAQ/Event-building tools set. This provides the advantages of sharing online software infrastructure with other Intensity Frontier experiments, and of being able to use any offline analysis module--unchanged--as a component of the online triggering decisions. The NOvA-artdaq architecture chosen has significant advantages, including graceful degradation if the triggering decision software fails or cannot be done quickly enough for some fraction of the time-slice ``events.'' We have tested and measured the performance and overhead of NOvA-DDT using an actual Hough transform based trigger decision module taken from the NOvA offline software. The results of these tests--98 ms mean time per event on only 1/16 of th e available processing power of a node, and overheads of about 2 ms per event--provide a proof of concept: NOvA-DDT is a viable strategy for data acquisition, event building, and trigger processing at the NOvA far detector.

Introduction to stochastic models in biology

DEFF Research Database (Denmark)

Ditlevsen, Susanne; Samson, Adeline

2013-01-01

This chapter is concerned with continuous time processes, which are often modeled as a system of ordinary differential equations (ODEs). These models assume that the observed dynamics are driven exclusively by internal, deterministic mechanisms. However, real biological systems will always be exp...

Physical mechanisms of biological molecular motors

Energy Technology Data Exchange (ETDEWEB)

Miller, John H. Jr. [Department of Physics and Texas Center for Superconductivity, University of Houston, 4800 Calhoun Road, Ste. 617 SR1 Houston, TX 77204-5005 (United States)], E-mail: jhmiller@uh.edu; Vajrala, Vijayanand; Infante, Hans L. [Department of Physics and Texas Center for Superconductivity, University of Houston, 4800 Calhoun Road, Ste. 617 SR1 Houston, TX 77204-5005 (United States); Claycomb, James R. [Department of Physics and Texas Center for Superconductivity, University of Houston, 4800 Calhoun Road, Ste. 617 SR1 Houston, TX 77204-5005 (United States); Department of Mathematics and Physics, Houston Baptist University, 7502 Fondren Road, Houston, TX 77074-3298 (United States); Palanisami, Akilan; Fang Jie; Mercier, George T. [Department of Physics and Texas Center for Superconductivity, University of Houston, 4800 Calhoun Road, Ste. 617 SR1 Houston, TX 77204-5005 (United States)

2009-03-01

Biological motors generally fall into two categories: (1) those that convert chemical into mechanical energy via hydrolysis of a nucleoside triphosphate, usually adenosine triphosphate, regarded as life's chemical currency of energy and (2) membrane bound motors driven directly by an ion gradient and/or membrane potential. Here we argue that electrostatic interactions play a vital role for both types of motors and, therefore, the tools of physics can greatly contribute to understanding biological motors.

Behaviour Driven Development a Scrum v korporátním prostředí

OpenAIRE

Kulhánková, Barbora

2015-01-01

Agile software development methodologies these days are not used only in small enterprises or startups, they are getting spread around large enterprises as well. An evidence of this fact could be, that Scrum is nowadays the most commonly used approach to software development. So this thesis focuses on usage of agile approaches, Scrum methodology in particular, in large enterprises. Author presents an approach called Behaviour Driven development and proposes how this approach could help dealin...

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

Directory of Open Access Journals (Sweden)

Falciani Francesco

2011-03-01

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

Supervised Semi-Automated Data Analysis Software for Gas Chromatography / Differential Mobility Spectrometry (GC/DMS) Metabolomics Applications.

Science.gov (United States)

Peirano, Daniel J; Pasamontes, Alberto; Davis, Cristina E

2016-09-01

Modern differential mobility spectrometers (DMS) produce complex and multi-dimensional data streams that allow for near-real-time or post-hoc chemical detection for a variety of applications. An active area of interest for this technology is metabolite monitoring for biological applications, and these data sets regularly have unique technical and data analysis end user requirements. While there are initial publications on how investigators have individually processed and analyzed their DMS metabolomic data, there are no user-ready commercial or open source software packages that are easily used for this purpose. We have created custom software uniquely suited to analyze gas chromatograph / differential mobility spectrometry (GC/DMS) data from biological sources. Here we explain the implementation of the software, describe the user features that are available, and provide an example of how this software functions using a previously-published data set. The software is compatible with many commercial or home-made DMS systems. Because the software is versatile, it can also potentially be used for other similarly structured data sets, such as GC/GC and other IMS modalities.

Constraint Network Analysis (CNA): a Python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function.

Science.gov (United States)

Pfleger, Christopher; Rathi, Prakash Chandra; Klein, Doris L; Radestock, Sebastian; Gohlke, Holger

2013-04-22

For deriving maximal advantage from information on biomacromolecular flexibility and rigidity, results from rigidity analyses must be linked to biologically relevant characteristics of a structure. Here, we describe the Python-based software package Constraint Network Analysis (CNA) developed for this task. CNA functions as a front- and backend to the graph-based rigidity analysis software FIRST. CNA goes beyond the mere identification of flexible and rigid regions in a biomacromolecule in that it (I) provides a refined modeling of thermal unfolding simulations that also considers the temperature-dependence of hydrophobic tethers, (II) allows performing rigidity analyses on ensembles of network topologies, either generated from structural ensembles or by using the concept of fuzzy noncovalent constraints, and (III) computes a set of global and local indices for quantifying biomacromolecular stability. This leads to more robust results from rigidity analyses and extends the application domain of rigidity analyses in that phase transition points ("melting points") and unfolding nuclei ("structural weak spots") are determined automatically. Furthermore, CNA robustly handles small-molecule ligands in general. Such advancements are important for applying rigidity analysis to data-driven protein engineering and for estimating the influence of ligand molecules on biomacromolecular stability. CNA maintains the efficiency of FIRST such that the analysis of a single protein structure takes a few seconds for systems of several hundred residues on a single core. These features make CNA an interesting tool for linking biomacromolecular structure, flexibility, (thermo-)stability, and function. CNA is available from http://cpclab.uni-duesseldorf.de/software for nonprofit organizations.

The fusion of biology, computer science, and engineering: towards efficient and successful synthetic biology.

Science.gov (United States)

Linshiz, Gregory; Goldberg, Alex; Konry, Tania; Hillson, Nathan J

2012-01-01

Synthetic biology is a nascent field that emerged in earnest only around the turn of the millennium. It aims to engineer new biological systems and impart new biological functionality, often through genetic modifications. The design and construction of new biological systems is a complex, multistep process, requiring multidisciplinary collaborative efforts from "fusion" scientists who have formal training in computer science or engineering, as well as hands-on biological expertise. The public has high expectations for synthetic biology and eagerly anticipates the development of solutions to the major challenges facing humanity. This article discusses laboratory practices and the conduct of research in synthetic biology. It argues that the fusion science approach, which integrates biology with computer science and engineering best practices, including standardization, process optimization, computer-aided design and laboratory automation, miniaturization, and systematic management, will increase the predictability and reproducibility of experiments and lead to breakthroughs in the construction of new biological systems. The article also discusses several successful fusion projects, including the development of software tools for DNA construction design automation, recursive DNA construction, and the development of integrated microfluidics systems.

A Survey of Bioinformatics Database and Software Usage through Mining the Literature.

Directory of Open Access Journals (Sweden)

Geraint Duck

Full Text Available Computer-based resources are central to much, if not most, biological and medical research. However, while there is an ever expanding choice of bioinformatics resources to use, described within the biomedical literature, little work to date has provided an evaluation of the full range of availability or levels of usage of database and software resources. Here we use text mining to process the PubMed Central full-text corpus, identifying mentions of databases or software within the scientific literature. We provide an audit of the resources contained within the biomedical literature, and a comparison of their relative usage, both over time and between the sub-disciplines of bioinformatics, biology and medicine. We find that trends in resource usage differs between these domains. The bioinformatics literature emphasises novel resource development, while database and software usage within biology and medicine is more stable and conservative. Many resources are only mentioned in the bioinformatics literature, with a relatively small number making it out into general biology, and fewer still into the medical literature. In addition, many resources are seeing a steady decline in their usage (e.g., BLAST, SWISS-PROT, though some are instead seeing rapid growth (e.g., the GO, R. We find a striking imbalance in resource usage with the top 5% of resource names (133 names accounting for 47% of total usage, and over 70% of resources extracted being only mentioned once each. While these results highlight the dynamic and creative nature of bioinformatics research they raise questions about software reuse, choice and the sharing of bioinformatics practice. Is it acceptable that so many resources are apparently never reused? Finally, our work is a step towards automated extraction of scientific method from text. We make the dataset generated by our study available under the CC0 license here: http://dx.doi.org/10.6084/m9.figshare.1281371.

A first-generation software product line for data acquisition systems in astronomy

Science.gov (United States)

López-Ruiz, J. C.; Heradio, Rubén; Cerrada Somolinos, José Antonio; Coz Fernandez, José Ramón; López Ramos, Pablo

2008-07-01

This article presents a case study on developing a software product line for data acquisition systems in astronomy based on the Exemplar Driven Development methodology and the Exemplar Flexibilization Language tool. The main strategies to build the software product line are based on the domain commonality and variability, the incremental scope and the use of existing artifacts. It consists on a lean methodology with little impact on the organization, suitable for small projects, which reduces product line start-up time. Software Product Lines focuses on creating a family of products instead of individual products. This approach has spectacular benefits on reducing the time to market, maintaining the know-how, reducing the development costs and increasing the quality of new products. The maintenance of the products is also enhanced since all the data acquisition systems share the same product line architecture.

Evolutionary perspectives into placental biology and disease

Directory of Open Access Journals (Sweden)

Edward B. Chuong

2013-12-01

Full Text Available In all mammals including humans, development takes place within the protective environment of the maternal womb. Throughout gestation, nutrients and waste products are continuously exchanged between mother and fetus through the placenta. Despite the clear importance of the placenta to successful pregnancy and the health of both mother and offspring, relatively little is understood about the biology of the placenta and its role in pregnancy-related diseases. Given that pre- and peri-natal diseases involving the placenta affect millions of women and their newborns worldwide, there is an urgent need to understand placenta biology and development. Here, we suggest that the placenta is an organ under unique selective pressures that have driven its rapid diversification throughout mammalian evolution. The high divergence of the placenta complicates the use of non-human animal models and necessitates an evolutionary perspective when studying its biology and role in disease. We suggest that diversifying evolution of the placenta is primarily driven by intraspecies evolutionary conflict between mother and fetus, and that many pregnancy diseases are a consequence of this evolutionary force. Understanding how maternal–fetal conflict shapes both basic placental and reproductive biology – in all species – will provide key insights into diseases of pregnancy.

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

International Nuclear Information System (INIS)

Glad, A.; Henline, P.; Gross, L.; McHarg, B.

1979-11-01

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

Close connections between open science and open-source software

Directory of Open Access Journals (Sweden)

YouHua Chen

2014-09-01

Full Text Available Open science is increasingly gaining attention in recent years. In this mini-review, we briefly discuss and summarize the reasons of introducing open science into academic publications for scientists. We argue that open-source software (like R and Python software can be the universal and important platforms for doing open science because of their appealing features: open source, easy-reading document, commonly used in various scientific disciplines like statistics, chemistry and biology. At last, the challenges and future perspectives of performing open science are discussed.

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.

Educational interactive multimedia software: The impact of interactivity on learning

Science.gov (United States)

Reamon, Derek Trent

This dissertation discusses the design, development, deployment and testing of two versions of educational interactive multimedia software. Both versions of the software are focused on teaching mechanical engineering undergraduates about the fundamentals of direct-current (DC) motor physics and selection. The two versions of Motor Workshop software cover the same basic materials on motors, but differ in the level of interactivity between the students and the software. Here, the level of interactivity refers to the particular role of the computer in the interaction between the user and the software. In one version, the students navigate through information that is organized by topic, reading text, and viewing embedded video clips; this is referred to as "low-level interactivity" software because the computer simply presents the content. In the other version, the students are given a task to accomplish---they must design a small motor-driven 'virtual' vehicle that competes against computer-generated opponents. The interaction is guided by the software which offers advice from 'experts' and provides contextual information; we refer to this as "high-level interactivity" software because the computer is actively participating in the interaction. The software was used in two sets of experiments, where students using the low-level interactivity software served as the 'control group,' and students using the highly interactive software were the 'treatment group.' Data, including pre- and post-performance tests, questionnaire responses, learning style characterizations, activity tracking logs and videotapes were collected for analysis. Statistical and observational research methods were applied to the various data to test the hypothesis that the level of interactivity effects the learning situation, with higher levels of interactivity being more effective for learning. The results show that both the low-level and high-level interactive versions of the software were effective

How can operations get the applications software that they want?

CERN Document Server

Bailey, R

1995-01-01

In SL division at CERN, any major development of application software to be used in the control room entails interaction and a division of responsibilities between people from operations, controls, accelerator physics and equipment groups. Providing the suite of applications for the operators to use for efficient exploitation of the machines is no exception to this. Indeed since routine operation accounts for the largest fraction of machine time, it should be regarded as the most important activity. We have found over 10 years that teams led by operations people, making pragmatic use of formal development methods, prove to be very effective in producing the software required for running the machines. This paper examines the modus operandi of some operations-driven projects, and contrasts this with some less successful ventures.

Integrating interactive computational modeling in biology curricula.

Directory of Open Access Journals (Sweden)

Tomáš Helikar

2015-03-01

Full Text Available While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

Integrating interactive computational modeling in biology curricula.

Science.gov (United States)

Helikar, Tomáš; Cutucache, Christine E; Dahlquist, Lauren M; Herek, Tyler A; Larson, Joshua J; Rogers, Jim A

2015-03-01

While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology) class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

Teaching structure: student use of software tools for understanding macromolecular structure in an undergraduate biochemistry course.

Science.gov (United States)

Jaswal, Sheila S; O'Hara, Patricia B; Williamson, Patrick L; Springer, Amy L

2013-01-01

Because understanding the structure of biological macromolecules is critical to understanding their function, students of biochemistry should become familiar not only with viewing, but also with generating and manipulating structural representations. We report a strategy from a one-semester undergraduate biochemistry course to integrate use of structural representation tools into both laboratory and homework activities. First, early in the course we introduce the use of readily available open-source software for visualizing protein structure, coincident with modules on amino acid and peptide bond properties. Second, we use these same software tools in lectures and incorporate images and other structure representations in homework tasks. Third, we require a capstone project in which teams of students examine a protein-nucleic acid complex and then use the software tools to illustrate for their classmates the salient features of the structure, relating how the structure helps explain biological function. To ensure engagement with a range of software and database features, we generated a detailed template file that can be used to explore any structure, and that guides students through specific applications of many of the software tools. In presentations, students demonstrate that they are successfully interpreting structural information, and using representations to illustrate particular points relevant to function. Thus, over the semester students integrate information about structural features of biological macromolecules into the larger discussion of the chemical basis of function. Together these assignments provide an accessible introduction to structural representation tools, allowing students to add these methods to their biochemical toolboxes early in their scientific development. © 2013 by The International Union of Biochemistry and Molecular Biology.

ROCKETSHIP: a flexible and modular software tool for the planning, processing and analysis of dynamic MRI studies

International Nuclear Information System (INIS)

Barnes, Samuel R.; Ng, Thomas S. C.; Santa-Maria, Naomi; Montagne, Axel; Zlokovic, Berislav V.; Jacobs, Russell E.

2015-01-01

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a promising technique to characterize pathology and evaluate treatment response. However, analysis of DCE-MRI data is complex and benefits from concurrent analysis of multiple kinetic models and parameters. Few software tools are currently available that specifically focuses on DCE-MRI analysis with multiple kinetic models. Here, we developed ROCKETSHIP, an open-source, flexible and modular software for DCE-MRI analysis. ROCKETSHIP incorporates analyses with multiple kinetic models, including data-driven nested model analysis. ROCKETSHIP was implemented using the MATLAB programming language. Robustness of the software to provide reliable fits using multiple kinetic models is demonstrated using simulated data. Simulations also demonstrate the utility of the data-driven nested model analysis. Applicability of ROCKETSHIP for both preclinical and clinical studies is shown using DCE-MRI studies of the human brain and a murine tumor model. A DCE-MRI software suite was implemented and tested using simulations. Its applicability to both preclinical and clinical datasets is shown. ROCKETSHIP was designed to be easily accessible for the beginner, but flexible enough for changes or additions to be made by the advanced user as well. The availability of a flexible analysis tool will aid future studies using DCE-MRI. A public release of ROCKETSHIP is available at (https://github.com/petmri/ROCKETSHIP)

Improvements to the APBS biomolecular solvation software suite.

Science.gov (United States)

Jurrus, Elizabeth; Engel, Dave; Star, Keith; Monson, Kyle; Brandi, Juan; Felberg, Lisa E; Brookes, David H; Wilson, Leighton; Chen, Jiahui; Liles, Karina; Chun, Minju; Li, Peter; Gohara, David W; Dolinsky, Todd; Konecny, Robert; Koes, David R; Nielsen, Jens Erik; Head-Gordon, Teresa; Geng, Weihua; Krasny, Robert; Wei, Guo-Wei; Holst, Michael J; McCammon, J Andrew; Baker, Nathan A

2018-01-01

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pK a values, and an improved web-based visualization tool for viewing electrostatics. © 2017 The Protein Society.

Software FMEA analysis for safety-related application software

International Nuclear Information System (INIS)

Park, Gee-Yong; Kim, Dong Hoon; Lee, Dong Young

2014-01-01

Highlights: • We develop a modified FMEA analysis suited for applying to software architecture. • A template for failure modes on a specific software language is established. • A detailed-level software FMEA analysis on nuclear safety software is presented. - Abstract: A method of a software safety analysis is described in this paper for safety-related application software. The target software system is a software code installed at an Automatic Test and Interface Processor (ATIP) in a digital reactor protection system (DRPS). For the ATIP software safety analysis, at first, an overall safety or hazard analysis is performed over the software architecture and modules, and then a detailed safety analysis based on the software FMEA (Failure Modes and Effect Analysis) method is applied to the ATIP program. For an efficient analysis, the software FMEA analysis is carried out based on the so-called failure-mode template extracted from the function blocks used in the function block diagram (FBD) for the ATIP software. The software safety analysis by the software FMEA analysis, being applied to the ATIP software code, which has been integrated and passed through a very rigorous system test procedure, is proven to be able to provide very valuable results (i.e., software defects) that could not be identified during various system tests

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...

Reconfiguring film studies through software cinema and procedural spectatorship

Directory of Open Access Journals (Sweden)

Marina Hassapopoulou

2014-12-01

Full Text Available The increasing use of software and database aesthetics in film and video production has created hybrid modes of spectatorship by altering the dynamic between media production and reception. Software-generated narratives (preprogrammed databases that create films through random selection and combination of discrete audio, visual, and/or textual tracks remove the viewer from the actual algorithmic process, drawing his/her attention instead on interactions between hardware and software. Here, the element of unpredictability that is part of cinematic pleasure lies in the recombination of discrete elements (audio, visuals, subtitles, and so on and the unexpected ways in which the software stitches those elements together. The subsequent reduction in the degree and compass of authorial control invites us to reconsider existing frameworks of spectatorship and narration within new contexts of mobility, performance, and databases. In this article I consider Soft Cinema films (Lev Manovich, Andreas Kratky, et al., 2003 as prototypical software-driven examples of this shift in viewing conditions and reception contexts. I argue that, despite its emerging and changing techniques and aesthetics, software-generated cinema retains one of the primitive socio-pedagogical functions of the cinema: training audiences to receive and buffer contemporary medial sensations. Just as early cinema prepared audiences and worked as a buffer for shocks of technological and industrial modernity, software cinema trains the viewer in new modes of film spectatorship and new modes of narrative and affective subjectivity that correspond to the hypertextual ways in which we interact with digital technologies. These viewing modes create a new form of procedural spectatorship that has been evident since the first pioneering experiments in generative cinema and a form that is, nonetheless, not entirely detached from existing theoretical paradigms of cinematic spectatorship and the

PHARMAVIRTUA: Educational Software for Teaching and Learning Basic Pharmacology

Science.gov (United States)

Fidalgo-Neto, Antonio Augusto; Alberto, Anael Viana Pinto; Bonavita, André Gustavo Calvano; Bezerra, Rômulo José Soares; Berçot, Felipe Faria; Lopes, Renato Matos; Alves, Luiz Anastacio

2014-01-01

Information and communication technologies have become important tools for teaching scientific subjects such as anatomy and histology as well as other, nondescriptive subjects like physiology and pharmacology. Software has been used to facilitate the learning of specific concepts at the cellular and molecular levels in the biological and health…

STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

KAUST Repository

Klingbeil, G.; Erban, R.; Giles, M.; Maini, P. K.

2011-01-01

Motivation: The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new

Developing BP-driven web application through the use of MDE techniques

OpenAIRE

Torres Bosch, Maria Victoria; Giner Blasco, Pau; Pelechano Ferragud, Vicente

2012-01-01

Model driven engineering (MDE) is a suitable approach for performing the construction of software systems (in particular in the Web application domain). There are different types of Web applications depending on their purpose (i.e., document-centric, interactive, transactional, workflow/business process-based, collaborative, etc). This work focusses on business process-based Web applications in order to be able to understand business processes in a broad sense, from the lightweight business p...

A Case Study of Horizontal Reuse in a Project-Driven Organisation

DEFF Research Database (Denmark)

Christensen, Henrik Bærbak; Røn, Henrik

2000-01-01

This experience paper presents observations, lessons learned, and recommendations based on a case study of reuse. The case study is concerned with the development, maturation, and reuse of a business domain independent software component (horizontal reuse) in a project-driven organisation that has...... knowledge is transferred within an organisation; (c) design patterns can be as risky as they can be beneficial; and (d) there is more to architectural mismatch than “merely ” packaging mismatch....

Software challenges in extreme scale systems

International Nuclear Information System (INIS)

Sarkar, Vivek; Harrod, William; Snavely, Allan E

2009-01-01

Computer systems anticipated in the 2015 - 2020 timeframe are referred to as Extreme Scale because they will be built using massive multi-core processors with 100's of cores per chip. The largest capability Extreme Scale system is expected to deliver Exascale performance of the order of 10 18 operations per second. These systems pose new critical challenges for software in the areas of concurrency, energy efficiency and resiliency. In this paper, we discuss the implications of the concurrency and energy efficiency challenges on future software for Extreme Scale Systems. From an application viewpoint, the concurrency and energy challenges boil down to the ability to express and manage parallelism and locality by exploring a range of strong scaling and new-era weak scaling techniques. For expressing parallelism and locality, the key challenges are the ability to expose all of the intrinsic parallelism and locality in a programming model, while ensuring that this expression of parallelism and locality is portable across a range of systems. For managing parallelism and locality, the OS-related challenges include parallel scalability, spatial partitioning of OS and application functionality, direct hardware access for inter-processor communication, and asynchronous rather than interrupt-driven events, which are accompanied by runtime system challenges for scheduling, synchronization, memory management, communication, performance monitoring, and power management. We conclude by discussing the importance of software-hardware co-design in addressing the fundamental challenges for application enablement on Extreme Scale systems.

Software support for SBGN maps: SBGN-ML and LibSBGN.

Science.gov (United States)

van Iersel, Martijn P; Villéger, Alice C; Czauderna, Tobias; Boyd, Sarah E; Bergmann, Frank T; Luna, Augustin; Demir, Emek; Sorokin, Anatoly; Dogrusoz, Ugur; Matsuoka, Yukiko; Funahashi, Akira; Aladjem, Mirit I; Mi, Huaiyu; Moodie, Stuart L; Kitano, Hiroaki; Le Novère, Nicolas; Schreiber, Falk

2012-08-01

LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner. Milestone 2 was released in December 2011. Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net. sbgn-libsbgn@lists.sourceforge.net.

Estudio de adopción de técnicas de desarrollo de software guiado por las pruebas

OpenAIRE

Maldonado, Calixto; Gastañaga, Iris; Inchaurrondo, Claudia Inés; Vaca, Pablo A.; Bueno, Matías; Romero, María Soledad; Peretti, Juan Pablo

2016-01-01

En el presente proyecto, dentro del Grupo de Investigación, Desarrollo y Transferencia de Sistemas de Información (GIDTSI), se estudiaron las implementaciones existentes de los frameworks aplicados en Test-Driven Development (TDD) y Behavior-Driven Development (BDD) y como resultado al final del mismo se prevé proponer una forma de integración entre distintas técnicas de (TDD) y (BDD). Para el estudio de campo entre las empresas de de desarrollo de software se ha creado un formulario de encue...

Test Driven Development of a Parameterized Ice Sheet Component

Science.gov (United States)

Clune, T.

2011-12-01

Test driven development (TDD) is a software development methodology that offers many advantages over traditional approaches including reduced development and maintenance costs, improved reliability, and superior design quality. Although TDD is widely accepted in many software communities, the suitability to scientific software is largely undemonstrated and warrants a degree of skepticism. Indeed, numerical algorithms pose several challenges to unit testing in general, and TDD in particular. Among these challenges are the need to have simple, non-redundant closed-form expressions to compare against the results obtained from the implementation as well as realistic error estimates. The necessity for serial and parallel performance raises additional concerns for many scientific applicaitons. In previous work I demonstrated that TDD performed well for the development of a relatively simple numerical model that simulates the growth of snowflakes, but the results were anecdotal and of limited relevance to far more complex software components typical of climate models. This investigation has now been extended by successfully applying TDD to the implementation of a substantial portion of a new parameterized ice sheet component within a full climate model. After a brief introduction to TDD, I will present techniques that address some of the obstacles encountered with numerical algorithms. I will conclude with some quantitative and qualitative comparisons against climate components developed in a more traditional manner.

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.

Secure Encapsulation and Publication of Biological Services in the Cloud Computing Environment

Science.gov (United States)

Zhang, Weizhe; Wang, Xuehui; Lu, Bo; Kim, Tai-hoon

2013-01-01

Secure encapsulation and publication for bioinformatics software products based on web service are presented, and the basic function of biological information is realized in the cloud computing environment. In the encapsulation phase, the workflow and function of bioinformatics software are conducted, the encapsulation interfaces are designed, and the runtime interaction between users and computers is simulated. In the publication phase, the execution and management mechanisms and principles of the GRAM components are analyzed. The functions such as remote user job submission and job status query are implemented by using the GRAM components. The services of bioinformatics software are published to remote users. Finally the basic prototype system of the biological cloud is achieved. PMID:24078906

Secure Encapsulation and Publication of Biological Services in the Cloud Computing Environment

Directory of Open Access Journals (Sweden)

Weizhe Zhang

2013-01-01

Full Text Available Secure encapsulation and publication for bioinformatics software products based on web service are presented, and the basic function of biological information is realized in the cloud computing environment. In the encapsulation phase, the workflow and function of bioinformatics software are conducted, the encapsulation interfaces are designed, and the runtime interaction between users and computers is simulated. In the publication phase, the execution and management mechanisms and principles of the GRAM components are analyzed. The functions such as remote user job submission and job status query are implemented by using the GRAM components. The services of bioinformatics software are published to remote users. Finally the basic prototype system of the biological cloud is achieved.

Secure encapsulation and publication of biological services in the cloud computing environment.

Science.gov (United States)

Zhang, Weizhe; Wang, Xuehui; Lu, Bo; Kim, Tai-hoon

2013-01-01

Secure encapsulation and publication for bioinformatics software products based on web service are presented, and the basic function of biological information is realized in the cloud computing environment. In the encapsulation phase, the workflow and function of bioinformatics software are conducted, the encapsulation interfaces are designed, and the runtime interaction between users and computers is simulated. In the publication phase, the execution and management mechanisms and principles of the GRAM components are analyzed. The functions such as remote user job submission and job status query are implemented by using the GRAM components. The services of bioinformatics software are published to remote users. Finally the basic prototype system of the biological cloud is achieved.

Software

Energy Technology Data Exchange (ETDEWEB)

Macedo, R.; Budd, G.; Ross, E.; Wells, P.

2010-07-15

The software section of this journal presented new software programs that have been developed to help in the exploration and development of hydrocarbon resources. Software provider IHS Inc. has made additions to its geological and engineering analysis software tool, IHS PETRA, a product used by geoscientists and engineers to visualize, analyze and manage well production, well log, drilling, reservoir, seismic and other related information. IHS PETRA also includes a directional well module and a decline curve analysis module to improve analysis capabilities in unconventional reservoirs. Petris Technology Inc. has developed a software to help manage the large volumes of data. PetrisWinds Enterprise (PWE) helps users find and manage wellbore data, including conventional wireline and MWD core data; analysis core photos and images; waveforms and NMR; and external files documentation. Ottawa-based Ambercore Software Inc. has been collaborating with Nexen on the Petroleum iQ software for steam assisted gravity drainage (SAGD) producers. Petroleum iQ integrates geology and geophysics data with engineering data in 3D and 4D. Calgary-based Envirosoft Corporation has developed a software that reduces the costly and time-consuming effort required to comply with Directive 39 of the Alberta Energy Resources Conservation Board. The product includes an emissions modelling software. Houston-based Seismic Micro-Technology (SMT) has developed the Kingdom software that features the latest in seismic interpretation. Holland-based Joa Oil and Gas and Calgary-based Computer Modelling Group have both supplied the petroleum industry with advanced reservoir simulation software that enables reservoir interpretation. The 2010 software survey included a guide to new software applications designed to facilitate petroleum exploration, drilling and production activities. Oil and gas producers can use the products for a range of functions, including reservoir characterization and accounting. In

Bigdata Driven Cloud Security: A Survey

Science.gov (United States)

Raja, K.; Hanifa, Sabibullah Mohamed

2017-08-01

Cloud Computing (CC) is a fast-growing technology to perform massive-scale and complex computing. It eliminates the need to maintain expensive computing hardware, dedicated space, and software. Recently, it has been observed that massive growth in the scale of data or big data generated through cloud computing. CC consists of a front-end, includes the users’ computers and software required to access the cloud network, and back-end consists of various computers, servers and database systems that create the cloud. In SaaS (Software as-a-Service - end users to utilize outsourced software), PaaS (Platform as-a-Service-platform is provided) and IaaS (Infrastructure as-a-Service-physical environment is outsourced), and DaaS (Database as-a-Service-data can be housed within a cloud), where leading / traditional cloud ecosystem delivers the cloud services become a powerful and popular architecture. Many challenges and issues are in security or threats, most vital barrier for cloud computing environment. The main barrier to the adoption of CC in health care relates to Data security. When placing and transmitting data using public networks, cyber attacks in any form are anticipated in CC. Hence, cloud service users need to understand the risk of data breaches and adoption of service delivery model during deployment. This survey deeply covers the CC security issues (covering Data Security in Health care) so as to researchers can develop the robust security application models using Big Data (BD) on CC (can be created / deployed easily). Since, BD evaluation is driven by fast-growing cloud-based applications developed using virtualized technologies. In this purview, MapReduce [12] is a good example of big data processing in a cloud environment, and a model for Cloud providers.

A Model-Driven Co-Design Framework for Fusing Control and Scheduling Viewpoints.

Science.gov (United States)

Sundharam, Sakthivel Manikandan; Navet, Nicolas; Altmeyer, Sebastian; Havet, Lionel

2018-02-20

Model-Driven Engineering (MDE) is widely applied in the industry to develop new software functions and integrate them into the existing run-time environment of a Cyber-Physical System (CPS). The design of a software component involves designers from various viewpoints such as control theory, software engineering, safety, etc. In practice, while a designer from one discipline focuses on the core aspects of his field (for instance, a control engineer concentrates on designing a stable controller), he neglects or considers less importantly the other engineering aspects (for instance, real-time software engineering or energy efficiency). This may cause some of the functional and non-functional requirements not to be met satisfactorily. In this work, we present a co-design framework based on timing tolerance contract to address such design gaps between control and real-time software engineering. The framework consists of three steps: controller design, verified by jitter margin analysis along with co-simulation, software design verified by a novel schedulability analysis, and the run-time verification by monitoring the execution of the models on target. This framework builds on CPAL (Cyber-Physical Action Language), an MDE design environment based on model-interpretation, which enforces a timing-realistic behavior in simulation through timing and scheduling annotations. The application of our framework is exemplified in the design of an automotive cruise control system.

A Model-Driven Co-Design Framework for Fusing Control and Scheduling Viewpoints

Science.gov (United States)

Navet, Nicolas; Havet, Lionel

2018-01-01

Model-Driven Engineering (MDE) is widely applied in the industry to develop new software functions and integrate them into the existing run-time environment of a Cyber-Physical System (CPS). The design of a software component involves designers from various viewpoints such as control theory, software engineering, safety, etc. In practice, while a designer from one discipline focuses on the core aspects of his field (for instance, a control engineer concentrates on designing a stable controller), he neglects or considers less importantly the other engineering aspects (for instance, real-time software engineering or energy efficiency). This may cause some of the functional and non-functional requirements not to be met satisfactorily. In this work, we present a co-design framework based on timing tolerance contract to address such design gaps between control and real-time software engineering. The framework consists of three steps: controller design, verified by jitter margin analysis along with co-simulation, software design verified by a novel schedulability analysis, and the run-time verification by monitoring the execution of the models on target. This framework builds on CPAL (Cyber-Physical Action Language), an MDE design environment based on model-interpretation, which enforces a timing-realistic behavior in simulation through timing and scheduling annotations. The application of our framework is exemplified in the design of an automotive cruise control system. PMID:29461489

A Model-Driven Co-Design Framework for Fusing Control and Scheduling Viewpoints

Directory of Open Access Journals (Sweden)

Sakthivel Manikandan Sundharam

2018-02-01

Full Text Available Model-Driven Engineering (MDE is widely applied in the industry to develop new software functions and integrate them into the existing run-time environment of a Cyber-Physical System (CPS. The design of a software component involves designers from various viewpoints such as control theory, software engineering, safety, etc. In practice, while a designer from one discipline focuses on the core aspects of his field (for instance, a control engineer concentrates on designing a stable controller, he neglects or considers less importantly the other engineering aspects (for instance, real-time software engineering or energy efficiency. This may cause some of the functional and non-functional requirements not to be met satisfactorily. In this work, we present a co-design framework based on timing tolerance contract to address such design gaps between control and real-time software engineering. The framework consists of three steps: controller design, verified by jitter margin analysis along with co-simulation, software design verified by a novel schedulability analysis, and the run-time verification by monitoring the execution of the models on target. This framework builds on CPAL (Cyber-Physical Action Language, an MDE design environment based on model-interpretation, which enforces a timing-realistic behavior in simulation through timing and scheduling annotations. The application of our framework is exemplified in the design of an automotive cruise control system.

Control and test software for IRAM WideX correlator

International Nuclear Information System (INIS)

Blanchet, S.; Broguiere, D.; Chavatte, P.; Morel, F.; Perrigouard, A.; Torres, M.

2012-01-01

IRAM is an international research institute for radio astronomy. It has designed a new correlator called WideX for the Plateau de Bure interferometer (an array of six 15-meter telescopes) in the French Alps. The device started its official service in February 2010. This correlator must be driven in real-time at 32 Hz for sending parameters and for data acquisition. With 3.67 million channels, distributed over 1792 dedicated chips, that produce a 1.87 Gbits/sec data output rate, the data acquisition and processing and also the automatic hardware-failure detection are big challenges for the software. This article presents the software that has been developed to drive and test the correlator. In particular it presents an innovative usage of a high speed optical link, initially developed for the CERN ALICE experiment, associated with real-time Linux (RTAI) to achieve our goals. (authors)

Software upgrade for the DIII-D neutral beam control systems

International Nuclear Information System (INIS)

Cummings, J.W.; Thurgood, P.A.

1991-11-01

The neutral beams are used to heat the plasma in the DIII-D tokamak, a fusion energy research experiment operated by General Atomics (GA) and funded by the Department of Energy (DOE). The experiment is dedicated to demonstrating noninductive current drive of high beta high temperature divertor plasma with good confinement. The neutral beam heating system for the DIII-D tokamak uses four MODCOMP Classic computers for data acquisition and control of the four beamlines. The Neutral Beam Software Upgrade project was launched in early 1990. The major goals were to upgrade the MAX IV operating system to the latest revision (K.1), use standard MODCOMP software (as much as possible), and to develop a very ''user friendly,'' versatile system. Accomplishing these goals required new software to be developed and modifications to existing applications software to make it compatible with the latest operating system. The custom operating system modules to handle the message service and interrupt handling were replaced by the standard MODCOMP Inter Task Communication (ITC) and interrupt routines that are part of the MAX IV operating system. The message service provides the mechanism for doing shot task sequencing (task scheduling). The interrupt routines are used to connect external interrupts to the system. The new software developed consists of a task dispatcher, screen manager, and interrupt tasks. The existing applications software had to be modified to be compatible with the MODCOMP ITC services and consists of the Modcomp Infinity Data Base Manager, a multi-user system, and menu-driven operating system interface routines using the Infinity Data Base Manager

The six critical attributes of the next generation of quality management software systems.

Science.gov (United States)

Clark, Kathleen

2011-07-01

Driven by both the need to meet regulatory requirements and a genuine desire to drive improved quality, quality management systems encompassing standard operating procedure, corrective and preventative actions and related processes have existed for many years, both in paper and electronic form. The impact of quality management systems on 'actual' quality, however, is often reported as far less than desired. A quality management software system that moves beyond formal forms-driven processes to include a true closed loop design, manage disparate processes across the enterprise, provide support for collaborative processes and deliver insight into the overall state of control has the potential to close the gap between simply accomplishing regulatory compliance and delivering measurable improvements in quality and efficiency.

An IT R&D-programme without new code?! –State driven IT-development in Denmark

DEFF Research Database (Denmark)

Koch, Christian; Haugen, Tore

2004-01-01

network theory to establish the point that the program theory and its initial program coalition is weaved into a political process, that makes the development a emergent process of network building. Some of the main elements of the program are: There is no funding for developing new software. Rather...... £) in combination with an estimated auto-financing of 30%. The main idea is moreover to adopt existing and developed generic software in the programme and configure this to support the developed basis. The program is developing a particular version of state driven development, namely one drawing on the power...

IFDOTMETER: A New Software Application for Automated Immunofluorescence Analysis.

Science.gov (United States)

Rodríguez-Arribas, Mario; Pizarro-Estrella, Elisa; Gómez-Sánchez, Rubén; Yakhine-Diop, S M S; Gragera-Hidalgo, Antonio; Cristo, Alejandro; Bravo-San Pedro, Jose M; González-Polo, Rosa A; Fuentes, José M

2016-04-01

Most laboratories interested in autophagy use different imaging software for managing and analyzing heterogeneous parameters in immunofluorescence experiments (e.g., LC3-puncta quantification and determination of the number and size of lysosomes). One solution would be software that works on a user's laptop or workstation that can access all image settings and provide quick and easy-to-use analysis of data. Thus, we have designed and implemented an application called IFDOTMETER, which can run on all major operating systems because it has been programmed using JAVA (Sun Microsystems). Briefly, IFDOTMETER software has been created to quantify a variety of biological hallmarks, including mitochondrial morphology and nuclear condensation. The program interface is intuitive and user-friendly, making it useful for users not familiar with computer handling. By setting previously defined parameters, the software can automatically analyze a large number of images without the supervision of the researcher. Once analysis is complete, the results are stored in a spreadsheet. Using software for high-throughput cell image analysis offers researchers the possibility of performing comprehensive and precise analysis of a high number of images in an automated manner, making this routine task easier. © 2015 Society for Laboratory Automation and Screening.

Development of software for management of radioactive waste in biological research and clinical assistance

International Nuclear Information System (INIS)

Maciel, Bianca; Mattos, Maria Fernanda S.S.; Medeiros, Regina B.; Franca Junior, Jose Antonio de

2011-01-01

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

Examining software complexity and quality for scientific software

International Nuclear Information System (INIS)

Kelly, D.; Shepard, T.

2005-01-01

Research has not found a simple relationship between software complexity and software quality, and particularly no relationship between commonly used software complexity metrics and the occurrence of software faults. A study with an example of scientific software from the nuclear power industry illustrates the importance of addressing cognitive complexity, the complexity related to understanding the intellectual content of the software. Simple practices such as aptly-named variables contributes more to high quality software than limiting code sizes. This paper examines the research into complexity and quality and reports on a longitudinal study using the example of nuclear software. (author)

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

Science.gov (United States)

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

2015-01-01

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

Introducing the RadBioStat Educational Software: Computer-Assisted Teaching of the Random Nature of Cell Killing

Directory of Open Access Journals (Sweden)

Safari A

2014-06-01

Full Text Available The interaction of radiation with cells and tissues has a random nature. Therefore, understanding the random nature of cell killing that is determined by Poisson distribution statistics is an essential point in education of radiation biology. RadBioStat is a newly developed educational MATLAB-based software designed for computer-assisted learning of the target theory in radiation biology. Although its potential applications is developing rapidly, currently RadBioStat software can be a useful tool in computerassisted education of radiobiological models such as single target single hit, multiple target single hit and multiple target multiple hit. Scholars’ feedback is valuable to the producers of this software and help them continuously improve this product, add new features and increase its desirability and functionality.

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)

Computer software summaries. Numbers 325 through 423

International Nuclear Information System (INIS)

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

Product-oriented Software Certification Process for Software Synthesis

Science.gov (United States)

Nelson, Stacy; Fischer, Bernd; Denney, Ewen; Schumann, Johann; Richardson, Julian; Oh, Phil

2004-01-01

The purpose of this document is to propose a product-oriented software certification process to facilitate use of software synthesis and formal methods. Why is such a process needed? Currently, software is tested until deemed bug-free rather than proving that certain software properties exist. This approach has worked well in most cases, but unfortunately, deaths still occur due to software failure. Using formal methods (techniques from logic and discrete mathematics like set theory, automata theory and formal logic as opposed to continuous mathematics like calculus) and software synthesis, it is possible to reduce this risk by proving certain software properties. Additionally, software synthesis makes it possible to automate some phases of the traditional software development life cycle resulting in a more streamlined and accurate development process.

Studies and analyses of the space shuttle main engine. Failure information propagation model data base and software

Science.gov (United States)

Tischer, A. E.

1987-01-01

The failure information propagation model (FIPM) data base was developed to store and manipulate the large amount of information anticipated for the various Space Shuttle Main Engine (SSME) FIPMs. The organization and structure of the FIPM data base is described, including a summary of the data fields and key attributes associated with each FIPM data file. The menu-driven software developed to facilitate and control the entry, modification, and listing of data base records is also discussed. The transfer of the FIPM data base and software to the NASA Marshall Space Flight Center is described. Complete listings of all of the data base definition commands and software procedures are included in the appendixes.

A concept of software testing for SMART MMIS software

International Nuclear Information System (INIS)

Seo, Yong Seok; Seong, Seung Hwan; Park, Keun Ok; Hur, Sub; Kim, Dong Hoon

2001-01-01

In order to achieve high quality of SMART MMIS software, the well-constructed software testing concept shall be required. This paper established software testing concept which is to be applied to SMART MMIS software, in terms of software testing organization, documentation. procedure, and methods. The software testing methods are classified into source code static analysis and dynamic testing. The software dynamic testing methods are discussed with two aspects: white-box and black-box testing. As software testing concept introduced in this paper is applied to the SMART MMIS software. the high quality of the software will be produced. In the future, software failure data will be collected through the construction of SMART MMIS prototyping facility which the software testing concept of this paper is applied to

Model-driven development of smart grid services using SoaML

DEFF Research Database (Denmark)

Kosek, Anna Magdalena; Gehrke, Oliver

2014-01-01

This paper presents a model-driven software devel- opment process which can be applied to the design of smart grid services. The Service Oriented Architecture Modelling Language (SoaML) is used to describe the architecture as well as the roles and interactions between service participants....... The individual modelling steps and an example design of a SoaML model for a voltage control service are presented and explained. Finally, the paper discusses a proof-of-concept implementation of the modelled service in a smart grid testing laboratory....

ImagePy: an open-source, Python-based and platform-independent software package for boimage analysis.

Science.gov (United States)

Wang, Anliang; Yan, Xiaolong; Wei, Zhijun

2018-04-27

This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis. ImagePy is free and open source software, with documentation and code available at https://github.com/Image-Py/imagepy under the BSD license. It has been tested on the Windows, Mac and Linux operating systems. wzjdlut@dlut.edu.cn or yxdragon@imagepy.org.

Converted vehicle for battery electric drive. Aspects on the design of the software-driven vehicle control unit

Energy Technology Data Exchange (ETDEWEB)

Giessler, Martin; Paul, Jens; Gauterin, Frank [Karlsruher Institut fuer Technologie (KIT), Karlsruhe (Germany). Inst. fuer Fahrzeugsystemtechnik (FAST); Fritz, Alexander; Sander, Oliver; Mueller-Glaser, Klaus D. [Karlsruher Institut fuer Technologie (KIT), Karlsruhe (Germany). Inst. fuer Technik der Informationsverarbeitung (ITIV)

2012-11-01

At the Karlsruher Institute of Technology (KIT) a vehicle was converted for full battery electric drive within a cooperation of several faculties under the direction of the chair of vehicle technology. Within this paper the developed software to control the main functions of the vehicle will be presented and potentials to increase the energy efficiency will be discussed. The software based vehicle control unit is the central control unit to realize drivers command with respect to the system parameters, which are important for safety, dynamics, range and comfort of the vehicle. The structure of the software architecture, the interaction with the main electric vehicle specific control units and components and the main implemented functions will be described within this paper. The converted vehicle consists mainly of one electric motor with water cooled power electronics that drives the front axle, 21 battery modules controlled and managed by the battery management system, one on board charging device and an universal control unit. Not only strategies for power recovery while braking, but also strategies for driving and operation can help increase the energy efficiency. Select measures to recover and safe energy are also shown. (orig.)

Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges.

Science.gov (United States)

Stein, Lincoln D

2008-09-01

Biology is an information-driven science. Large-scale data sets from genomics, physiology, population genetics and imaging are driving research at a dizzying rate. Simultaneously, interdisciplinary collaborations among experimental biologists, theorists, statisticians and computer scientists have become the key to making effective use of these data sets. However, too many biologists have trouble accessing and using these electronic data sets and tools effectively. A 'cyberinfrastructure' is a combination of databases, network protocols and computational services that brings people, information and computational tools together to perform science in this information-driven world. This article reviews the components of a biological cyberinfrastructure, discusses current and pending implementations, and notes the many challenges that lie ahead.

Active machine learning-driven experimentation to determine compound effects on protein patterns.

Science.gov (United States)

Naik, Armaghan W; Kangas, Joshua D; Sullivan, Devin P; Murphy, Robert F

2016-02-03

High throughput screening determines the effects of many conditions on a given biological target. Currently, to estimate the effects of those conditions on other targets requires either strong modeling assumptions (e.g. similarities among targets) or separate screens. Ideally, data-driven experimentation could be used to learn accurate models for many conditions and targets without doing all possible experiments. We have previously described an active machine learning algorithm that can iteratively choose small sets of experiments to learn models of multiple effects. We now show that, with no prior knowledge and with liquid handling robotics and automated microscopy under its control, this learner accurately learned the effects of 48 chemical compounds on the subcellular localization of 48 proteins while performing only 29% of all possible experiments. The results represent the first practical demonstration of the utility of active learning-driven biological experimentation in which the set of possible phenotypes is unknown in advance.

Static and Dynamic Verification of Critical Software for Space Applications

Science.gov (United States)

Moreira, F.; Maia, R.; Costa, D.; Duro, N.; Rodríguez-Dapena, P.; Hjortnaes, K.

Space technology is no longer used only for much specialised research activities or for sophisticated manned space missions. Modern society relies more and more on space technology and applications for every day activities. Worldwide telecommunications, Earth observation, navigation and remote sensing are only a few examples of space applications on which we rely daily. The European driven global navigation system Galileo and its associated applications, e.g. air traffic management, vessel and car navigation, will significantly expand the already stringent safety requirements for space based applications Apart from their usefulness and practical applications, every single piece of onboard software deployed into the space represents an enormous investment. With a long lifetime operation and being extremely difficult to maintain and upgrade, at least when comparing with "mainstream" software development, the importance of ensuring their correctness before deployment is immense. Verification &Validation techniques and technologies have a key role in ensuring that the onboard software is correct and error free, or at least free from errors that can potentially lead to catastrophic failures. Many RAMS techniques including both static criticality analysis and dynamic verification techniques have been used as a means to verify and validate critical software and to ensure its correctness. But, traditionally, these have been isolated applied. One of the main reasons is the immaturity of this field in what concerns to its application to the increasing software product(s) within space systems. This paper presents an innovative way of combining both static and dynamic techniques exploiting their synergy and complementarity for software fault removal. The methodology proposed is based on the combination of Software FMEA and FTA with Fault-injection techniques. The case study herein described is implemented with support from two tools: The SoftCare tool for the SFMEA and SFTA

Quality assurance for CORAL and COOL within the LCG software stack for the LHC experiments

CERN Multimedia

CERN. Geneva

2015-01-01

CORAL and COOL are software packages used by the LHC experiments for managing different categories of physics data using a variety of relational database technologies. The core components are written in C++, but Python bindings are also provided. CORAL is a generic relational access layer, while COOL includes the implementation of a specific relational data model and optimization of SQL queries for "conditions data". The software is the result of more than 10 years of development in colaboration between the IT department and the LHC experiments. The packages are built and released within the LCG software stack, for which automatic nightly builds and release installations are provided by PH-SFT (cmake, jenkins, cdash) for many different platforms, compilers and software version configurations. Test-driven development and functional tests of both C++ and Python components (CppUnit, unittest) have been key elements in the success of the projects. Dedicated test suites have also been prepared to commission and ma...

Development strategies for the satellite flight software on-board Meteosat Third Generation

Science.gov (United States)

Tipaldi, Massimo; Legendre, Cedric; Koopmann, Olliver; Ferraguto, Massimo; Wenker, Ralf; D'Angelo, Gianni

2018-04-01

Nowadays, satellites are becoming increasingly software dependent. Satellite Flight Software (FSW), that is to say, the application software running on the satellite main On-Board Computer (OBC), plays a relevant role in implementing complex space mission requirements. In this paper, we examine relevant technical approaches and programmatic strategies adopted for the development of the Meteosat Third Generation Satellite (MTG) FSW. To begin with, we present its layered model-based architecture, and the means for ensuring a robust and reliable interaction among the FSW components. Then, we focus on the selection of an effective software development life cycle model. In particular, by combining plan-driven and agile approaches, we can fulfill the need of having preliminary SW versions. They can be used for the elicitation of complex system-level requirements as well as for the initial satellite integration and testing activities. Another important aspect can be identified in the testing activities. Indeed, very demanding quality requirements have to be fulfilled in satellite SW applications. This manuscript proposes a test automation framework, which uses an XML-based test procedure language independent of the underlying test environment. Finally, a short overview of the MTG FSW sizing and timing budgets concludes the paper.

Software Maintenance and Evolution: The Implication for Software ...

African Journals Online (AJOL)

Software Maintenance and Evolution: The Implication for Software Development. ... Software maintenance is the process of modifying existing operational software by correcting errors, ... EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT

Artificial cognitive memory—changing from density driven to functionality driven

Science.gov (United States)

Shi, L. P.; Yi, K. J.; Ramanathan, K.; Zhao, R.; Ning, N.; Ding, D.; Chong, T. C.

2011-03-01

Increasing density based on bit size reduction is currently a main driving force for the development of data storage technologies. However, it is expected that all of the current available storage technologies might approach their physical limits in around 15 to 20 years due to miniaturization. To further advance the storage technologies, it is required to explore a new development trend that is different from density driven. One possible direction is to derive insights from biological counterparts. Unlike physical memories that have a single function of data storage, human memory is versatile. It contributes to functions of data storage, information processing, and most importantly, cognitive functions such as adaptation, learning, perception, knowledge generation, etc. In this paper, a brief review of current data storage technologies are presented, followed by discussions of future storage technology development trend. We expect that the driving force will evolve from density to functionality, and new memory modules associated with additional functions other than only data storage will appear. As an initial step toward building a future generation memory technology, we propose Artificial Cognitive Memory (ACM), a memory based intelligent system. We also present the characteristics of ACM, new technologies that can be used to develop ACM components such as bioinspired element cells (silicon, memristor, phase change, etc.), and possible methodologies to construct a biologically inspired hierarchical system.

ATLAS tile calorimeter cesium calibration control and analysis software

International Nuclear Information System (INIS)

Solovyanov, O; Solodkov, A; Starchenko, E; Karyukhin, A; Isaev, A; Shalanda, N

2008-01-01

An online control system to calibrate and monitor ATLAS Barrel hadronic calorimeter (TileCal) with a movable radioactive source, driven by liquid flow, is described. To read out and control the system an online software has been developed, using ATLAS TDAQ components like DVS (Diagnostic and Verification System) to verify the hardware before running, IS (Information Server) for data and status exchange between networked computers, and other components like DDC (DCS to DAQ Connection), to connect to PVSS-based slow control systems of Tile Calorimeter, high voltage and low voltage. A system of scripting facilities, based on Python language, is used to handle all the calibration and monitoring processes from hardware perspective to final data storage, including various abnormal situations. A QT based graphical user interface to display the status of the calibration system during the cesium source scan is described. The software for analysis of the detector response, using online data, is discussed. Performance of the system and first experience from the ATLAS pit are presented

ATLAS tile calorimeter cesium calibration control and analysis software

Energy Technology Data Exchange (ETDEWEB)

Solovyanov, O; Solodkov, A; Starchenko, E; Karyukhin, A; Isaev, A; Shalanda, N [Institute for High Energy Physics, Protvino 142281 (Russian Federation)], E-mail: Oleg.Solovyanov@ihep.ru

2008-07-01

An online control system to calibrate and monitor ATLAS Barrel hadronic calorimeter (TileCal) with a movable radioactive source, driven by liquid flow, is described. To read out and control the system an online software has been developed, using ATLAS TDAQ components like DVS (Diagnostic and Verification System) to verify the hardware before running, IS (Information Server) for data and status exchange between networked computers, and other components like DDC (DCS to DAQ Connection), to connect to PVSS-based slow control systems of Tile Calorimeter, high voltage and low voltage. A system of scripting facilities, based on Python language, is used to handle all the calibration and monitoring processes from hardware perspective to final data storage, including various abnormal situations. A QT based graphical user interface to display the status of the calibration system during the cesium source scan is described. The software for analysis of the detector response, using online data, is discussed. Performance of the system and first experience from the ATLAS pit are presented.

Advanced software development workstation. Comparison of two object-oriented development methodologies

Science.gov (United States)

Izygon, Michel E.

1992-01-01

This report is an attempt to clarify some of the concerns raised about the OMT method, specifically that OMT is weaker than the Booch method in a few key areas. This interim report specifically addresses the following issues: (1) is OMT object-oriented or only data-driven?; (2) can OMT be used as a front-end to implementation in C++?; (3) the inheritance concept in OMT is in contradiction with the 'pure and real' inheritance concept found in object-oriented (OO) design; (4) low support for software life-cycle issues, for project and risk management; (5) uselessness of functional modeling for the ROSE project; and (6) problems with event-driven and simulation systems. The conclusion of this report is that both Booch's method and Rumbaugh's method are good OO methods, each with strengths and weaknesses in different areas of the development process.

Model format for a vaccine stability report and software solutions.

Science.gov (United States)

Shin, Jinho; Southern, James; Schofield, Timothy

2009-11-01

A session of the International Association for Biologicals Workshop on Stability Evaluation of Vaccine, a Life Cycle Approach was devoted to a model format for a vaccine stability report, and software solutions. Presentations highlighted the utility of a model format that will conform to regulatory requirements and the ICH common technical document. However, there need be flexibility to accommodate individual company practices. Adoption of a model format is premised upon agreement regarding content between industry and regulators, and ease of use. Software requirements will include ease of use and protections against inadvertent misspecification of stability design or misinterpretation of program output.

Comparative exploration of multidimensional flow cytometry software: a model approach evaluating T cell polyfunctional behavior.

Science.gov (United States)

Spear, Timothy T; Nishimura, Michael I; Simms, Patricia E

2017-08-01

Advancement in flow cytometry reagents and instrumentation has allowed for simultaneous analysis of large numbers of lineage/functional immune cell markers. Highly complex datasets generated by polychromatic flow cytometry require proper analytical software to answer investigators' questions. A problem among many investigators and flow cytometry Shared Resource Laboratories (SRLs), including our own, is a lack of access to a flow cytometry-knowledgeable bioinformatics team, making it difficult to learn and choose appropriate analysis tool(s). Here, we comparatively assess various multidimensional flow cytometry software packages for their ability to answer a specific biologic question and provide graphical representation output suitable for publication, as well as their ease of use and cost. We assessed polyfunctional potential of TCR-transduced T cells, serving as a model evaluation, using multidimensional flow cytometry to analyze 6 intracellular cytokines and degranulation on a per-cell basis. Analysis of 7 parameters resulted in 128 possible combinations of positivity/negativity, far too complex for basic flow cytometry software to analyze fully. Various software packages were used, analysis methods used in each described, and representative output displayed. Of the tools investigated, automated classification of cellular expression by nonlinear stochastic embedding (ACCENSE) and coupled analysis in Pestle/simplified presentation of incredibly complex evaluations (SPICE) provided the most user-friendly manipulations and readable output, evaluating effects of altered antigen-specific stimulation on T cell polyfunctionality. This detailed approach may serve as a model for other investigators/SRLs in selecting the most appropriate software to analyze complex flow cytometry datasets. Further development and awareness of available tools will help guide proper data analysis to answer difficult biologic questions arising from incredibly complex datasets. © Society

WE-G-BRA-02: SafetyNet: Automating Radiotherapy QA with An Event Driven Framework

International Nuclear Information System (INIS)

Hadley, S; Kessler, M; Litzenberg, D; Lee, C; Irrer, J; Chen, X; Acosta, E; Weyburne, G; Lam, K; Younge, K; Matuszak, M; Keranen, W; Covington, E; Moran, J

2015-01-01

Purpose: Quality assurance is an essential task in radiotherapy that often requires many manual tasks. We investigate the use of an event driven framework in conjunction with software agents to automate QA and eliminate wait times. Methods: An in house developed subscription-publication service, EventNet, was added to the Aria OIS to be a message broker for critical events occurring in the OIS and software agents. Software agents operate without user intervention and perform critical QA steps. The results of the QA are documented and the resulting event is generated and passed back to EventNet. Users can subscribe to those events and receive messages based on custom filters designed to send passing or failing results to physicists or dosimetrists. Agents were developed to expedite the following QA tasks: Plan Revision, Plan 2nd Check, SRS Winston-Lutz isocenter, Treatment History Audit, Treatment Machine Configuration. Results: Plan approval in the Aria OIS was used as the event trigger for plan revision QA and Plan 2nd check agents. The agents pulled the plan data, executed the prescribed QA, stored the results and updated EventNet for publication. The Winston Lutz agent reduced QA time from 20 minutes to 4 minutes and provided a more accurate quantitative estimate of radiation isocenter. The Treatment Machine Configuration agent automatically reports any changes to the Treatment machine or HDR unit configuration. The agents are reliable, act immediately, and execute each task identically every time. Conclusion: An event driven framework has inverted the data chase in our radiotherapy QA process. Rather than have dosimetrists and physicists push data to QA software and pull results back into the OIS, the software agents perform these steps immediately upon receiving the sentinel events from EventNet. Mr Keranen is an employee of Varian Medical Systems. Dr. Moran’s institution receives research support for her effort for a linear accelerator QA project from

WE-G-BRA-02: SafetyNet: Automating Radiotherapy QA with An Event Driven Framework

Energy Technology Data Exchange (ETDEWEB)

Hadley, S; Kessler, M [The University of Michigan, Ann Arbor, MI (United States); Litzenberg, D [Univ Michigan, Ann Arbor, MI (United States); Lee, C; Irrer, J; Chen, X; Acosta, E; Weyburne, G; Lam, K; Younge, K; Matuszak, M [University of Michigan, Ann Arbor, MI (United States); Keranen, W [Varian Medical Systems, Palo Alto, CA (United States); Covington, E [University of Michigan Hospital and Health System, Ann Arbor, MI (United States); Moran, J [Univ Michigan Medical Center, Ann Arbor, MI (United States)

2015-06-15

Purpose: Quality assurance is an essential task in radiotherapy that often requires many manual tasks. We investigate the use of an event driven framework in conjunction with software agents to automate QA and eliminate wait times. Methods: An in house developed subscription-publication service, EventNet, was added to the Aria OIS to be a message broker for critical events occurring in the OIS and software agents. Software agents operate without user intervention and perform critical QA steps. The results of the QA are documented and the resulting event is generated and passed back to EventNet. Users can subscribe to those events and receive messages based on custom filters designed to send passing or failing results to physicists or dosimetrists. Agents were developed to expedite the following QA tasks: Plan Revision, Plan 2nd Check, SRS Winston-Lutz isocenter, Treatment History Audit, Treatment Machine Configuration. Results: Plan approval in the Aria OIS was used as the event trigger for plan revision QA and Plan 2nd check agents. The agents pulled the plan data, executed the prescribed QA, stored the results and updated EventNet for publication. The Winston Lutz agent reduced QA time from 20 minutes to 4 minutes and provided a more accurate quantitative estimate of radiation isocenter. The Treatment Machine Configuration agent automatically reports any changes to the Treatment machine or HDR unit configuration. The agents are reliable, act immediately, and execute each task identically every time. Conclusion: An event driven framework has inverted the data chase in our radiotherapy QA process. Rather than have dosimetrists and physicists push data to QA software and pull results back into the OIS, the software agents perform these steps immediately upon receiving the sentinel events from EventNet. Mr Keranen is an employee of Varian Medical Systems. Dr. Moran’s institution receives research support for her effort for a linear accelerator QA project from

Small-scale fixed wing airplane software verification flight test

Science.gov (United States)

Miller, Natasha R.

The increased demand for micro Unmanned Air Vehicles (UAV) driven by military requirements, commercial use, and academia is creating a need for the ability to quickly and accurately conduct low Reynolds Number aircraft design. There exist several open source software programs that are free or inexpensive that can be used for large scale aircraft design, but few software programs target the realm of low Reynolds Number flight. XFLR5 is an open source, free to download, software program that attempts to take into consideration viscous effects that occur at low Reynolds Number in airfoil design, 3D wing design, and 3D airplane design. An off the shelf, remote control airplane was used as a test bed to model in XFLR5 and then compared to flight test collected data. Flight test focused on the stability modes of the 3D plane, specifically the phugoid mode. Design and execution of the flight tests were accomplished for the RC airplane using methodology from full scale military airplane test procedures. Results from flight test were not conclusive in determining the accuracy of the XFLR5 software program. There were several sources of uncertainty that did not allow for a full analysis of the flight test results. An off the shelf drone autopilot was used as a data collection device for flight testing. The precision and accuracy of the autopilot is unknown. Potential future work should investigate flight test methods for small scale UAV flight.

Model-driven engineering of information systems principles, techniques, and practice

CERN Document Server

Cretu, Liviu Gabriel

2015-01-01

Model-driven engineering (MDE) is the automatic production of software from simplified models of structure and functionality. It mainly involves the automation of the routine and technologically complex programming tasks, thus allowing developers to focus on the true value-adding functionality that the system needs to deliver. This book serves an overview of some of the core topics in MDE. The volume is broken into two sections offering a selection of papers that helps the reader not only understand the MDE principles and techniques, but also learn from practical examples. Also covered are the

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.

Solution Proposals for Japan-Oriented Offshore Software Development in China

Science.gov (United States)

Zhang, Lei; Zhang, Xuan; Chai, Meiping; Tan, Yibing; Miyake, Shigeru; Taniguchi, Yoji; Hosoya, Jun; Mibe, Ryota

Surveys on the Japan-oriented vendors in China were conducted twice to find out the existent problems in the Japan-oriented offshore software development. From these survey results, four main problems were found out, which were the frequent requirement changes from the product owner, the misunderstanding of the requirement specification in the vendor side, the heavy overhead of the project management and the low-efficiency communication between the product owner and the vendor. Several solutions are proposed to solve these four problems, which mainly consist of the improvement of the offshore software development process and the development of the offshore development supporting tools. The proposed offshore development process is based on the application of the prototype development, the iteration development and the customer test driven development processes. The proposed offshore development supporting tools include the project management assistant tool and the communication assistant tool.

Interactive analysis of systems biology molecular expression data

Directory of Open Access Journals (Sweden)

Prabhakar Sunil

2008-02-01

Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

Software quality assurance plans for safety-critical software

International Nuclear Information System (INIS)

Liddle, P.

2006-01-01

Application software is defined as safety-critical if a fault in the software could prevent the system components from performing their nuclear-safety functions. Therefore, for nuclear-safety systems, the AREVA TELEPERM R XS (TXS) system is classified 1E, as defined in the Inst. of Electrical and Electronics Engineers (IEEE) Std 603-1998. The application software is classified as Software Integrity Level (SIL)-4, as defined in IEEE Std 7-4.3.2-2003. The AREVA NP Inc. Software Program Manual (SPM) describes the measures taken to ensure that the TELEPERM XS application software attains a level of quality commensurate with its importance to safety. The manual also describes how TELEPERM XS correctly performs the required safety functions and conforms to established technical and documentation requirements, conventions, rules, and standards. The program manual covers the requirements definition, detailed design, integration, and test phases for the TELEPERM XS application software, and supporting software created by AREVA NP Inc. The SPM is required for all safety-related TELEPERM XS system applications. The program comprises several basic plans and practices: 1. A Software Quality-Assurance Plan (SQAP) that describes the processes necessary to ensure that the software attains a level of quality commensurate with its importance to safety function. 2. A Software Safety Plan (SSP) that identifies the process to reasonably ensure that safety-critical software performs as intended during all abnormal conditions and events, and does not introduce any new hazards that could jeopardize the health and safety of the public. 3. A Software Verification and Validation (V and V) Plan that describes the method of ensuring the software is in accordance with the requirements. 4. A Software Configuration Management Plan (SCMP) that describes the method of maintaining the software in an identifiable state at all times. 5. A Software Operations and Maintenance Plan (SO and MP) that

The Evolution of Software and Its Impact on Complex System Design in Robotic Spacecraft Embedded Systems

Science.gov (United States)

Butler, Roy

2013-01-01

The growth in computer hardware performance, coupled with reduced energy requirements, has led to a rapid expansion of the resources available to software systems, driving them towards greater logical abstraction, flexibility, and complexity. This shift in focus from compacting functionality into a limited field towards developing layered, multi-state architectures in a grand field has both driven and been driven by the history of embedded processor design in the robotic spacecraft industry.The combinatorial growth of interprocess conditions is accompanied by benefits (concurrent development, situational autonomy, and evolution of goals) and drawbacks (late integration, non-deterministic interactions, and multifaceted anomalies) in achieving mission success, as illustrated by the case of the Mars Reconnaissance Orbiter. Approaches to optimizing the benefits while mitigating the drawbacks have taken the form of the formalization of requirements, modular design practices, extensive system simulation, and spacecraft data trend analysis. The growth of hardware capability and software complexity can be expected to continue, with future directions including stackable commodity subsystems, computer-generated algorithms, runtime reconfigurable processors, and greater autonomy.

RSYST: From nuclear reactor calculations towards a highly sophisticated scientific software integration environment

International Nuclear Information System (INIS)

Noack, M.; Seybold, J.; Ruehle, R.

1996-01-01

The software environment RSYST was originally used to solve problems of reactor physics. The consideration of advanced scientific simulation requirements and the strict application of modern software design principles led to a system which is perfectly suitable to solve problems in various complex scientific problem domains. Starting with a review of the early days of RSYST, we describe the straight evolution driven by the need of software environment which combines the advantages of a high-performance database system with the capability to integrate sophisticated scientific technical applications. The RSYST architecture is presented and the data modelling capabilities are described. To demonstrate the powerful possibilities and flexibility of the RSYST environment, we describe a wide range of RSYST applications, e.g., mechanical simulations of multibody systems, which are used in biomechanical research, civil engineering and robotics. In addition, a hypermedia system which is used for scientific technical training and documentation is presented. (orig.) [de

Intellectual Property Protection of Software – At the Crossroads of Software Patents and Open Source Software

OpenAIRE

Tantarimäki, Maria

2018-01-01

The thesis considers the intellectual property protection of software in Europe and in the US, which is increasingly important subject as the world is globalizing and digitalizing. The special nature of software has challenges the intellectual property rights. The current protection of software is based on copyright protection but in this thesis, two other options are considered: software patents and open source software. Software patents provide strong protection for software whereas the pur...

Molecular dynamics for irradiation driven chemistry: application to the FEBID process*

Science.gov (United States)

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

2016-10-01

A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields 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 parameters for the fragments of the molecular system arising in the course of irradiation one can reproduce reasonably well experimental observations and make predictions about the morphology and molecular composition of nanostructures that emerge on the surface during the FEBID process.

A novel industry grade dataset for fault prediction based on model-driven developed automotive embedded software

NARCIS (Netherlands)

Altinger, H.; Siegl, S.; Dajsuren, Y.; Wotawa, F.

2015-01-01

In this paper, we present a novel industry dataset on static software and change metrics for Matlab/Simulink models and their corresponding auto-generated C source code. The data set comprises data of three automotive projects developed and tested accordingly to industry standards and restrictive

Software Quality Assurance in Software Projects: A Study of Pakistan

OpenAIRE

Faisal Shafique Butt; Sundus Shaukat; M. Wasif Nisar; Ehsan Ullah Munir; Muhammad Waseem; Kashif Ayyub

2013-01-01

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 Qu...

Intrafirm knowledge transfer of agile software practices: barriers and their relations

DEFF Research Database (Denmark)

Tordrup Heeager, Lise; Nielsen, Peter Axel

2018-01-01

to knowledge transfer, we modify and extend the framework to transferring knowledge of agile practices. This framework is subsequently applied for interpreting and analyzing the case study data. The analysis shows how these barriers (e.g., the organizational culture, time and resources, knowledge strategy......Agile software practices are widely used in a great variety of organizations, and the shift from traditional plan-driven approaches entails a redefinition of processes in these organizations. Intrafirm knowledge transfer of agile software practices between projects is a key concern...... in this redefinition. While knowledge transfer is essential for an organization to develop or keep its competitive advantage, it is also both difficult and time consuming, due to a wide range of barriers. Transferring knowledge on agile practices is even more complex due to there being a high degree of tacit knowledge...

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

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

Science.gov (United States)

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

2015-01-01

To develop expeditiously a pragmatic, modular, and extensible software framework for understanding and improving healthcare value (costs relative to outcomes). In 2012, a multidisciplinary team was assembled by the leadership of the University of Utah Health Sciences Center and charged with rapidly developing a pragmatic and actionable analytics framework for understanding and enhancing healthcare value. Based on an analysis of relevant prior work, a value analytics framework known as Value Driven Outcomes (VDO) was developed using an agile methodology. Evaluation consisted of measurement against project objectives, including implementation timeliness, system performance, completeness, accuracy, extensibility, adoption, satisfaction, and the ability to support value improvement. A modular, extensible framework was developed to allocate clinical care costs to individual patient encounters. For example, labor costs in a hospital unit are allocated to patients based on the hours they spent in the unit; actual medication acquisition costs are allocated to patients based on utilization; and radiology costs are allocated based on the minutes required for study performance. Relevant process and outcome measures are also available. A visualization layer facilitates the identification of value improvement opportunities, such as high-volume, high-cost case types with high variability in costs across providers. Initial implementation was completed within 6 months, and all project objectives were fulfilled. The framework has been improved iteratively and is now a foundational tool for delivering high-value care. The framework described can be expeditiously implemented to provide a pragmatic, modular, and extensible approach to understanding and improving healthcare value. © The Author 2014. Published by Oxford University Press on behalf of the American Medical Informatics Association.

A software engineering process for safety-critical software application

International Nuclear Information System (INIS)

Kang, Byung Heon; Kim, Hang Bae; Chang, Hoon Seon; Jeon, Jong Sun

1995-01-01

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)

Precision medicine driven by cancer systems biology.

Science.gov (United States)

Filipp, Fabian V

2017-03-01

Molecular insights from genome and systems biology are influencing how cancer is diagnosed and treated. We critically evaluate big data challenges in precision medicine. The melanoma research community has identified distinct subtypes involving chronic sun-induced damage and the mitogen-activated protein kinase driver pathway. In addition, despite low mutation burden, non-genomic mitogen-activated protein kinase melanoma drivers are found in membrane receptors, metabolism, or epigenetic signaling with the ability to bypass central mitogen-activated protein kinase molecules and activating a similar program of mitogenic effectors. Mutation hotspots, structural modeling, UV signature, and genomic as well as non-genomic mechanisms of disease initiation and progression are taken into consideration to identify resistance mutations and novel drug targets. A comprehensive precision medicine profile of a malignant melanoma patient illustrates future rational drug targeting strategies. Network analysis emphasizes an important role of epigenetic and metabolic master regulators in oncogenesis. Co-occurrence of driver mutations in signaling, metabolic, and epigenetic factors highlights how cumulative alterations of our genomes and epigenomes progressively lead to uncontrolled cell proliferation. Precision insights have the ability to identify independent molecular pathways suitable for drug targeting. Synergistic treatment combinations of orthogonal modalities including immunotherapy, mitogen-activated protein kinase inhibitors, epigenetic inhibitors, and metabolic inhibitors have the potential to overcome immune evasion, side effects, and drug resistance.

Software architecture analysis tool : software architecture metrics collection

NARCIS (Netherlands)

Muskens, J.; Chaudron, M.R.V.; Westgeest, R.

2002-01-01

The Software Engineering discipline lacks the ability to evaluate software architectures. Here we describe a tool for software architecture analysis that is based on metrics. Metrics can be used to detect possible problems and bottlenecks in software architectures. Even though metrics do not give a

Customer Interaction in Software Development: A Comparison of Software Methodologies Deployed in Namibian Software Firms

CSIR Research Space (South Africa)

Iyawa, GE

2016-01-01

Full Text Available within the Namibian context. An implication for software project managers and software developers is that customer interaction should be properly managed to ensure that the software methodologies for improving software development processes...

Structure and software tools of AIDA.

Science.gov (United States)

Duisterhout, J S; Franken, B; Witte, F

1987-01-01

AIDA consists of a set of software tools to allow for fast development and easy-to-maintain Medical Information Systems. AIDA supports all aspects of such a system both during development and operation. It contains tools to build and maintain forms for interactive data entry and on-line input validation, a database management system including a data dictionary and a set of run-time routines for database access, and routines for querying the database and output formatting. Unlike an application generator, the user of AIDA may select parts of the tools to fulfill his needs and program other subsystems not developed with AIDA. The AIDA software uses as host language the ANSI-standard programming language MUMPS, an interpreted language embedded in an integrated database and programming environment. This greatly facilitates the portability of AIDA applications. The database facilities supported by AIDA are based on a relational data model. This data model is built on top of the MUMPS database, the so-called global structure. This relational model overcomes the restrictions of the global structure regarding string length. The global structure is especially powerful for sorting purposes. Using MUMPS as a host language allows the user an easy interface between user-defined data validation checks or other user-defined code and the AIDA tools. AIDA has been designed primarily for prototyping and for the construction of Medical Information Systems in a research environment which requires a flexible approach. The prototyping facility of AIDA operates terminal independent and is even to a great extent multi-lingual. Most of these features are table-driven; this allows on-line changes in the use of terminal type and language, but also causes overhead. AIDA has a set of optimizing tools by which it is possible to build a faster, but (of course) less flexible code from these table definitions. By separating the AIDA software in a source and a run-time version, one is able to write

Cancer: a profit-driven biosystem?

Science.gov (United States)

Deisboeck, Thomas S

2008-08-01

The argument is made that solid malignant tumors behave as profit-driven biological systems in that they expand their nutrient-uptaking surface to increase energetic revenue, at a comparably low metabolic cost. Within this conceptual framework, cancer cell migration is a critical mechanism as it maximizes systemic surface expansion while minimizing diffusion distance. Treating these tumor systems with adjuvant anti-proliferative regimen only should increase the energetic net gain of the viable cancer cells left behind, hence would facilitate tumor recurrence. Therapeutic attempts to better control tumor (re)growth should therefore aim primarily at containing its surface expansion, thus reducing its energetic revenue, or increasing its metabolic costs or better yet, both.

A SOFTWARE RELIABILITY ESTIMATION METHOD TO NUCLEAR SAFETY SOFTWARE

Directory of Open Access Journals (Sweden)

GEE-YONG PARK

2014-02-01

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

Setting Parameters for Biological Models With ANIMO

NARCIS (Netherlands)

Schivo, Stefano; Scholma, Jetse; Karperien, Hermanus Bernardus Johannes; Post, Janine Nicole; van de Pol, Jan Cornelis; Langerak, Romanus; André, Étienne; Frehse, Goran

2014-01-01

ANIMO (Analysis of Networks with Interactive MOdeling) is a software for modeling biological networks, such as e.g. signaling, metabolic or gene networks. An ANIMO model is essentially the sum of a network topology and a number of interaction parameters. The topology describes the interactions

Building Software, Building Community: Lessons from the Ropensci Project

Science.gov (United States)

Boettiger, C.

2014-12-01

rOpenSci is a developer collective originally formed in 2011 by graduate students and post-docs from ecology and evolutionary biology to collaborate on building software tools to facilitate a more open and synthetic approach in the face of transformative rise of large and heterogeneous data. Born on the internet (the collective only began through chance discussions over social media), we have grown into a widely recognized effort that supports an ecosystem of some 45software packages, engages scores of collaborators, has taught dozens of workshops around the world, and has secured over $480,000 in grant support. As young scientists working in an academic context largely without direct support for our efforts, we have first hand experience with most of the the technical and social challenges in developing sustainable scientific software. I will summarize our experiences, the challenges we have faced, and describe our approach and success in building an effective and diverse community around the rOpenSci project.

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.

Synthetic Biology with Cytochromes P450 Using Photosynthetic Chassis

DEFF Research Database (Denmark)

Gnanasekaran, Thiyagarajan

, this modern field of synthetic biology is completely dependent on the nature of the chassis - the host organisms - for its endeavor. Of all the chassis, photosynthetic organisms such as cyanobacteria and plants gains special attention due to the remarkable amount of sunlight that is striking the Earth...... in cyanobacteria and plant chloroplasts for the purpose of light driven synthesis of bioactive compounds by using synthetic biology approaches. As model pathways, in this thesis, the pathway involved in the synthesis of the cyanogenic glucoside dhurrin from Sorghum bicolor, and the pathway involved......Synthetic biology is a rapidly growing engineering discipline in biology. It aims at building novel biological systems that do not exist in nature by selecting the interchangeable standardized biological parts that are already available in the nature, and assembling them in a specific order. Today...

Combining Domain-driven Design and Mashups for Service Development

Science.gov (United States)

Iglesias, Carlos A.; Fernández-Villamor, José Ignacio; Del Pozo, David; Garulli, Luca; García, Boni

This chapter presents the Romulus project approach to Service Development using Java-based web technologies. Romulus aims at improving productivity of service development by providing a tool-supported model to conceive Java-based web applications. This model follows a Domain Driven Design approach, which states that the primary focus of software projects should be the core domain and domain logic. Romulus proposes a tool-supported model, Roma Metaframework, that provides an abstraction layer on top of existing web frameworks and automates the application generation from the domain model. This metaframework follows an object centric approach, and complements Domain Driven Design by identifying the most common cross-cutting concerns (security, service, view, ...) of web applications. The metaframework uses annotations for enriching the domain model with these cross-cutting concerns, so-called aspects. In addition, the chapter presents the usage of mashup technology in the metaframework for service composition, using the web mashup editor MyCocktail. This approach is applied to a scenario of the Mobile Phone Service Portability case study for the development of a new service.

Rules of thumb to increase the software quality through testing

Science.gov (United States)

Buttu, M.; Bartolini, M.; Migoni, C.; Orlati, A.; Poppi, S.; Righini, S.

2016-07-01

The software maintenance typically requires 40-80% of the overall project costs, and this considerable variability mostly depends on the software internal quality: the more the software is designed and implemented to constantly welcome new changes, the lower will be the maintenance costs. The internal quality is typically enforced through testing, which in turn also affects the development and maintenance costs. This is the reason why testing methodologies have become a major concern for any company that builds - or is involved in building - software. Although there is no testing approach that suits all contexts, we infer some general guidelines learned during the Development of the Italian Single-dish COntrol System (DISCOS), which is a project aimed at producing the control software for the three INAF radio telescopes (the Medicina and Noto dishes, and the newly-built SRT). These guidelines concern both the development and the maintenance phases, and their ultimate goal is to maximize the DISCOS software quality through a Behavior-Driven Development (BDD) workflow beside a continuous delivery pipeline. We consider different topics and patterns; they involve the proper apportion of the tests (from end-to-end to low-level tests), the choice between hardware simulators and mockers, why and how to apply TDD and the dependency injection to increase the test coverage, the emerging technologies available for test isolation, bug fixing, how to protect the system from the external resources changes (firmware updating, hardware substitution, etc.) and, eventually, how to accomplish BDD starting from functional tests and going through integration and unit tests. We discuss pros and cons of each solution and point out the motivations of our choices either as a general rule or narrowed in the context of the DISCOS project.

Cloudweaver: Adaptive and Data-Driven Workload Manager for Generic Clouds

Science.gov (United States)

Li, Rui; Chen, Lei; Li, Wen-Syan

Cloud computing denotes the latest trend in application development for parallel computing on massive data volumes. It relies on clouds of servers to handle tasks that used to be managed by an individual server. With cloud computing, software vendors can provide business intelligence and data analytic services for internet scale data sets. Many open source projects, such as Hadoop, offer various software components that are essential for building a cloud infrastructure. Current Hadoop (and many others) requires users to configure cloud infrastructures via programs and APIs and such configuration is fixed during the runtime. In this chapter, we propose a workload manager (WLM), called CloudWeaver, which provides automated configuration of a cloud infrastructure for runtime execution. The workload management is data-driven and can adapt to dynamic nature of operator throughput during different execution phases. CloudWeaver works for a single job and a workload consisting of multiple jobs running concurrently, which aims at maximum throughput using a minimum set of processors.

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.

Design Automation in Synthetic Biology.

Science.gov (United States)

Appleton, Evan; Madsen, Curtis; Roehner, Nicholas; Densmore, Douglas

2017-04-03

Design automation refers to a category of software tools for designing systems that work together in a workflow for designing, building, testing, and analyzing systems with a target behavior. In synthetic biology, these tools are called bio-design automation (BDA) tools. In this review, we discuss the BDA tools areas-specify, design, build, test, and learn-and introduce the existing software tools designed to solve problems in these areas. We then detail the functionality of some of these tools and show how they can be used together to create the desired behavior of two types of modern synthetic genetic regulatory networks. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Simulation on the Performance of a Driven Fan Made by Polyester/Epoxy interpenetrate polymer network (IPN)

Science.gov (United States)

Fahrul Hassan, Mohd; Jamri, Azmil; Nawawi, Azli; Zaini Yunos, Muhamad; Fauzi Ahmad, Md; Adzila, Sharifah; Nasrull Abdol Rahman, Mohd

2017-08-01

The main purpose of this study is to investigate the performance of a driven fan design made by Polyester/Epoxy interpenetrate polymer network (IPN) material that specifically used for turbocharger compressor. Polyester/Epoxy IPN is polymer plastics that was used as replacements for traditional polymers and has been widely used in a variety of applications because of their limitless conformations. Simulation based on several parameters which are air pressure, air velocity and air temperature have been carried out for a driven fan design performance of two different materials, aluminum alloy (existing driven fan design) and Polyester/Epoxy IPN using SolidWorks Flow Simulation software. Results from both simulations were analyzed and compared where both materials show similar performance in terms of air pressure and air velocity due to similar geometric and dimension, but Polyester/Epoxy IPN produces lower air temperature than aluminum alloy. This study shows a preliminary result of the potential Polyester/Epoxy IPN to be used as a driven fan design material. In the future, further studies will be conducted on detail simulation and experimental analysis.

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.

Culture, Urbanism and Changing Human Biology.

Science.gov (United States)

Schell, L M

2014-04-03

Anthropologists have long known that human activity driven by culture changes the environment. This is apparent in the archaeological record and through the study of the modern environment. Perhaps the largest change since the paleolithic era is the organization of human populations in cities. New environments can reshape human biology through evolution as shown by the evolution of the hominid lineage. Evolution is not the only process capable of reshaping our biology. Some changes in our human biology are adaptive and evolutionary while others are pathological. What changes in human biology may be wrought by the modern urban environment? One significant new change in the environment is the introduction of pollutants largely through urbanization. Pollutants can affect human biology in myriad ways. Evidence shows that human growth, reproduction, and cognitive functioning can be altered by some pollutants, and altered in different ways depending on the pollutant. Thus, pollutants have significance for human biologists and anthropologists generally. Further, they illustrate the bio-cultural interaction characterizing human change. Humans adapt by changing the environment, a cultural process, and then change biologically to adjust to that new environment. This ongoing, interactive process is a fundamental characteristic of human change over the millennia.

Design of pressure-driven microfluidic networks using electric circuit analogy.

Science.gov (United States)

Oh, Kwang W; Lee, Kangsun; Ahn, Byungwook; Furlani, Edward P

2012-02-07

This article reviews the application of electric circuit methods for the analysis of pressure-driven microfluidic networks with an emphasis on concentration- and flow-dependent systems. The application of circuit methods to microfluidics is based on the analogous behaviour of hydraulic and electric circuits with correlations of pressure to voltage, volumetric flow rate to current, and hydraulic to electric resistance. Circuit analysis enables rapid predictions of pressure-driven laminar flow in microchannels and is very useful for designing complex microfluidic networks in advance of fabrication. This article provides a comprehensive overview of the physics of pressure-driven laminar flow, the formal analogy between electric and hydraulic circuits, applications of circuit theory to microfluidic network-based devices, recent development and applications of concentration- and flow-dependent microfluidic networks, and promising future applications. The lab-on-a-chip (LOC) and microfluidics community will gain insightful ideas and practical design strategies for developing unique microfluidic network-based devices to address a broad range of biological, chemical, pharmaceutical, and other scientific and technical challenges.

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...

Data processing software for purex plant process control laboratory

International Nuclear Information System (INIS)

Kansara, V.P.; Achuthan, P.V.; Sridhar, S.; Ramanujam, A.; Dhumwad, R.K.

1990-01-01

A software has been developed at the Fuel Reprocessing Division, Trombay to meet the data processing needs of the Control Laboratory of a reprocessing plant. During the normal plant operations contents of over one hundred process tanks have to be sampled and analysed for regular monitoring. In order to speed up the computation and the reporting of results as well as to obtain the process performance data over a period of time a software has been developed. The package has been sucessfully demonstrated and implemented at the Plutonium Plant, Trombay. This has been in continuous use since May 1987 with highly satisfactory performance. The software is a totally menu-driven package which can be used by the laboratory analysts with a few hours of training. The features include data validation involving source tank identification, the nature of the sample, the range of expected results, any duplication in sample numbering etc. Audio indication of deviations from the expected input or output values are given with an option to override in case of abnormal samples. The progress of analysis can be obtained for a given sample at any given time. Incorporated in the software is the help menu for quick reference of analytical protocol to be followed for a given tank/method. The computations for the determinations are carried out after obtaining input values on a screen-form. Th e results can be displayed on the monitor or obtained in the form of a hard copy i n any desired format. (author). 17 figs., 2 refs

Software system safety

Science.gov (United States)

Uber, James G.

1988-01-01

Software itself is not hazardous, but since software and hardware share common interfaces there is an opportunity for software to create hazards. Further, these software systems are complex, and proven methods for the design, analysis, and measurement of software safety are not yet available. Some past software failures, future NASA software trends, software engineering methods, and tools and techniques for various software safety analyses are reviewed. Recommendations to NASA are made based on this review.

On Rank Driven Dynamical Systems

Science.gov (United States)

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

2014-08-01

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

Using systems and structure biology tools to dissect cellular phenotypes.

Science.gov (United States)

Floratos, Aris; Honig, Barry; Pe'er, Dana; Califano, Andrea

2012-01-01

The Center for the Multiscale Analysis of Genetic Networks (MAGNet, http://magnet.c2b2.columbia.edu) was established in 2005, with the mission of providing the biomedical research community with Structural and Systems Biology algorithms and software tools for the dissection of molecular interactions and for the interaction-based elucidation of cellular phenotypes. Over the last 7 years, MAGNet investigators have developed many novel analysis methodologies, which have led to important biological discoveries, including understanding the role of the DNA shape in protein-DNA binding specificity and the discovery of genes causally related to the presentation of malignant phenotypes, including lymphoma, glioma, and melanoma. Software tools implementing these methodologies have been broadly adopted by the research community and are made freely available through geWorkbench, the Center's integrated analysis platform. Additionally, MAGNet has been instrumental in organizing and developing key conferences and meetings focused on the emerging field of systems biology and regulatory genomics, with special focus on cancer-related research.

For fun and profit a history of the free and open source software revolution

CERN Document Server

Tozzi, Christopher

2017-01-01

In the 1980s, there was a revolution with far-reaching consequences -- a revolution to restore software freedom. In the early 1980s, after decades of making source code available with programs, most programmers ceased sharing code freely. A band of revolutionaries, self-described "hackers," challenged this new norm by building operating systems with source code that could be freely shared. In For Fun and Profit, Christopher Tozzi offers an account of the free and open source software (FOSS) revolution, from its origins as an obscure, marginal effort by a small group of programmers to the widespread commercial use of open source software today. Tozzi explains FOSS's historical trajectory, shaped by eccentric personalities -- including Richard Stallman and Linus Torvalds -- and driven both by ideology and pragmatism, by fun and profit. Tozzi examines hacker culture and its influence on the Unix operating system, the reaction to Unix's commercialization, and the history of early Linux development. He describes ...

Classification Systems, their Digitization and Consequences for Data-Driven Decision Making

DEFF Research Database (Denmark)

Stein, Mari-Klara; Newell, Sue; Galliers, Robert D.

2013-01-01

Classification systems are foundational in many standardized software tools. This digitization of classification systems gives them a new ‘materiality’ that, jointly with the social practices of information producers/consumers, has significant consequences on the representational quality of such ...... and the foundational role of representational quality in understanding the success and consequences of data-driven decision-making.......-narration and meta-narration), and three different information production/consumption situations. We contribute to the relational theorization of representational quality and extend classification systems research by drawing explicit attention to the importance of ‘materialization’ of classification systems...

Pulsed radiobiology with laser-driven plasma accelerators

Science.gov (United States)

Giulietti, Antonio; Grazia Andreassi, Maria; Greco, Carlo

2011-05-01

Recently, a high efficiency regime of acceleration in laser plasmas has been discovered, allowing table top equipment to deliver doses of interest for radiotherapy with electron bunches of suitable kinetic energy. In view of an R&D program aimed to the realization of an innovative class of accelerators for medical uses, a radiobiological validation is needed. At the present time, the biological effects of electron bunches from the laser-driven electron accelerator are largely unknown. In radiobiology and radiotherapy, it is known that the early spatial distribution of energy deposition following ionizing radiation interactions with DNA molecule is crucial for the prediction of damages at cellular or tissue levels and during the clinical responses to this irradiation. The purpose of the present study is to evaluate the radio-biological effects obtained with electron bunches from a laser-driven electron accelerator compared with bunches coming from a IORT-dedicated medical Radio-frequency based linac's on human cells by the cytokinesis block micronucleus assay (CBMN). To this purpose a multidisciplinary team including radiotherapists, biologists, medical physicists, laser and plasma physicists is working at CNR Campus and University of Pisa. Dose on samples is delivered alternatively by the "laser-linac" operating at ILIL lab of Istituto Nazionale di Ottica and an RF-linac operating for IORT at Pisa S. Chiara Hospital. Experimental data are analyzed on the basis of suitable radiobiological models as well as with numerical simulation based on Monte Carlo codes. Possible collective effects are also considered in the case of ultrashort, ultradense bunches of ionizing radiation.

Documentation Driven Software Development

Science.gov (United States)

2010-06-01

governmental organizations, and private companies and volunteer organizations. There is usually very little overlap between each of the aforementioned...Process Variables in Complex B2B Systems Integration Assessment,” Proceedings of the IEEE International Conference on E-Commerce Technology (CEC 2004...Innovation Engine for Online Analytics and Information Assurance in Enterprise B2B Infrastructure,” Paper presented at the Fifth International

Integrated Biological Warfare Technology Platform (IBWTP). Intelligent Software Supporting Situation Awareness, Response, and Operations

Science.gov (United States)

2007-01-01

phases of the technology, QLI used a common software development and maintenance environment, called the Quantum Leap Uber Build System (QLUBS). QLI...May be used in internal tools and application. Using internally developed code on internal application ( Eating your own dogfood) provides

Small-scale laser based electron accelerators for biology and medicine: a comparative study of the biological effectiveness

Science.gov (United States)

Labate, Luca; Andreassi, Maria Grazia; Baffigi, Federica; Basta, Giuseppina; Bizzarri, Ranieri; Borghini, Andrea; Candiano, Giuliana C.; Casarino, Carlo; Cresci, Monica; Di Martino, Fabio; Fulgentini, Lorenzo; Ghetti, Francesco; Gilardi, Maria Carla; Giulietti, Antonio; Köster, Petra; Lenci, Francesco; Levato, Tadzio; Oishi, Yuji; Russo, Giorgio; Sgarbossa, Antonella; Traino, Claudio; Gizzi, Leonida A.

2013-05-01

Laser-driven electron accelerators based on the Laser Wakefield Acceleration process has entered a mature phase to be considered as alternative devices to conventional radiofrequency linear accelerators used in medical applications. Before entering the medical practice, however, deep studies of the radiobiological effects of such short bunches as the ones produced by laser-driven accelerators have to be performed. Here we report on the setup, characterization and first test of a small-scale laser accelerator for radiobiology experiments. A brief description of the experimental setup will be given at first, followed by an overview of the electron bunch characterization, in particular in terms of dose delivered to the samples. Finally, the first results from the irradiation of biological samples will be briefly discussed.

Avoidable Software Procurements

Science.gov (United States)

2012-09-01

software license, software usage, ELA, Software as a Service , SaaS , Software Asset...PaaS Platform as a Service SaaS Software as a Service SAM Software Asset Management SMS System Management Server SEWP Solutions for Enterprise Wide...delivery of full Cloud Services , we will see the transition of the Cloud Computing service model from Iaas to SaaS , or Software as a Service . Software

Event management for large scale event-driven digital hardware spiking neural networks.

Science.gov (United States)

Caron, Louis-Charles; D'Haene, Michiel; Mailhot, Frédéric; Schrauwen, Benjamin; Rouat, Jean

2013-09-01

The interest in brain-like computation has led to the design of a plethora of innovative neuromorphic systems. Individually, spiking neural networks (SNNs), event-driven simulation and digital hardware neuromorphic systems get a lot of attention. Despite the popularity of event-driven SNNs in software, very few digital hardware architectures are found. This is because existing hardware solutions for event management scale badly with the number of events. This paper introduces the structured heap queue, a pipelined digital hardware data structure, and demonstrates its suitability for event management. The structured heap queue scales gracefully with the number of events, allowing the efficient implementation of large scale digital hardware event-driven SNNs. The scaling is linear for memory, logarithmic for logic resources and constant for processing time. The use of the structured heap queue is demonstrated on a field-programmable gate array (FPGA) with an image segmentation experiment and a SNN of 65,536 neurons and 513,184 synapses. Events can be processed at the rate of 1 every 7 clock cycles and a 406×158 pixel image is segmented in 200 ms. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

Concurrent software system design supported by SARA at the age of one

Energy Technology Data Exchange (ETDEWEB)

Campos, I.M.; Estrin, G.

A multilevel modeling method suitable for the design of concurrent hardware or software systems is presented. The methodology is requirement driven and uses tools incorporated in a programming system called SARA (Systems ARchitect's Apprentice). Both top-down refinement and bottom-up abstraction are supported. The design of an asynchronous sender-receiver illustrates the key steps in going smoothly from programing in the large to programing in the small or actual code. The same methodology can be used to design hardware systems by applying different pragmatics from those proposed for software systems. SARA consists of a set of interactive tools implemented both at UCLA and also on the MIT-Multics system. Although SARA continues in long-term development, completed design tools are accessible for experimentation by authorized users at either location via the ARPANET. 9 figures, 2 tables.

Using CONFIG for Simulation of Operation of Water Recovery Subsystems for Advanced Control Software Evaluation

Science.gov (United States)

Malin, Jane T.; Flores, Luis; Fleming, Land; Throop, Daiv

2002-01-01

A hybrid discrete/continuous simulation tool, CONFIG, has been developed to support evaluation of the operability life support systems. CON FIG simulates operations scenarios in which flows and pressures change continuously while system reconfigurations occur as discrete events. In simulations, intelligent control software can interact dynamically with hardware system models. CONFIG simulations have been used to evaluate control software and intelligent agents for automating life support systems operations. A CON FIG model of an advanced biological water recovery system has been developed to interact with intelligent control software that is being used in a water system test at NASA Johnson Space Center

Ultra-Structure database design methodology for managing systems biology data and analyses

Directory of Open Access Journals (Sweden)

Hemminger Bradley M

2009-08-01

Full Text Available Abstract Background Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these factors, systems designed to manage and integrate modern biological data sets often end up as large, unwieldy databases that become difficult to maintain or evolve. The novel rule-based approach of the Ultra-Structure design methodology presents a potential solution to this problem. By representing both data and processes as formal rules within a database, an Ultra-Structure system constitutes a flexible framework that enables users to explicitly store domain knowledge in both a machine- and human-readable form. End users themselves can change the system's capabilities without programmer intervention, simply by altering database contents; no computer code or schemas need be modified. This provides flexibility in adapting to change, and allows integration of disparate, heterogenous data sets within a small core set of database tables, facilitating joint analysis and visualization without becoming unwieldy. Here, we examine the application of Ultra-Structure to our ongoing research program for the integration of large proteomic and genomic data sets (proteogenomic mapping. Results We transitioned our proteogenomic mapping information system from a traditional entity-relationship design to one based on Ultra-Structure. Our system integrates tandem mass spectrum data, genomic annotation sets, and spectrum/peptide mappings, all within a small, general framework implemented within a standard relational database system. General software procedures driven by user-modifiable rules can perform tasks such as logical deduction and location-based computations. The system is not tied specifically to proteogenomic research, but is rather designed to accommodate virtually any kind of biological research. Conclusion We find

Free software, Open source software, licenses. A short presentation including a procedure for research software and data dissemination

OpenAIRE

Gomez-Diaz , Teresa

2014-01-01

4 pages. Spanish version: Software libre, software de código abierto, licencias. Donde se propone un procedimiento de distribución de software y datos de investigación; The main goal of this document is to help the research community to understand the basic concepts of software distribution: Free software, Open source software, licenses. This document also includes a procedure for research software and data dissemination.

An Unprecedented Revolution in Medicinal Chemistry Driven by the Progress of Biological Science.

Science.gov (United States)

Chou, Kuo-Chen

2017-01-01

The eternal or ultimate goal of medicinal chemistry is to find most effective ways to treat various diseases and extend human beings' life as long as possible. Human being is a biological entity. To realize such an ultimate goal, the inputs or breakthroughs from the advances in biological science are no doubt most important that may even drive medicinal science into a revolution. In this review article, we are to address this from several different angles. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Model-driven Privacy Assessment in the Smart Grid

Energy Technology Data Exchange (ETDEWEB)

Knirsch, Fabian [Salzburg Univ. (Austria); Engel, Dominik [Salzburg Univ. (Austria); Neureiter, Christian [Salzburg Univ. (Austria); Frincu, Marc [Univ. of Southern California, Los Angeles, CA (United States); Prasanna, Viktor [Univ. of Southern California, Los Angeles, CA (United States)

2015-02-09

In a smart grid, data and information are transported, transmitted, stored, and processed with various stakeholders having to cooperate effectively. Furthermore, personal data is the key to many smart grid applications and therefore privacy impacts have to be taken into account. For an effective smart grid, well integrated solutions are crucial and for achieving a high degree of customer acceptance, privacy should already be considered at design time of the system. To assist system engineers in early design phase, frameworks for the automated privacy evaluation of use cases are important. For evaluation, use cases for services and software architectures need to be formally captured in a standardized and commonly understood manner. In order to ensure this common understanding for all kinds of stakeholders, reference models have recently been developed. In this paper we present a model-driven approach for the automated assessment of such services and software architectures in the smart grid that builds on the standardized reference models. The focus of qualitative and quantitative evaluation is on privacy. For evaluation, the framework draws on use cases from the University of Southern California microgrid.

The Program for Climate Model Diagnosis and Intercomparison (PCMDI) Software Development: Applications, Infrastructure, and Middleware/Networks

Energy Technology Data Exchange (ETDEWEB)

Williams, Dean N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2011-06-30

The status of and future plans for the Program for Climate Model Diagnosis and Intercomparison (PCMDI) hinge on software that PCMDI is either currently distributing or plans to distribute to the climate community in the near future. These software products include standard conventions, national and international federated infrastructures, and community analysis and visualization tools. This report also mentions other secondary software not necessarily led by or developed at PCMDI to provide a complete picture of the overarching applications, infrastructures, and middleware/networks. Much of the software described anticipates the use of future technologies envisioned over the span of next year to 10 years. These technologies, together with the software, will be the catalyst required to address extreme-scale data warehousing, scalability issues, and service-level requirements for a diverse set of well-known projects essential for predicting climate change. These tools, unlike the previous static analysis tools of the past, will support the co-existence of many users in a productive, shared virtual environment. This advanced technological world driven by extreme-scale computing and the data it generates will increase scientists’ productivity, exploit national and international relationships, and push research to new levels of understanding.

Chaste: an open source C++ library for computational physiology and biology.

KAUST Repository

Mirams, Gary R; Arthurs, Christopher J; Bernabeu, Miguel O; Bordas, Rafel; Cooper, Jonathan; Corrias, Alberto; Davit, Yohan; Dunn, Sara-Jane; Fletcher, Alexander G; Harvey, Daniel G; Marsh, Megan E; Osborne, James M; Pathmanathan, Pras; Pitt-Francis, Joe; Southern, James; Zemzemi, Nejib; Gavaghan, David J

2013-01-01

Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to 're-invent the wheel' with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials.

Chaste: an open source C++ library for computational physiology and biology.

Directory of Open Access Journals (Sweden)

Gary R Mirams

Full Text Available Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs. Re-use of these components avoids the need for researchers to 're-invent the wheel' with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials.

Chaste: an open source C++ library for computational physiology and biology.

KAUST Repository

Mirams, Gary R

2013-03-14

Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to \\'re-invent the wheel\\' with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials.

Implementing a modeling software for animated protein-complex interactions using a physics simulation library.

Science.gov (United States)

Ueno, Yutaka; Ito, Shuntaro; Konagaya, Akihiko

2014-12-01

To better understand the behaviors and structural dynamics of proteins within a cell, novel software tools are being developed that can create molecular animations based on the findings of structural biology. This study proposes our method developed based on our prototypes to detect collisions and examine the soft-body dynamics of molecular models. The code was implemented with a software development toolkit for rigid-body dynamics simulation and a three-dimensional graphics library. The essential functions of the target software system included the basic molecular modeling environment, collision detection in the molecular models, and physical simulations of the movement of the model. Taking advantage of recent software technologies such as physics simulation modules and interpreted scripting language, the functions required for accurate and meaningful molecular animation were implemented efficiently.

Value Co-creation in the Cloud : Understanding Software-as-a-Service-Driven Convergence of the Enterprise Systems and Financial Services Industries

NARCIS (Netherlands)

Teracino, Elizabeth Anne

2017-01-01

Enterprise systemen worden meer en meer gehost in de cloud en aangeboden als een dienst, volgens het zogenaamde software-als-een-dienst (Software-as-a-Service, of afgekort, SaaS) business model. Ook financiële dienstverleners zijn SaaS aan het invoeren en passen hierdoor de wijze waarop zij hun

Performance analysis and optimization of an advanced pharmaceutical wastewater treatment plant through a visual basic software tool (PWWT.VB).

Science.gov (United States)

Pal, Parimal; Thakura, Ritwik; Chakrabortty, Sankha

2016-05-01

A user-friendly, menu-driven simulation software tool has been developed for the first time to optimize and analyze the system performance of an advanced continuous membrane-integrated pharmaceutical wastewater treatment plant. The software allows pre-analysis and manipulation of input data which helps in optimization and shows the software performance visually on a graphical platform. Moreover, the software helps the user to "visualize" the effects of the operating parameters through its model-predicted output profiles. The software is based on a dynamic mathematical model, developed for a systematically integrated forward osmosis-nanofiltration process for removal of toxic organic compounds from pharmaceutical wastewater. The model-predicted values have been observed to corroborate well with the extensive experimental investigations which were found to be consistent under varying operating conditions like operating pressure, operating flow rate, and draw solute concentration. Low values of the relative error (RE = 0.09) and high values of Willmott-d-index (d will = 0.981) reflected a high degree of accuracy and reliability of the software. This software is likely to be a very efficient tool for system design or simulation of an advanced membrane-integrated treatment plant for hazardous wastewater.

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…

The NUKDOS software for dosimetry in molecular radiotherapy

International Nuclear Information System (INIS)

Kletting, P.; Schimmel, S.; Haenscheid, H.; Fernandez, M.; Lassmann, M.; Broer, J.; Nosske, D.; Glatting, G.

2015-01-01

Full text of publication follows. Aim: The NUKDOS software is developed to improve and standardize therapy planning in molecular radiotherapy (MRT). Methods: NUKDOS is developed in Matlab, based on the MIRD formalism, modularly structured and currently allows dosimetry for Y-90, Lu-177, I-131. First, the user enters the basic patient data and specifies the injected activities. Second, 3D or 2D images can be loaded. Based on the voxel-size and the used nuclide the corresponding voxel S-values (>1 mm) are calculated. Serum, probe or urine data can be entered and processed. To get the activity distribution of the organs for all serial measurements, the user is led to the image processing tool. This tool includes all functionality for defining the regions or volumes of interest (ROIs/VOIs). ROIs/VOIs can also be created in a corresponding CT image and subsequently transferred to the SPECT/PET images. Time activity curves (TACs) derived from 2D scans are scaled using the averaged organ activity of a 3D image. To determine the time-integrated activity coefficients A, the areas under the time activity curves are calculated. For this purpose, a set of fit functions can be chosen. The selection of the most suitable function is based on the Akaike Information Criterion and statistical measures. The most suitable TACs are integrated analytically and including the standard errors. Absorbed dose coefficients are calculated by convolution using the voxel based A and S value matrices. Depending on the absorbed dose (or biologically effective dose) for the limiting organ the activity to administer along with the pertaining organ doses is calculated using the absorbed dose coefficients. Results: proper implementation of the mathematical methods of each module of the software was tested by comparing the results to currently available software. The applicability of the software was investigated using phantom measurement and examples from MRT. User interaction is minimized

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....

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.

Science.gov (United States)

Rose, Peter W; Prlić, Andreas; Bi, Chunxiao; Bluhm, Wolfgang F; Christie, Cole H; Dutta, Shuchismita; Green, Rachel Kramer; Goodsell, David S; Westbrook, John D; Woo, Jesse; Young, Jasmine; Zardecki, Christine; Berman, Helen M; Bourne, Philip E; Burley, Stephen K

2015-01-01

The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Cellular potts models multiscale extensions and biological applications

CERN Document Server

Scianna, Marco

2013-01-01

A flexible, cell-level, and lattice-based technique, the cellular Potts model accurately describes the phenomenological mechanisms involved in many biological processes. Cellular Potts Models: Multiscale Extensions and Biological Applications gives an interdisciplinary, accessible treatment of these models, from the original methodologies to the latest developments. The book first explains the biophysical bases, main merits, and limitations of the cellular Potts model. It then proposes several innovative extensions, focusing on ways to integrate and interface the basic cellular Potts model at the mesoscopic scale with approaches that accurately model microscopic dynamics. These extensions are designed to create a nested and hybrid environment, where the evolution of a biological system is realistically driven by the constant interplay and flux of information between the different levels of description. Through several biological examples, the authors demonstrate a qualitative and quantitative agreement with t...

A market-driven approach based on Markov decision theory for optimal use of resources in software development

NARCIS (Netherlands)

Noppen, J.A.R.; Eisenbach, S.; Aksit, Mehmet; Nicola, V.F.; Tekinerdogan, B.

2004-01-01

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

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

A software for parameter optimization with Differential Evolution Entirely Parallel method

Directory of Open Access Journals (Sweden)

Konstantin Kozlov

2016-08-01

Full Text Available Summary. Differential Evolution Entirely Parallel (DEEP package is a software for finding unknown real and integer parameters in dynamical models of biological processes by minimizing one or even several objective functions that measure the deviation of model solution from data. Numerical solutions provided by the most efficient global optimization methods are often problem-specific and cannot be easily adapted to other tasks. In contrast, DEEP allows a user to describe both mathematical model and objective function in any programming language, such as R, Octave or Python and others. Being implemented in C, DEEP demonstrates as good performance as the top three methods from CEC-2014 (Competition on evolutionary computation benchmark and was successfully applied to several biological problems. Availability. DEEP method is an open source and free software distributed under the terms of GPL licence version 3. The sources are available at http://deepmethod.sourceforge.net/ and binary packages for Fedora GNU/Linux are provided for RPM package manager at https://build.opensuse.org/project/repositories/home:mackoel:compbio.

Software Epistemology

Science.gov (United States)

2016-03-01

in-vitro decision to incubate a startup, Lexumo [7], which is developing a commercial Software as a Service ( SaaS ) vulnerability assessment...LTS Label Transition System MUSE Mining and Understanding Software Enclaves RTEMS Real-Time Executive for Multi-processor Systems SaaS Software ...as a Service SSA Static Single Assignment SWE Software Epistemology UD/DU Def-Use/Use-Def Chains (Dataflow Graph)

The SOFIA Mission Control System Software

Science.gov (United States)

Heiligman, G. M.; Brock, D. R.; Culp, S. D.; Decker, P. H.; Estrada, J. C.; Graybeal, J. B.; Nichols, D. M.; Paluzzi, P. R.; Sharer, P. J.; Pampell, R. J.; Papke, B. L.; Salovich, R. D.; Schlappe, S. B.; Spriestersbach, K. K.; Webb, G. L.

1999-05-01

The Stratospheric Observatory for Infrared Astronomy (SOFIA) will be delivered with a computerized mission control system (MCS). The MCS communicates with the aircraft's flight management system and coordinates the operations of the telescope assembly, mission-specific subsystems, and the science instruments. The software for the MCS must be reliable and flexible. It must be easily usable by many teams of observers with widely differing needs, and it must support non-intrusive access for education and public outreach. The technology must be appropriate for SOFIA's 20-year lifetime. The MCS software development process is an object-oriented, use case driven approach. The process is iterative: delivery will be phased over four "builds"; each build will be the result of many iterations; and each iteration will include analysis, design, implementation, and test activities. The team is geographically distributed, coordinating its work via Web pages, teleconferences, T.120 remote collaboration, and CVS (for Internet-enabled configuration management). The MCS software architectural design is derived in part from other observatories' experience. Some important features of the MCS are: * distributed computing over several UNIX and VxWorks computers * fast throughput of time-critical data * use of third-party components, such as the Adaptive Communications Environment (ACE) and the Common Object Request Broker Architecture (CORBA) * extensive configurability via stored, editable configuration files * use of several computer languages so developers have "the right tool for the job". C++, Java, scripting languages, Interactive Data Language (from Research Systems, Int'l.), XML, and HTML will all be used in the final deliverables. This paper reports on work in progress, with the final product scheduled for delivery in 2001. This work was performed for Universities Space Research Association for NASA under contract NAS2-97001.

NASA Data Acquisition System Software Development for Rocket Propulsion Test Facilities

Science.gov (United States)

Herbert, Phillip W., Sr.; Elliot, Alex C.; Graves, Andrew R.

2015-01-01

Current NASA propulsion test facilities include Stennis Space Center in Mississippi, Marshall Space Flight Center in Alabama, Plum Brook Station in Ohio, and White Sands Test Facility in New Mexico. Within and across these centers, a diverse set of data acquisition systems exist with different hardware and software platforms. The NASA Data Acquisition System (NDAS) is a software suite designed to operate and control many critical aspects of rocket engine testing. The software suite combines real-time data visualization, data recording to a variety formats, short-term and long-term acquisition system calibration capabilities, test stand configuration control, and a variety of data post-processing capabilities. Additionally, data stream conversion functions exist to translate test facility data streams to and from downstream systems, including engine customer systems. The primary design goals for NDAS are flexibility, extensibility, and modularity. Providing a common user interface for a variety of hardware platforms helps drive consistency and error reduction during testing. In addition, with an understanding that test facilities have different requirements and setups, the software is designed to be modular. One engine program may require real-time displays and data recording; others may require more complex data stream conversion, measurement filtering, or test stand configuration management. The NDAS suite allows test facilities to choose which components to use based on their specific needs. The NDAS code is primarily written in LabVIEW, a graphical, data-flow driven language. Although LabVIEW is a general-purpose programming language; large-scale software development in the language is relatively rare compared to more commonly used languages. The NDAS software suite also makes extensive use of a new, advanced development framework called the Actor Framework. The Actor Framework provides a level of code reuse and extensibility that has previously been difficult

NeuroDebian Virtual Machine Deployment Facilitates Trainee-Driven Bedside Neuroimaging Research.

Science.gov (United States)

Cohen, Alexander; Kenney-Jung, Daniel; Botha, Hugo; Tillema, Jan-Mendelt

2017-01-01

Freely available software, derived from the past 2 decades of neuroimaging research, is significantly more flexible for research purposes than presently available clinical tools. Here, we describe and demonstrate the utility of rapidly deployable analysis software to facilitate trainee-driven translational neuroimaging research. A recipe and video tutorial were created to guide the creation of a NeuroDebian-based virtual computer that conforms to current neuroimaging research standards and can exist within a HIPAA-compliant system. This allows for retrieval of clinical imaging data, conversion to standard file formats, and rapid visualization and quantification of individual patients' cortical and subcortical anatomy. As an example, we apply this pipeline to a pediatric patient's data to illustrate the advantages of research-derived neuroimaging tools in asking quantitative questions "at the bedside." Our goal is to provide a path of entry for trainees to become familiar with common neuroimaging tools and foster an increased interest in translational research.

Data Driven - Android based displays on data acquisition and system status

CERN Document Server

Canilho, Paulo

2014-01-01

For years, both hardware and software engineers have struggled with the acquisition of device information in a flexible and fast perspective, numerous devices cannot have their status quickly tested due to time limitation associated with the travelling to a computer terminal. For instance, in order to test a scintillator status, one has to inject beam into the device and quickly return to a terminal to see the results, this is not only time demanding but extremely inconvenient for the person responsible, it consumes time that would be used in more pressing matters. In this train of thoughts, the proposal of creating an interface to bring a stable, flexible, user friendly and data driven solution to this problem was created. Being the most common operative system for mobile display, the Android API proved to have the best efficient in financing, since it is based on an open source software, and in implementation difficulty since it’s backend development resides in JAVA calls and XML for visual representation...

Computer software.

Science.gov (United States)

Rosenthal, L E

1986-10-01

Software is the component in a computer system that permits the hardware to perform the various functions that a computer system is capable of doing. The history of software and its development can be traced to the early nineteenth century. All computer systems are designed to utilize the "stored program concept" as first developed by Charles Babbage in the 1850s. The concept was lost until the mid-1940s, when modern computers made their appearance. Today, because of the complex and myriad tasks that a computer system can perform, there has been a differentiation of types of software. There is software designed to perform specific business applications. There is software that controls the overall operation of a computer system. And there is software that is designed to carry out specialized tasks. Regardless of types, software is the most critical component of any computer system. Without it, all one has is a collection of circuits, transistors, and silicone chips.

Leaf-GP: an open and automated software application for measuring growth phenotypes for arabidopsis and wheat.

Science.gov (United States)

Zhou, Ji; Applegate, Christopher; Alonso, Albor Dobon; Reynolds, Daniel; Orford, Simon; Mackiewicz, Michal; Griffiths, Simon; Penfield, Steven; Pullen, Nick

2017-01-01

Plants demonstrate dynamic growth phenotypes that are determined by genetic and environmental factors. Phenotypic analysis of growth features over time is a key approach to understand how plants interact with environmental change as well as respond to different treatments. Although the importance of measuring dynamic growth traits is widely recognised, available open software tools are limited in terms of batch image processing, multiple traits analyses, software usability and cross-referencing results between experiments, making automated phenotypic analysis problematic. Here, we present Leaf-GP (Growth Phenotypes), an easy-to-use and open software application that can be executed on different computing platforms. To facilitate diverse scientific communities, we provide three software versions, including a graphic user interface (GUI) for personal computer (PC) users, a command-line interface for high-performance computer (HPC) users, and a well-commented interactive Jupyter Notebook (also known as the iPython Notebook) for computational biologists and computer scientists. The software is capable of extracting multiple growth traits automatically from large image datasets. We have utilised it in Arabidopsis thaliana and wheat ( Triticum aestivum ) growth studies at the Norwich Research Park (NRP, UK). By quantifying a number of growth phenotypes over time, we have identified diverse plant growth patterns between different genotypes under several experimental conditions. As Leaf-GP has been evaluated with noisy image series acquired by different imaging devices (e.g. smartphones and digital cameras) and still produced reliable biological outputs, we therefore believe that our automated analysis workflow and customised computer vision based feature extraction software implementation can facilitate a broader plant research community for their growth and development studies. Furthermore, because we implemented Leaf-GP based on open Python-based computer vision, image

Workshop and conference on Grand Challenges applications and software technology

Energy Technology Data Exchange (ETDEWEB)

1993-12-31

On May 4--7, 1993, nine federal agencies sponsored a four-day meeting on Grand Challenge applications and software technology. The objective was to bring High-Performance Computing and Communications (HPCC) Grand Challenge applications research groups supported under the federal HPCC program together with HPCC software technologists to: discuss multidisciplinary computational science research issues and approaches, identify major technology challenges facing users and providers, and refine software technology requirements for Grand Challenge applications research. The first day and a half focused on applications. Presentations were given by speakers from universities, national laboratories, and government agencies actively involved in Grand Challenge research. Five areas of research were covered: environmental and earth sciences; computational physics; computational biology, chemistry, and materials sciences; computational fluid and plasma dynamics; and applications of artificial intelligence. The next day and a half was spent in working groups in which the applications researchers were joined by software technologists. Nine breakout sessions took place: I/0, Data, and File Systems; Parallel Programming Paradigms; Performance Characterization and Evaluation of Massively Parallel Processing Applications; Program Development Tools; Building Multidisciplinary Applications; Algorithm and Libraries I; Algorithms and Libraries II; Graphics and Visualization; and National HPCC Infrastructure.

Studying cell biology in the skin.

Science.gov (United States)

Morrow, Angel; Lechler, Terry

2015-11-15

Advances in cell biology have often been driven by studies in diverse organisms and cell types. Although there are technical reasons for why different cell types are used, there are also important physiological reasons. For example, ultrastructural studies of vesicle transport were aided by the use of professional secretory cell types. The use of tissues/primary cells has the advantage not only of using cells that are adapted to the use of certain cell biological machinery, but also of highlighting the physiological roles of this machinery. Here we discuss advantages of the skin as a model system. We discuss both advances in cell biology that used the skin as a driving force and future prospects for use of the skin to understand basic cell biology. A unique combination of characteristics and tools makes the skin a useful in vivo model system for many cell biologists. © 2015 Morrow and Lechler. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Biocellion: accelerating computer simulation of multicellular biological system models.

Science.gov (United States)

Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

2014-11-01

Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A Comparative Evaluation of Videodiscs for General Biology.

Science.gov (United States)

Ralph, Charles L.

1995-01-01

Provides a brief profile of the currently available videodiscs for general biology, with comparable information for each. An introduction discusses benefits and problems associated with videodisc use in the classroom. Profiles contain information on description, good and bad features, still images, animations and movies, audio, software,…

Software engineering laboratory series: Annotated bibliography of software engineering laboratory literature

Science.gov (United States)

Morusiewicz, Linda; Valett, Jon

1992-01-01

This document is an annotated bibliography of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory. More than 100 publications are summarized. These publications cover many areas of software engineering and range from research reports to software documentation. This document has been updated and reorganized substantially since the original version (SEL-82-006, November 1982). All materials have been grouped into eight general subject areas for easy reference: (1) the Software Engineering Laboratory; (2) the Software Engineering Laboratory: Software Development Documents; (3) Software Tools; (4) Software Models; (5) Software Measurement; (6) Technology Evaluations; (7) Ada Technology; and (8) Data Collection. This document contains an index of these publications classified by individual author.

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.

From Software Development to Software Assembly

NARCIS (Netherlands)

Sneed, Harry M.; Verhoef, Chris

2016-01-01

The lack of skilled programming personnel and the growing burden of maintaining customized software are forcing organizations to quit producing their own software. It's high time they turned to ready-made, standard components to fulfill their business requirements. Cloud services might be one way to

Fast and predictable video compression in software design and implementation of an H.261 codec

Science.gov (United States)

Geske, Dagmar; Hess, Robert

1998-09-01

The use of software codecs for video compression becomes commonplace in several videoconferencing applications. In order to reduce conflicts with other applications used at the same time, mechanisms for resource reservation on endsystems need to determine an upper bound for computing time used by the codec. This leads to the demand for predictable execution times of compression/decompression. Since compression schemes as H.261 inherently depend on the motion contained in the video, an adaptive admission control is required. This paper presents a data driven approach based on dynamical reduction of the number of processed macroblocks in peak situations. Besides the absolute speed is a point of interest. The question, whether and how software compression of high quality video is feasible on today's desktop computers, is examined.

A Software Reuse Approach and Its Effect On Software Quality, An Empirical Study for The Software Industry

OpenAIRE

Mateen, Ahmed; Kausar, Samina; Sattar, Ahsan Raza

2017-01-01

Software reusability has become much interesting because of increased quality and reduce cost. A good process of software reuse leads to enhance the reliability, productivity, quality and the reduction of time and cost. Current reuse techniques focuses on the reuse of software artifact which grounded on anticipated functionality whereas, the non-functional (quality) aspect are also important. So, Software reusability used here to expand quality and productivity of software. It improves overal...

Software quality assurance: in large scale and complex software-intensive systems

NARCIS (Netherlands)

Mistrik, I.; Soley, R.; Ali, N.; Grundy, J.; Tekinerdogan, B.

2015-01-01

Software Quality Assurance in Large Scale and Complex Software-intensive Systems presents novel and high-quality research related approaches that relate the quality of software architecture to system requirements, system architecture and enterprise-architecture, or software testing. Modern software

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.

Software Tools for Emittance Measurement and Matching for 12 GeV CEBAF

Energy Technology Data Exchange (ETDEWEB)

Turner, Dennis L. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States)

2016-05-01

This paper discusses model-driven setup of the Continuous Electron Beam Accelerator Facility (CEBAF) for the 12GeV era, focusing on qsUtility. qsUtility is a set of software tools created to perform emittance measurements, analyze those measurements, and compute optics corrections based upon the measurements.qsUtility was developed as a toolset to facilitate reducing machine configuration time and reproducibility by way of an accurate accelerator model, and to provide Operations staff with tools to measure and correct machine optics with little or no assistance from optics experts.

Model-driven discovery of underground metabolic functions in Escherichia coli

DEFF Research Database (Denmark)

Guzmán, Gabriela I.; Utrilla, José; Nurk, Sergey

2015-01-01

-scale models, which have been widely used for predicting growth phenotypes in various environments or following a genetic perturbation; however, these predictions occasionally fail. Failed predictions of gene essentiality offer an opportunity for targeting biological discovery, suggesting the presence......E, and gltA and prpC. This study demonstrates how a targeted model-driven approach to discovery can systematically fill knowledge gaps, characterize underground metabolism, and elucidate regulatory mechanisms of adaptation in response to gene KO perturbations....

An Analysis of Security and Privacy Issues in Smart Grid Software Architectures on Clouds

Energy Technology Data Exchange (ETDEWEB)

Simmhan, Yogesh; Kumbhare, Alok; Cao, Baohua; Prasanna, Viktor K.

2011-07-09

Power utilities globally are increasingly upgrading to Smart Grids that use bi-directional communication with the consumer to enable an information-driven approach to distributed energy management. Clouds offer features well suited for Smart Grid software platforms and applications, such as elastic resources and shared services. However, the security and privacy concerns inherent in an information rich Smart Grid environment are further exacerbated by their deployment on Clouds. Here, we present an analysis of security and privacy issues in a Smart Grids software architecture operating on different Cloud environments, in the form of a taxonomy. We use the Los Angeles Smart Grid Project that is underway in the largest U.S. municipal utility to drive this analysis that will benefit both Cloud practitioners targeting Smart Grid applications, and Cloud researchers investigating security and privacy.

[Application of microelectronics CAD tools to synthetic biology].

Science.gov (United States)

Madec, Morgan; Haiech, Jacques; Rosati, Élise; Rezgui, Abir; Gendrault, Yves; Lallement, Christophe

2017-02-01

Synthetic biology is an emerging science that aims to create new biological functions that do not exist in nature, based on the knowledge acquired in life science over the last century. Since the beginning of this century, several projects in synthetic biology have emerged. The complexity of the developed artificial bio-functions is relatively low so that empirical design methods could be used for the design process. Nevertheless, with the increasing complexity of biological circuits, this is no longer the case and a large number of computer aided design softwares have been developed in the past few years. These tools include languages for the behavioral description and the mathematical modelling of biological systems, simulators at different levels of abstraction, libraries of biological devices and circuit design automation algorithms. All of these tools already exist in other fields of engineering sciences, particularly in microelectronics. This is the approach that is put forward in this paper. © 2017 médecine/sciences – Inserm.

Computer-Aided Software Engineering - An approach to real-time software development

Science.gov (United States)

Walker, Carrie K.; Turkovich, John J.

1989-01-01

A new software engineering discipline is Computer-Aided Software Engineering (CASE), a technology aimed at automating the software development process. This paper explores the development of CASE technology, particularly in the area of real-time/scientific/engineering software, and a history of CASE is given. The proposed software development environment for the Advanced Launch System (ALS CASE) is described as an example of an advanced software development system for real-time/scientific/engineering (RT/SE) software. The Automated Programming Subsystem of ALS CASE automatically generates executable code and corresponding documentation from a suitably formatted specification of the software requirements. Software requirements are interactively specified in the form of engineering block diagrams. Several demonstrations of the Automated Programming Subsystem are discussed.

A finite volume method for density driven flows in porous media

Directory of Open Access Journals (Sweden)

Hilhorst Danielle

2013-01-01

Full Text Available In this paper, we apply a semi-implicit finite volume method for the numerical simulation of density driven flows in porous media; this amounts to solving a nonlinear convection-diffusion parabolic equation for the concentration coupled with an elliptic equation for the pressure. We compute the solutions for two specific problems: a problem involving a rotating interface between salt and fresh water and the classical but difficult Henry’s problem. All solutions are compared to results obtained by running FEflow, a commercial software package for the simulation of groundwater flow, mass and heat transfer in porous media.

The National Water-Quality Assessment Program Invertebrate Data Analysis System (IDAS) Software: Version 3 (User's Manual)

National Research Council Canada - National Science Library

Cuffney, Thomas F

2003-01-01

... as part of the National Water-Quality Assessment Program and stored in the Biological Transactional Database (Bio-TDB). The IDAS software is a stand-alone program for personal computers that run Microsoft...

Model-Based Software Testing for Object-Oriented Software

Science.gov (United States)

Biju, Soly Mathew

2008-01-01

Model-based testing is one of the best solutions for testing object-oriented software. It has a better test coverage than other testing styles. Model-based testing takes into consideration behavioural aspects of a class, which are usually unchecked in other testing methods. An increase in the complexity of software has forced the software industry…

Software Atom: An approach towards software components structuring to improve reusability

Directory of Open Access Journals (Sweden)

Muhammad Hussain Mughal

2017-12-01

Full Text Available Diversity of application domain compelled to design sustainable classification scheme for significantly amassing software repository. The atomic reusable software components are articulated to improve the software component reusability in volatile industry.  Numerous approaches of software classification have been proposed over past decades. Each approach has some limitations related to coupling and cohesion. In this paper, we proposed a novel approach by constituting the software based on radical functionalities to improve software reusability. We analyze the element's semantics in Periodic Table used in chemistry to design our classification approach, and present this approach using tree-based classification to curtail software repository search space complexity and further refined based on semantic search techniques. We developed a Global unique Identifier (GUID for indexing the functions and related components. We have exploited the correlation between chemistry element and software elements to simulate one to one mapping between them. Our approach is inspired from sustainability chemical periodic table. We have proposed software periodic table (SPT representing atomic software components extracted from real application software. Based on SPT classified repository tree parsing & extraction to enable the user to program their software by customizing the ingredients of software requirements. The classified repository of software ingredients assist user to exploits their requirements to software engineer and enable requirement engineer to develop a rapid large-scale prototype with great essence. Furthermore, we would predict the usability of the categorized repository based on feedback of users.  The continuous evolution of that proposed repository will be fine-tuned based on utilization and SPT would be gradually optimized by ant colony optimization techniques. Succinctly would provoke automating the software development process.

Mining biological networks from full-text articles.

Science.gov (United States)

Czarnecki, Jan; Shepherd, Adrian J

2014-01-01

The study of biological networks is playing an increasingly important role in the life sciences. Many different kinds of biological system can be modelled as networks; perhaps the most important examples are protein-protein interaction (PPI) networks, metabolic pathways, gene regulatory networks, and signalling networks. Although much useful information is easily accessible in publicly databases, a lot of extra relevant data lies scattered in numerous published papers. Hence there is a pressing need for automated text-mining methods capable of extracting such information from full-text articles. Here we present practical guidelines for constructing a text-mining pipeline from existing code and software components capable of extracting PPI networks from full-text articles. This approach can be adapted to tackle other types of biological network.

Advances in software development for intelligent interfaces for alarm and emergency management consoles

International Nuclear Information System (INIS)

Moseley, M.R.; Olson, C.E.

1986-01-01

Recent advances in technology allow features like voice synthesis, voice and speech recognition, image understanding, and intelligent data base management to be incorporated in computer driven alarm and emergency management information systems. New software development environments make it possible to do rapid prototyping of custom applications. Three examples using these technologies are discussed. (1) Maximum use is made of high-speed graphics and voice synthesis to implement a state-of-the-art alarm processing and display system with features that make the operator-machine interface efficient and accurate. Although very functional, this system is not portable or flexible; the software would have to be substantially rewritten for other applications. (2) An application generator which has the capability of ''building'' a specific alarm processing and display application in a matter of a few hours, using the site definition developed in the security planning phase to produce the custom application. This package is based on a standardized choice of hardware, within which it is capable of building a system to order, automatically constructing graphics, data tables, alarm prioritization rules, and interfaces to peripherals. (3) A software tool, the User Interface Management System (UIMS), is described which permits rapid prototyping of human-machine interfaces for a variety of applications including emergency management, alarm display and process information display. The object-oriented software of the UIMS achieves rapid prototyping of a new interface by standardizing to a class library of software objects instead of hardware objects

A Systems’ Biology Approach to Study MicroRNA-Mediated Gene Regulatory Networks

Directory of Open Access Journals (Sweden)

Xin Lai

2013-01-01

Full Text Available MicroRNAs (miRNAs are potent effectors in gene regulatory networks where aberrant miRNA expression can contribute to human diseases such as cancer. For a better understanding of the regulatory role of miRNAs in coordinating gene expression, we here present a systems biology approach combining data-driven modeling and model-driven experiments. Such an approach is characterized by an iterative process, including biological data acquisition and integration, network construction, mathematical modeling and experimental validation. To demonstrate the application of this approach, we adopt it to investigate mechanisms of collective repression on p21 by multiple miRNAs. We first construct a p21 regulatory network based on data from the literature and further expand it using algorithms that predict molecular interactions. Based on the network structure, a detailed mechanistic model is established and its parameter values are determined using data. Finally, the calibrated model is used to study the effect of different miRNA expression profiles and cooperative target regulation on p21 expression levels in different biological contexts.